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

Optimal community structure for social contagions

NASA Astrophysics Data System (ADS)

Su, Zhen; Wang, Wei; Li, Lixiang; Stanley, H. Eugene; Braunstein, Lidia A.

2018-05-01

Community structure is an important factor in the behavior of real-world networks because it strongly affects the stability and thus the phase transition order of the spreading dynamics. We here propose a reversible social contagion model of community networks that includes the factor of social reinforcement. In our model an individual adopts a social contagion when the number of received units of information exceeds its adoption threshold. We use mean-field approximation to describe our proposed model, and the results agree with numerical simulations. The numerical simulations and theoretical analyses both indicate that there is a first-order phase transition in the spreading dynamics, and that a hysteresis loop emerges in the system when there is a variety of initially adopted seeds. We find an optimal community structure that maximizes spreading dynamics. We also find a rich phase diagram with a triple point that separates the no-diffusion phase from the two diffusion phases.

Complexity and dynamics of topological and community structure in complex networks

NASA Astrophysics Data System (ADS)

Berec, Vesna

2017-07-01

Complexity is highly susceptible to variations in the network dynamics, reflected on its underlying architecture where topological organization of cohesive subsets into clusters, system's modular structure and resulting hierarchical patterns, are cross-linked with functional dynamics of the system. Here we study connection between hierarchical topological scales of the simplicial complexes and the organization of functional clusters - communities in complex networks. The analysis reveals the full dynamics of different combinatorial structures of q-th-dimensional simplicial complexes and their Laplacian spectra, presenting spectral properties of resulting symmetric and positive semidefinite matrices. The emergence of system's collective behavior from inhomogeneous statistical distribution is induced by hierarchically ordered topological structure, which is mapped to simplicial complex where local interactions between the nodes clustered into subcomplexes generate flow of information that characterizes complexity and dynamics of the full system.

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.

Flowering and floral visitation predict changes in community structure provided that mycorrhizas remain intact.

PubMed

Bennett, Jonathan A; Cahill, James F

2018-06-01

Pollination is critical for plant fitness and population dynamics, yet little attention is paid to the role of flowering and plant-pollinator interactions in structuring plant communities, including community responses to environmental change. Changes in arbuscular mycorrhizal fungi (AMF), nutrient abundances, and plant litter all affect plant access to different resources, and are known regulators of community structure. Each factor can also affect flowering and plant-pollinator interactions, potentially contributing to changes in community structure. To test whether AMF, nutrients, and litter influenced the relationship between pollination and community structure, we conducted a 5-yr field experiment applying fungicide, adding fertilizer, and removing plant litter in native grassland. We measured the distribution of flowers and floral visits among species in year three and linked these measures to changes in plant composition and species richness between years three and five. We hypothesized that an uneven distribution of flowers and visits among species would lead to greater community change, but that the treatments would disrupt this relationship by altering sexual allocation and recruitment. Consistent with our hypothesis, communities with uneven flower distributions exhibited greater changes in community composition and richness under ambient conditions. However, AMF suppression neutralized this relationship and regulated the other treatment effects, highlighting the potential importance of AMF for stabilizing recruitment dynamics. Combined, AMF suppression and nutrient addition caused species losses when few species flowered, likely by compounding stresses for those species. The treatment effects on the relationship between flowering and community composition were more nuanced, but were likely driven by increased competition and altered flowering among species. By contrast, community composition was more stable when visitation rates were uneven among species, irrespective of any treatments. This suggests that some species require high visitation rates to maintain their populations due to greater dependence on sexual reproduction. Combined, these results highlight the importance of flowering and floral visitation to the dynamics of grassland communities. They also suggest that altered recruitment dynamics is a major, yet understudied, mechanism by which environmental change affects communities. Consequently, understanding the effects of environmental change on plant communities will require study of both plant growth and sexual reproduction. © 2018 by the Ecological Society of America.

Emergence of bursts and communities in evolving weighted networks.

PubMed

Jo, Hang-Hyun; Pan, Raj Kumar; Kaski, Kimmo

2011-01-01

Understanding the patterns of human dynamics and social interaction and the way they lead to the formation of an organized and functional society are important issues especially for techno-social development. Addressing these issues of social networks has recently become possible through large scale data analysis of mobile phone call records, which has revealed the existence of modular or community structure with many links between nodes of the same community and relatively few links between nodes of different communities. The weights of links, e.g., the number of calls between two users, and the network topology are found correlated such that intra-community links are stronger compared to the weak inter-community links. This feature is known as Granovetter's "The strength of weak ties" hypothesis. In addition to this inhomogeneous community structure, the temporal patterns of human dynamics turn out to be inhomogeneous or bursty, characterized by the heavy tailed distribution of time interval between two consecutive events, i.e., inter-event time. In this paper, we study how the community structure and the bursty dynamics emerge together in a simple evolving weighted network model. The principal mechanisms behind these patterns are social interaction by cyclic closure, i.e., links to friends of friends and the focal closure, links to individuals sharing similar attributes or interests, and human dynamics by task handling process. These three mechanisms have been implemented as a network model with local attachment, global attachment, and priority-based queuing processes. By comprehensive numerical simulations we show that the interplay of these mechanisms leads to the emergence of heavy tailed inter-event time distribution and the evolution of Granovetter-type community structure. Moreover, the numerical results are found to be in qualitative agreement with empirical analysis results from mobile phone call dataset.

A multistate dynamic site occupancy model for spatially aggregated sessile communities

USGS Publications Warehouse

Fukaya, Keiichi; Royle, J. Andrew; Okuda, Takehiro; Nakaoka, Masahiro; Noda, Takashi

2017-01-01

Estimation of transition probabilities of sessile communities seems easy in principle but may still be difficult in practice because resampling error (i.e. a failure to resample exactly the same location at fixed points) may cause significant estimation bias. Previous studies have developed novel analytical methods to correct for this estimation bias. However, they did not consider the local structure of community composition induced by the aggregated distribution of organisms that is typically observed in sessile assemblages and is very likely to affect observations.We developed a multistate dynamic site occupancy model to estimate transition probabilities that accounts for resampling errors associated with local community structure. The model applies a nonparametric multivariate kernel smoothing methodology to the latent occupancy component to estimate the local state composition near each observation point, which is assumed to determine the probability distribution of data conditional on the occurrence of resampling error.By using computer simulations, we confirmed that an observation process that depends on local community structure may bias inferences about transition probabilities. By applying the proposed model to a real data set of intertidal sessile communities, we also showed that estimates of transition probabilities and of the properties of community dynamics may differ considerably when spatial dependence is taken into account.Results suggest the importance of accounting for resampling error and local community structure for developing management plans that are based on Markovian models. Our approach provides a solution to this problem that is applicable to broad sessile communities. It can even accommodate an anisotropic spatial correlation of species composition, and may also serve as a basis for inferring complex nonlinear ecological dynamics.

Mesoscopic Community Structure of Financial Markets Revealed by Price and Sign Fluctuations.

PubMed

Almog, Assaf; Besamusca, Ferry; MacMahon, Mel; Garlaschelli, Diego

2015-01-01

The mesoscopic organization of complex systems, from financial markets to the brain, is an intermediate between the microscopic dynamics of individual units (stocks or neurons, in the mentioned cases), and the macroscopic dynamics of the system as a whole. The organization is determined by "communities" of units whose dynamics, represented by time series of activity, is more strongly correlated internally than with the rest of the system. Recent studies have shown that the binary projections of various financial and neural time series exhibit nontrivial dynamical features that resemble those of the original data. This implies that a significant piece of information is encoded into the binary projection (i.e. the sign) of such increments. Here, we explore whether the binary signatures of multiple time series can replicate the same complex community organization of the financial market, as the original weighted time series. We adopt a method that has been specifically designed to detect communities from cross-correlation matrices of time series data. Our analysis shows that the simpler binary representation leads to a community structure that is almost identical with that obtained using the full weighted representation. These results confirm that binary projections of financial time series contain significant structural information.

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction.

PubMed

Zhang, Ping; Wu, Wei-Min; Van Nostrand, Joy D; Deng, Ye; He, Zhili; Gihring, Thomas; Zhang, Gengxin; Schadt, Chris W; Watson, David; Jardine, Phil; Criddle, Craig S; Brooks, Scott; Marsh, Terence L; Tiedje, James M; Arkin, Adam P; Zhou, Jizhong

2015-06-15

A pilot-scale field experiment demonstrated that a one-time amendment of emulsified vegetable oil (EVO) reduced groundwater U(VI) concentrations for 1 year in a fast-flowing aquifer. However, little is known about how EVO amendment stimulates the functional gene composition, structure, and dynamics of groundwater microbial communities toward prolonged U(VI) reduction. In this study, we hypothesized that EVO amendment would shift the functional gene composition and structure of groundwater microbial communities and stimulate key functional genes/groups involved in EVO biodegradation and reduction of electron acceptors in the aquifer. To test these hypotheses, groundwater microbial communities after EVO amendment were analyzed using a comprehensive functional gene microarray. Our results showed that EVO amendment stimulated sequential shifts in the functional composition and structure of groundwater microbial communities. Particularly, the relative abundance of key functional genes/groups involved in EVO biodegradation and the reduction of NO3 (-), Mn(IV), Fe(III), U(VI), and SO4 (2-) significantly increased, especially during the active U(VI) reduction period. The relative abundance for some of these key functional genes/groups remained elevated over 9 months. Montel tests suggested that the dynamics in the abundance, composition, and structure of these key functional genes/groups were significantly correlated with groundwater concentrations of acetate, NO3 (-), Mn(II), Fe(II), U(VI), and SO4 (2-). Our results suggest that EVO amendment stimulated dynamic succession of key functional microbial communities. This study improves our understanding of the composition, structure, and function changes needed for groundwater microbial communities to sustain a long-term U(VI) reduction. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction

PubMed Central

Zhang, Ping; Wu, Wei-Min; Van Nostrand, Joy D.; Deng, Ye; He, Zhili; Gihring, Thomas; Zhang, Gengxin; Schadt, Chris W.; Watson, David; Jardine, Phil; Criddle, Craig S.; Brooks, Scott; Marsh, Terence L.; Tiedje, James M.; Arkin, Adam P.

2015-01-01

A pilot-scale field experiment demonstrated that a one-time amendment of emulsified vegetable oil (EVO) reduced groundwater U(VI) concentrations for 1 year in a fast-flowing aquifer. However, little is known about how EVO amendment stimulates the functional gene composition, structure, and dynamics of groundwater microbial communities toward prolonged U(VI) reduction. In this study, we hypothesized that EVO amendment would shift the functional gene composition and structure of groundwater microbial communities and stimulate key functional genes/groups involved in EVO biodegradation and reduction of electron acceptors in the aquifer. To test these hypotheses, groundwater microbial communities after EVO amendment were analyzed using a comprehensive functional gene microarray. Our results showed that EVO amendment stimulated sequential shifts in the functional composition and structure of groundwater microbial communities. Particularly, the relative abundance of key functional genes/groups involved in EVO biodegradation and the reduction of NO3−, Mn(IV), Fe(III), U(VI), and SO42− significantly increased, especially during the active U(VI) reduction period. The relative abundance for some of these key functional genes/groups remained elevated over 9 months. Montel tests suggested that the dynamics in the abundance, composition, and structure of these key functional genes/groups were significantly correlated with groundwater concentrations of acetate, NO3−, Mn(II), Fe(II), U(VI), and SO42−. Our results suggest that EVO amendment stimulated dynamic succession of key functional microbial communities. This study improves our understanding of the composition, structure, and function changes needed for groundwater microbial communities to sustain a long-term U(VI) reduction. PMID:25862231

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction

DOE PAGES

Zhang, Ping; Wu, Wei-Min; Van Nostrand, Joy D.; ...

2015-04-10

A pilot-scale field experiment demonstrated that a one-time amendment of emulsified vegetable oil (EVO) reduced groundwater U(VI) concentrations for 1 year in a fast-flowing aquifer. However, little is known about how EVO amendment stimulates the functional gene composition, structure, and dynamics of groundwater microbial communities toward prolonged U(VI) reduction. In this paper, we hypothesized that EVO amendment would shift the functional gene composition and structure of groundwater microbial communities and stimulate key functional genes/groups involved in EVO biodegradation and reduction of electron acceptors in the aquifer. To test these hypotheses, groundwater microbial communities after EVO amendment were analyzed using amore » comprehensive functional gene microarray. Our results showed that EVO amendment stimulated sequential shifts in the functional composition and structure of groundwater microbial communities. Particularly, the relative abundance of key functional genes/groups involved in EVO biodegradation and the reduction of NO 3 -, Mn(IV), Fe(III), U(VI), and SO 4 2- significantly increased, especially during the active U(VI) reduction period. The relative abundance for some of these key functional genes/groups remained elevated over 9 months. Montel tests suggested that the dynamics in the abundance, composition, and structure of these key functional genes/groups were significantly correlated with groundwater concentrations of acetate, NO 3 -, Mn(II), Fe(II), U(VI), and SO 4 2-. Our results suggest that EVO amendment stimulated dynamic succession of key functional microbial communities. Finally, this study improves our understanding of the composition, structure, and function changes needed for groundwater microbial communities to sustain a long-term U(VI) reduction.« less

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction

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

Zhang, Ping; Wu, Wei-Min; Van Nostrand, Joy D.

A pilot-scale field experiment demonstrated that a one-time amendment of emulsified vegetable oil (EVO) reduced groundwater U(VI) concentrations for 1 year in a fast-flowing aquifer. However, little is known about how EVO amendment stimulates the functional gene composition, structure, and dynamics of groundwater microbial communities toward prolonged U(VI) reduction. In this paper, we hypothesized that EVO amendment would shift the functional gene composition and structure of groundwater microbial communities and stimulate key functional genes/groups involved in EVO biodegradation and reduction of electron acceptors in the aquifer. To test these hypotheses, groundwater microbial communities after EVO amendment were analyzed using amore » comprehensive functional gene microarray. Our results showed that EVO amendment stimulated sequential shifts in the functional composition and structure of groundwater microbial communities. Particularly, the relative abundance of key functional genes/groups involved in EVO biodegradation and the reduction of NO 3 -, Mn(IV), Fe(III), U(VI), and SO 4 2- significantly increased, especially during the active U(VI) reduction period. The relative abundance for some of these key functional genes/groups remained elevated over 9 months. Montel tests suggested that the dynamics in the abundance, composition, and structure of these key functional genes/groups were significantly correlated with groundwater concentrations of acetate, NO 3 -, Mn(II), Fe(II), U(VI), and SO 4 2-. Our results suggest that EVO amendment stimulated dynamic succession of key functional microbial communities. Finally, this study improves our understanding of the composition, structure, and function changes needed for groundwater microbial communities to sustain a long-term U(VI) reduction.« less

Dynamic structure of stock communities: a comparative study between stock returns and turnover rates

NASA Astrophysics Data System (ADS)

Su, Li-Ling; Jiang, Xiong-Fei; Li, Sai-Ping; Zhong, Li-Xin; Ren, Fei

2017-07-01

The detection of community structure in stock market is of theoretical and practical significance for the study of financial dynamics and portfolio risk estimation. We here study the community structures in Chinese stock markets from the aspects of both price returns and turnover rates, by using a combination of the PMFG and infomap methods based on a distance matrix. An empirical study using the overall data set shows that for both returns and turnover rates the largest communities are composed of specific industrial or conceptional sectors and the correlation inside a sector is generally larger than the correlation between different sectors. However, the community structure for turnover rates is more complex than that for returns, which indicates that the interactions between stocks revealed by turnover rates may contain more information. This conclusion is further confirmed by the analysis of the changes in the dynamics of community structures over five sub-periods. Sectors like banks, real estate, health care and New Shanghai take turns to comprise a few of the largest communities in different sub-periods, and more interestingly several specific sectors appear in the communities with different rank orders for returns and turnover rates even in the same sub-period. To better understand their differences, a comparison between the evolution of the returns and turnover rates of the stocks from these sectors is conducted. We find that stock prices only had large changes around important events while turnover rates surged after each of these events relevant to specific sectors, which shows strong evidence that the turnover rates are more susceptible to exogenous shocks than returns and its measurement for community detection may contain more useful information about market structure.

Influence of static habitat attributes on local and regional Rocky intertidal community structure

USGS Publications Warehouse

Konar, B.; Iken, K.; Coletti, H.; Monson, Daniel H.; Weitzman, Ben P.

2016-01-01

Rocky intertidal communities are structured by local environmental drivers, which can be dynamic, fluctuating on various temporal scales, or static and not greatly varying across years. We examined the role of six static drivers (distance to freshwater, tidewater glacial presence, wave exposure, fetch, beach slope, and substrate composition) on intertidal community structure across the northern Gulf of Alaska. We hypothesized that community structure is less similar at the local scale compared with the regional scale, coinciding with static drivers being less similar on smaller than larger scales. We also hypothesized that static attributes mainly drive local biological community structure. For this, we surveyed five to six sites in each of the six regions in the mid and low intertidal strata. Across regions, static attributes were not consistently different and only small clusters of sites had similar attributes. Additionally, intertidal communities were less similar on the site compared with the region level. These results suggest that these biological communities are not strongly influenced by the local static attributes measured in this study. An alternative explanation is that static attributes among our regions are not different enough to influence the biological communities. This lack of evidence for a strong static driver may be a result of our site selection, which targeted rocky sheltered communities. This suggests that this habitat may be ideal to examine the influence of dynamic drivers. We recommend that future analyses of dynamic attributes may best be performed after analyses have demonstrated that sites do not differ in static attributes.

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.

Comparison of bacterial community structure and dynamics during the thermophilic composting of different types of solid wastes: anaerobic digestion residue, pig manure and chicken manure

PubMed Central

Song, Caihong; Li, Mingxiao; Jia, Xuan; Wei, Zimin; Zhao, Yue; Xi, Beidou; Zhu, Chaowei; Liu, Dongming

2014-01-01

This study investigated the impact of composting substrate types on the bacterial community structure and dynamics during composting processes. To this end, pig manure (PM), chicken manure (CM), a mixture of PM and CM (PM + CM), and a mixture of PM, CM and anaerobic digestion residue (ADR) (PM + CM + ADR) were selected for thermophilic composting. The bacterial community structure and dynamics during the composting process were detected and analysed by polymerase chain reaction–denaturing gradient gel electrophoresis (DGGE) coupled with a statistic analysis. The physical-chemical analyses indicated that compared to single-material composting (PM, CM), co-composting (PM + CM, PM + CM + ADR) could promote the degradation of organic matter and strengthen the ability of conserving nitrogen. A DGGE profile and statistical analysis demonstrated that co-composting, especially PM + CM + ADR, could improve the bacterial community structure and functional diversity, even in the thermophilic stage. Therefore, co-composting could weaken the screening effect of high temperature on bacterial communities. Dominant sequencing analyses indicated a dramatic shift in the dominant bacterial communities from single-material composting to co-composting. Notably, compared with PM, PM + CM increased the quantity of xylan-degrading bacteria and reduced the quantity of human pathogens. PMID:24963997

Optimal multi-community network modularity for information diffusion

NASA Astrophysics Data System (ADS)

Wu, Jiaocan; Du, Ruping; Zheng, Yingying; Liu, Dong

2016-02-01

Studies demonstrate that community structure plays an important role in information spreading recently. In this paper, we investigate the impact of multi-community structure on information diffusion with linear threshold model. We utilize extended GN network that contains four communities and analyze dynamic behaviors of information that spreads on it. And we discover the optimal multi-community network modularity for information diffusion based on the social reinforcement. Results show that, within the appropriate range, multi-community structure will facilitate information diffusion instead of hindering it, which accords with the results derived from two-community network.

Fragmentation alters stream fish community structure in dendritic ecological networks.

PubMed

Perkin, Joshuah S; Gido, Keith B

2012-12-01

Effects of fragmentation on the ecology of organisms occupying dendritic ecological networks (DENs) have recently been described through both conceptual and mathematical models, but few hypotheses have been tested in complex, real-world ecosystems. Stream fishes provide a model system for assessing effects of fragmentation on the structure of communities occurring within DENs, including how fragmentation alters metacommunity dynamics and biodiversity. A recently developed habitat-availability measure, the "dendritic connectivity index" (DCI), allows for assigning quantitative measures of connectivity in DENs regardless of network extent or complexity, and might be used to predict fish community response to fragmentation. We characterized stream fish community structure in 12 DENs in the Great Plains, USA, during periods of dynamic (summer) and muted (fall) discharge regimes to test the DCI as a predictive model of fish community response to fragmentation imposed by road crossings. Results indicated that fish communities in stream segments isolated by road crossings had reduced species richness (alpha diversity) relative to communities that maintained connectivity with the surrounding DEN during summer and fall. Furthermore, isolated communities had greater dissimilarity (beta diversity) to downstream sites notisolated by road crossings during summer and fall. Finally, dissimilarity among communities within DENs decreased as a function of increased habitat connectivity (measured using the DCI) for summer and fall, suggesting that communities within highly connected DENs tend to be more homogeneous. Our results indicate that the DCI is sensitive to community effects of fragmentation in riverscapes and might be used by managers to predict ecological responses to changes in habitat connectivity. Moreover, our findings illustrate that relating structural connectivity of riverscapes to functional connectivity among communities might aid in maintaining metacommunity dynamics and biodiversity in complex dendritic ecosystems.

Biophysical controls on cluster dynamics and architectural differentiation of microbial biofilms in contrasting flow environments

PubMed Central

Hödl, Iris; Mari, Lorenzo; Bertuzzo, Enrico; Suweis, Samir; Besemer, Katharina; Rinaldo, Andrea; Battin, Tom J

2014-01-01

Ecology, with a traditional focus on plants and animals, seeks to understand the mechanisms underlying structure and dynamics of communities. In microbial ecology, the focus is changing from planktonic communities to attached biofilms that dominate microbial life in numerous systems. Therefore, interest in the structure and function of biofilms is on the rise. Biofilms can form reproducible physical structures (i.e. architecture) at the millimetre-scale, which are central to their functioning. However, the spatial dynamics of the clusters conferring physical structure to biofilms remains often elusive. By experimenting with complex microbial communities forming biofilms in contrasting hydrodynamic microenvironments in stream mesocosms, we show that morphogenesis results in ‘ripple-like’ and ‘star-like’ architectures – as they have also been reported from monospecies bacterial biofilms, for instance. To explore the potential contribution of demographic processes to these architectures, we propose a size-structured population model to simulate the dynamics of biofilm growth and cluster size distribution. Our findings establish that basic physical and demographic processes are key forces that shape apparently universal biofilm architectures as they occur in diverse microbial but also in single-species bacterial biofilms. PMID:23879839

The dynamic bacterial communities of a melting High Arctic glacier snowpack

PubMed Central

Hell, Katherina; Edwards, Arwyn; Zarsky, Jakub; Podmirseg, Sabine M; Girdwood, Susan; Pachebat, Justin A; Insam, Heribert; Sattler, Birgit

2013-01-01

Snow environments can occupy over a third of land surface area, but little is known about the dynamics of snowpack bacteria. The effect of snow melt on bacterial community structure and diversity of surface environments of a Svalbard glacier was examined using analyses of 16S rRNA genes via T-RFLP, qPCR and 454 pyrosequencing. Distinct community structures were found in different habitat types, with changes over 1 week apparent, in particular for the dominant bacterial class present, Betaproteobacteria. The differences observed were consistent with influences from depositional mode (snowfall vs aeolian dusts), contrasting snow with dust-rich snow layers and near-surface ice. Contrary to that, slush as the decompositional product of snow harboured distinct lineages of bacteria, further implying post-depositional changes in community structure. Taxa affiliated to the betaproteobacterial genus Polaromonas were particularly dynamic, and evidence for the presence of betaproteobacterial ammonia-oxidizing bacteria was uncovered, inviting the prospect that the dynamic bacterial communities associated with snowpacks may be active in supraglacial nitrogen cycling and capable of rapid responses to changes induced by snowmelt. Furthermore the potential of supraglacial snowpack ecosystems to respond to transient yet spatially extensive melting episodes such as that observed across most of Greenland's ice sheet in 2012 merits further investigation. PMID:23552623

The dynamic bacterial communities of a melting High Arctic glacier snowpack.

PubMed

Hell, Katherina; Edwards, Arwyn; Zarsky, Jakub; Podmirseg, Sabine M; Girdwood, Susan; Pachebat, Justin A; Insam, Heribert; Sattler, Birgit

2013-09-01

Snow environments can occupy over a third of land surface area, but little is known about the dynamics of snowpack bacteria. The effect of snow melt on bacterial community structure and diversity of surface environments of a Svalbard glacier was examined using analyses of 16S rRNA genes via T-RFLP, qPCR and 454 pyrosequencing. Distinct community structures were found in different habitat types, with changes over 1 week apparent, in particular for the dominant bacterial class present, Betaproteobacteria. The differences observed were consistent with influences from depositional mode (snowfall vs aeolian dusts), contrasting snow with dust-rich snow layers and near-surface ice. Contrary to that, slush as the decompositional product of snow harboured distinct lineages of bacteria, further implying post-depositional changes in community structure. Taxa affiliated to the betaproteobacterial genus Polaromonas were particularly dynamic, and evidence for the presence of betaproteobacterial ammonia-oxidizing bacteria was uncovered, inviting the prospect that the dynamic bacterial communities associated with snowpacks may be active in supraglacial nitrogen cycling and capable of rapid responses to changes induced by snowmelt. Furthermore the potential of supraglacial snowpack ecosystems to respond to transient yet spatially extensive melting episodes such as that observed across most of Greenland's ice sheet in 2012 merits further investigation.

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.

Structural stability, microbial biomass and community composition of sediments affected by the hydric dynamics of an urban stormwater infiltration basin. Dynamics of physical and microbial characteristics of stormwater sediment.

PubMed

Badin, Anne Laure; Monier, Armelle; Volatier, Laurence; Geremia, Roberto A; Delolme, Cécile; Bedell, Jean-Philippe

2011-05-01

The sedimentary layer deposited at the surface of stormwater infiltration basins is highly organic and multicontaminated. It undergoes considerable moisture content fluctuations due to the drying and inundation cycles (called hydric dynamics) of these basins. Little is known about the microflora of the sediments and its dynamics; hence, the purpose of this study is to describe the physicochemical and biological characteristics of the sediments at different hydric statuses of the infiltration basin. Sediments were sampled at five time points following rain events and dry periods. They were characterized by physical (aggregation), chemical (nutrients and heavy metals), and biological (total, bacterial and fungal biomasses, and genotypic fingerprints of total bacterial and fungal communities) parameters. Data were processed using statistical analyses which indicated that heavy metal (1,841 μg/g dry weight (DW)) and organic matter (11%) remained stable through time. By contrast, aggregation, nutrient content (NH₄⁺, 53-717 μg/g DW), pH (6.9-7.4), and biological parameters were shown to vary with sediment water content and sediment biomass, and were higher consecutive to stormwater flows into the basin (up to 7 mg C/g DW) than during dry periods (0.6 mg C/g DW). Coinertia analysis revealed that the structure of the bacterial communities is driven by the hydric dynamics of the infiltration basin, although no such trend was found for fungal communities. Hydric dynamics more than rain events appear to be more relevant for explaining variations of aggregation, microbial biomass, and shift in the microbial community composition. We concluded that the hydric dynamics of stormwater infiltration basins greatly affects the structural stability of the sedimentary layer, the biomass of the microbial community living in it and its dynamics. The decrease in aggregation consecutive to rewetting probably enhances access to organic matter (OM), explaining the consecutive release of NH₄⁺, the bloom of the microbial biomass, and the change in structure of the bacterial community. These results open new perspectives for basin management since the risk of OM and pollutant transfer to the aquifer is greatly affected by alternating dry and flood periods.

Inferring the relative resilience of alternative states

USGS Publications Warehouse

Angeler, David G.; Allen, Craig R.; Rojo, Carmen; Alvarez-Cobelas, Miguel; Rodrigo, Maria A.; Sanchez-Carrillo, Salvador

2013-01-01

Ecological systems may occur in alternative states that differ in ecological structures, functions and processes. Resilience is the measure of disturbance an ecological system can absorb before changing states. However, how the intrinsic structures and processes of systems that characterize their states affects their resilience remains unclear. We analyzed time series of phytoplankton communities at three sites in a floodplain in central Spain to assess the dominant frequencies or “temporal scales” in community dynamics and compared the patterns between a wet and a dry alternative state. The identified frequencies and cross-scale structures are expected to arise from positive feedbacks that are thought to reinforce processes in alternative states of ecological systems and regulate emergent phenomena such as resilience. Our analyses show a higher species richness and diversity but lower evenness in the dry state. Time series modeling revealed a decrease in the importance of short-term variability in the communities, suggesting that community dynamics slowed down in the dry relative to the wet state. The number of temporal scales at which community dynamics manifested, and the explanatory power of time series models, was lower in the dry state. The higher diversity, reduced number of temporal scales and the lower explanatory power of time series models suggest that species dynamics tended to be more stochastic in the dry state. From a resilience perspective our results highlight a paradox: increasing species richness may not necessarily enhance resilience. The loss of cross-scale structure (i.e. the lower number of temporal scales) in community dynamics across sites suggests that resilience erodes during drought. Phytoplankton communities in the dry state are therefore likely less resilient than in the wet state. Our case study demonstrates the potential of time series modeling to assess attributes that mediate resilience. The approach is useful for assessing resilience of alternative states across ecological and other complex systems.

Detecting brain dynamics during resting state: a tensor based evolutionary clustering approach

NASA Astrophysics Data System (ADS)

Al-sharoa, Esraa; Al-khassaweneh, Mahmood; Aviyente, Selin

2017-08-01

Human brain is a complex network with connections across different regions. Understanding the functional connectivity (FC) of the brain is important both during resting state and task; as disruptions in connectivity patterns are indicators of different psychopathological and neurological diseases. In this work, we study the resting state functional connectivity networks (FCNs) of the brain from fMRI BOLD signals. Recent studies have shown that FCNs are dynamic even during resting state and understanding the temporal dynamics of FCNs is important for differentiating between different conditions. Therefore, it is important to develop algorithms to track the dynamic formation and dissociation of FCNs of the brain during resting state. In this paper, we propose a two step tensor based community detection algorithm to identify and track the brain network community structure across time. First, we introduce an information-theoretic function to reduce the dynamic FCN and identify the time points that are similar topologically to combine them into a tensor. These time points will be used to identify the different FC states. Second, a tensor based spectral clustering approach is developed to identify the community structure of the constructed tensors. The proposed algorithm applies Tucker decomposition to the constructed tensors and extract the orthogonal factor matrices along the connectivity mode to determine the common subspace within each FC state. The detected community structure is summarized and described as FC states. The results illustrate the dynamic structure of resting state networks (RSNs), including the default mode network, somatomotor network, subcortical network and visual network.

Comparison of bacterial community structure and dynamics during the thermophilic composting of different types of solid wastes: anaerobic digestion residue, pig manure and chicken manure.

PubMed

Song, Caihong; Li, Mingxiao; Jia, Xuan; Wei, Zimin; Zhao, Yue; Xi, Beidou; Zhu, Chaowei; Liu, Dongming

2014-09-01

This study investigated the impact of composting substrate types on the bacterial community structure and dynamics during composting processes. To this end, pig manure (PM), chicken manure (CM), a mixture of PM and CM (PM + CM), and a mixture of PM, CM and anaerobic digestion residue (ADR) (PM + CM + ADR) were selected for thermophilic composting. The bacterial community structure and dynamics during the composting process were detected and analysed by polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) coupled with a statistic analysis. The physical-chemical analyses indicated that compared to single-material composting (PM, CM), co-composting (PM + CM, PM + CM + ADR) could promote the degradation of organic matter and strengthen the ability of conserving nitrogen. A DGGE profile and statistical analysis demonstrated that co-composting, especially PM + CM + ADR, could improve the bacterial community structure and functional diversity, even in the thermophilic stage. Therefore, co-composting could weaken the screening effect of high temperature on bacterial communities. Dominant sequencing analyses indicated a dramatic shift in the dominant bacterial communities from single-material composting to co-composting. Notably, compared with PM, PM + CM increased the quantity of xylan-degrading bacteria and reduced the quantity of human pathogens. © 2014 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Seasonal dynamics in the community structure and trophic structure of testate amoebae inhabiting the Sanjiang peatlands, Northeast China.

PubMed

Song, Lihong; Li, Hongkai; Wang, Kehong; Yan, Xiumin; Wu, Donghui

2018-04-01

Peatlands cover 3% of the earth's land surface but contain 30% of the world's soil carbon pool. Microbial communities constitute a crucial detrital food web for nutrient and carbon cycling in peatlands. Heterotrophic protozoans are considered top predators in the microbial food web; however, they are not yet well understood. In this study, we investigated seasonal dynamics in the community and the trophic structure of testate amoebae in four peatlands. Testate amoebae density and biomass in August were significantly higher than those in May and October. The highest density, 6.7 × 10 4 individual g -1 dry moss, was recorded in August 2014. The highest biomass, 7.7 × 10 2  μg C g -1 dry moss, was recorded in August 2013. Redundancy analyses showed that water-table depth was the most important factor, explaining over one third of the variance in fauna communities in all sampled seasons. High trophic position taxa dominated testate amoebae communities. The Shannon diversity index and community size structure index declined from August to October in 2013 and from May to October in 2014. These seasonal patterns of testate amoebae indicated the seasonal variations of the peatlands' microbial food web and are possibly related to the seasonal carbon dynamics in Northeast Chinese peatlands. Copyright © 2018 Elsevier GmbH. All rights reserved.

Toward Gleasonian landscape ecology: From communities to species, from patches to pixels

Treesearch

Samuel A. Cushman; Jeffrey S. Evans; Kevin McGarigal; Joseph M. Kiesecker

2010-01-01

The fusion of individualistic community ecology with the Hutchinsonian niche concept enabled a broad integration of ecological theory, spanning all the way from the niche characteristics of individual species, to the composition, structure, and dynamics of ecological communities. Landscape ecology has been variously described as the study of the structure, function,...

Microbial communities in methane seep sediments along US Atlantic Margin are structured by organic matter and seepage dynamics

NASA Astrophysics Data System (ADS)

Graw, M. F.; Pohlman, J.; Treude, T.; Ruppel, C. D.; Colwell, F. S.

2016-12-01

Methane seeps are dynamic environments on continental margins where subsurface methane reaches the ocean. Microbial communities play a critical role in carbon cycling within seep sediments via organic carbon degradation, methane production, and anaerobic oxidation of methane (AOM), which consumes 20-80% of methane in seep sediments. However, biogeochemical controls on microbial community structure at seeps on a margin-wide scale remain unclear. The passive US Atlantic Margin (USAM) has been identified as a region of active methane seepage. Passive margin seeps have traditionally been understudied relative to seeps on active margins. Passive margins exhibit large cross-margin variability in organic carbon deposition and are anticipated to have divergent seep dynamics from active margins. Thus, the USAM offers a unique opportunity to investigate controls on microbial communities in seep sediments. We undertook analysis of microbial communities inhabiting seep sediments at 6 biogeochemically distinct sites along the USAM. Microbiological samples were co-located with measurements of sediment geochemistry and AOM and sulfate reduction rates. Illumina sequencing of the 16S rRNA gene, using both universal (83 samples) and archaeal-specific (64 samples) primers, and the mcrA gene (18 samples) identified 44 bacterial phyla and 7 archaeal phyla. Seeps in canyons and on open slope, likely representing high and low organic content sediments, hosted distinct communities; the former was dominated by ammonia-oxidizing Marine Group I Thaumarchaeota and the latter by mixotrophic Hadesarchaeota. Seep stability also impacted microbial community structure, and in particular the establishment of an AOM community rather than a Bathyarchaeota-dominated community. These findings contribute to understanding how microbial communities are structured within methane seep sediments and pave the way for investigating broad differences in carbon cycling between seeps on passive and active margins.

The Influential Role of Sociocultural Feedbacks on Community-Managed Irrigation System Behaviors During times of Water Stress

DOE PAGES

Gunda, Thushara; Turner, B. L.; Tidwell, Vincent C.

2018-03-14

Sociohydrological studies use interdisciplinary approaches to explore the complex interactions between physical and social water systems and increase our understanding of emergent and paradoxical system behaviors. The dynamics of community values and social cohesion, however, have received little attention in modeling studies due to quantification challenges. Social structures associated with community-managed irrigation systems around the world, in particular, reflect these communities' experiences with a multitude of natural and social shocks. Using the Valdez acequia (a communally-managed irrigation community in northern New Mexico) as a simulation case study, we evaluate the impact of that community's social structure in governing its responsesmore » to water availability stresses posed by climate change. Specifically, a system dynamics model (developed using insights from community stakeholders and multiple disciplines that captures biophysical, socioeconomic, and sociocultural dynamics of acequia systems) was used to generate counterfactual trajectories to explore how the community would behave with streamflow conditions expected under climate change. We found that earlier peak flows, combined with adaptive measures of shifting crop selection, allowed for greater production of higher value crops and fewer people leaving the acequia. The economic benefits were lost, however, if downstream water pressures increased. Even with significant reductions in agricultural profitability, feedbacks associated with community cohesion buffered the community's population and land parcel sizes from more detrimental impacts, indicating the community's resilience under natural and social stresses. In conclusion, continued exploration of social structures is warranted to better understand these systems' responses to stress and identify possible leverage points for strengthening community resilience.« less

The Influential Role of Sociocultural Feedbacks on Community-Managed Irrigation System Behaviors During times of Water Stress

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

Gunda, Thushara; Turner, B. L.; Tidwell, Vincent C.

Sociohydrological studies use interdisciplinary approaches to explore the complex interactions between physical and social water systems and increase our understanding of emergent and paradoxical system behaviors. The dynamics of community values and social cohesion, however, have received little attention in modeling studies due to quantification challenges. Social structures associated with community-managed irrigation systems around the world, in particular, reflect these communities' experiences with a multitude of natural and social shocks. Using the Valdez acequia (a communally-managed irrigation community in northern New Mexico) as a simulation case study, we evaluate the impact of that community's social structure in governing its responsesmore » to water availability stresses posed by climate change. Specifically, a system dynamics model (developed using insights from community stakeholders and multiple disciplines that captures biophysical, socioeconomic, and sociocultural dynamics of acequia systems) was used to generate counterfactual trajectories to explore how the community would behave with streamflow conditions expected under climate change. We found that earlier peak flows, combined with adaptive measures of shifting crop selection, allowed for greater production of higher value crops and fewer people leaving the acequia. The economic benefits were lost, however, if downstream water pressures increased. Even with significant reductions in agricultural profitability, feedbacks associated with community cohesion buffered the community's population and land parcel sizes from more detrimental impacts, indicating the community's resilience under natural and social stresses. In conclusion, continued exploration of social structures is warranted to better understand these systems' responses to stress and identify possible leverage points for strengthening community resilience.« less

The Influential Role of Sociocultural Feedbacks on Community-Managed Irrigation System Behaviors During Times of Water Stress

NASA Astrophysics Data System (ADS)

Gunda, T.; Turner, B. L.; Tidwell, V. C.

2018-04-01

Sociohydrological studies use interdisciplinary approaches to explore the complex interactions between physical and social water systems and increase our understanding of emergent and paradoxical system behaviors. The dynamics of community values and social cohesion, however, have received little attention in modeling studies due to quantification challenges. Social structures associated with community-managed irrigation systems around the world, in particular, reflect these communities' experiences with a multitude of natural and social shocks. Using the Valdez acequia (a communally-managed irrigation community in northern New Mexico) as a simulation case study, we evaluate the impact of that community's social structure in governing its responses to water availability stresses posed by climate change. Specifically, a system dynamics model (developed using insights from community stakeholders and multiple disciplines that captures biophysical, socioeconomic, and sociocultural dynamics of acequia systems) was used to generate counterfactual trajectories to explore how the community would behave with streamflow conditions expected under climate change. We found that earlier peak flows, combined with adaptive measures of shifting crop selection, allowed for greater production of higher value crops and fewer people leaving the acequia. The economic benefits were lost, however, if downstream water pressures increased. Even with significant reductions in agricultural profitability, feedbacks associated with community cohesion buffered the community's population and land parcel sizes from more detrimental impacts, indicating the community's resilience under natural and social stresses. Continued exploration of social structures is warranted to better understand these systems' responses to stress and identify possible leverage points for strengthening community resilience.

Structure and dynamics of stock market in times of crisis

NASA Astrophysics Data System (ADS)

Zhao, Longfeng; Li, Wei; Cai, Xu

2016-02-01

Daily correlations among 322 S&P 500 constituent stocks are investigated by means of correlation-based (CB) network. By using the heterogeneous time scales, we identify global expansion and local clustering market behaviors during crises, which are mainly caused by community splits and inter-sector edge number decreases. The CB networks display distinctive community and sector structures. Graph edit distance is applied to capturing the dynamics of CB networks in which drastic structure reconfigurations can be observed during crisis periods. Edge statistics reveal the power-law nature of edges' duration time distribution. Despite the networks' strong structural changes during crises, we still find some long-duration edges that serve as the backbone of the stock market. Finally the dynamical change of network structure has shown its capability in predicting the implied volatility index (VIX).

Historical changes in the structure and functioning of the benthic community in the lagoon of Venice

NASA Astrophysics Data System (ADS)

Pranovi, Fabio; Da Ponte, Filippo; Torricelli, Patrizia

2008-03-01

One of the main challenges in environmental management is how to manage the dynamics of natural environments. In this context, having information about historical changes of the structure of the biological communities could represent a useful tool to improve management strategies, contributing to refine the policy objectives, since it gives reference states with which to compare the present. The Venice lagoon represents an interesting case study, since it is a highly dynamic, but sensitive, environment which requires the adoption of prudent management. In its recent history the lagoon ecosystem has been exposed to different kinds of disturbance, from the discharge of pollutants and nutrients, to the invasion of alien species and the exploitation of its biological resources by using highly impacting fishing gears. The analysis of available data about the macro-benthic community, from 1935 to 2004, allows the description of changes of the community structure over almost 70 years, showing a sharp decrease in its diversity. In order to obtain information about its functioning, it is necessary to know how these changes have affected processes at the community and system level. In shallow water ecosystems, as the control is mainly due to the benthic compartment, variations in the structure of the benthic community can induce modifications in processes at different hierarchical levels. The trophic structure analysis has revealed major changes during the period; from a well-assorted structure in 1935, to an herbivore-detritivore dominated one in the 1990s, and finally to a filter feeder dominated structure during the last decade. This has produced variations in the secondary production and it has induced modifications in the type of the ecosystem control. These changes are discussed in the light of the dynamics of the main driving forces.

Capturing the Interplay of Dynamics and Networks through Parameterizations of Laplacian Operators

DTIC Science & Technology

2016-08-24

important vertices and communities in the network. Specifically, for each dynamical process in this framework, we define a centrality measure that...vertices as a potential cluster (or community ) with respect to this process. We show that the subset-quality function generalizes the traditional conductance...compare the different perspectives they create on network structure. Subjects Network Science and Online Social Networks Keywords Network, Community

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

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.

Changes of soil prokaryotic communities after clear-cutting in a karst forest: evidences for cutting-based disturbance promoting deterministic processes.

PubMed

Zhang, Xiao; Liu, Shirong; Li, Xiangzhen; Wang, Jingxin; Ding, Qiong; Wang, Hui; Tian, Chao; Yao, Minjie; An, Jiaxing; Huang, Yongtao

2016-03-01

To understand the temporal responses of soil prokaryotic communities to clear-cutting disturbance, we examined the changes in soil bacterial and archaeal community composition, structure and diversity along a chronosequence of forest successional restoration using high-throughput 16S rRNA gene sequencing. Our results demonstrated that clear-cutting significantly altered soil bacterial community structure, while no significant shifts of soil archaeal communities were observed. The hypothesis that soil bacterial communities would become similar to those of surrounding intact primary forest with natural regeneration was supported by the shifts in the bacterial community composition and structure. Bacterial community diversity patterns induced by clear-cutting were consistent with the intermediate disturbance hypothesis. Dynamics of bacterial communities was mostly driven by soil properties, which collectively explained more than 70% of the variation in bacterial community composition. Community assembly data revealed that clear-cutting promoted the importance of the deterministic processes in shaping bacterial communities, coinciding with the resultant low resource environments. But assembly processes in the secondary forest returned a similar level compared to the intact primary forest. These findings suggest that bacterial community dynamics may be predictable during the natural recovery process. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

CEAS/AIAA/ICASE/NASA Langley International Forum on Aeroelasticity and Structural Dynamics 1999. Pt. 1

NASA Technical Reports Server (NTRS)

Woodrow Whitlow, Jr. (Editor); Todd, Emily N. (Editor)

1999-01-01

These proceedings represent a collection of the latest advances in aeroelasticity and structural dynamics from the world community. Research in the areas of unsteady aerodynamics and aeroelasticity, structural modeling and optimization, active control and adaptive structures, landing dynamics, certification and qualification, and validation testing are highlighted in the collection of papers. The wide range of results will lead to advances in the prediction and control of the structural response of aircraft and spacecraft.

Soil fungal communities respond to grassland plant community richness and soil edaphics

USDA-ARS?s Scientific Manuscript database

Fungal communities in soil have significant influences on terrestrial ecosystem dynamics, yet our understanding of the drivers of fungal diversity and community structure in soil is limited. Fungal communities associated with the rhizosphere of four native perennial grassland plant species grown in ...

Efficient community-based control strategies in adaptive networks

NASA Astrophysics Data System (ADS)

Yang, Hui; Tang, Ming; Zhang, Hai-Feng

2012-12-01

Most studies on adaptive networks concentrate on the properties of steady state, but neglect transient dynamics. In this study, we pay attention to the emergence of community structure in the transient process and the effects of community-based control strategies on epidemic spreading. First, by normalizing the modularity, we investigate the evolution of community structure during the transient process, and find that a strong community structure is induced by the rewiring mechanism in the early stage of epidemic dynamics, which, remarkably, delays the outbreak of disease. We then study the effects of control strategies started at different stages on the prevalence. Both immunization and quarantine strategies indicate that it is not ‘the earlier, the better’ for the implementation of control measures. And the optimal control effect is obtained if control measures can be efficiently implemented in the period of a strong community structure. For the immunization strategy, immunizing the susceptible nodes on susceptible-infected links and immunizing susceptible nodes randomly have similar control effects. However, for the quarantine strategy, quarantining the infected nodes on susceptible-infected links can yield a far better result than quarantining infected nodes randomly. More significantly, the community-based quarantine strategy performs better than the community-based immunization strategy. This study may shed new light on the forecast and the prevention of epidemics among humans.

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

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.

Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy

PubMed Central

Ulrich, Nikea; Rosenberger, Abigail; Brislawn, Colin; Wright, Justin; Kessler, Collin; Toole, David; Solomon, Caroline; Strutt, Steven; McClure, Erin

2016-01-01

ABSTRACT Bacterial community composition and longitudinal fluctuations were monitored in a riverine system during and after Superstorm Sandy to better characterize inter- and intracommunity responses associated with the disturbance associated with a 100-year storm event. High-throughput sequencing of the 16S rRNA gene was used to assess microbial community structure within water samples from Muddy Creek Run, a second-order stream in Huntingdon, PA, at 12 different time points during the storm event (29 October to 3 November 2012) and under seasonally matched baseline conditions. High-throughput sequencing of the 16S rRNA gene was used to track changes in bacterial community structure and divergence during and after Superstorm Sandy. Bacterial community dynamics were correlated to measured physicochemical parameters and fecal indicator bacteria (FIB) concentrations. Bioinformatics analyses of 2.1 million 16S rRNA gene sequences revealed a significant increase in bacterial diversity in samples taken during peak discharge of the storm. Beta-diversity analyses revealed longitudinal shifts in the bacterial community structure. Successional changes were observed, in which Betaproteobacteria and Gammaproteobacteria decreased in 16S rRNA gene relative abundance, while the relative abundance of members of the Firmicutes increased. Furthermore, 16S rRNA gene sequences matching pathogenic bacteria, including strains of Legionella, Campylobacter, Arcobacter, and Helicobacter, as well as bacteria of fecal origin (e.g., Bacteroides), exhibited an increase in abundance after peak discharge of the storm. This study revealed a significant restructuring of in-stream bacterial community structure associated with hydric dynamics of a storm event. IMPORTANCE In order to better understand the microbial risks associated with freshwater environments during a storm event, a more comprehensive understanding of the variations in aquatic bacterial diversity is warranted. This study investigated the bacterial communities during and after Superstorm Sandy to provide fine time point resolution of dynamic changes in bacterial composition. This study adds to the current literature by revealing the variation in bacterial community structure during the course of a storm. This study employed high-throughput DNA sequencing, which generated a deep analysis of inter- and intracommunity responses during a significant storm event. This study has highlighted the utility of applying high-throughput sequencing for water quality monitoring purposes, as this approach enabled a more comprehensive investigation of the bacterial community structure. Altogether, these data suggest a drastic restructuring of the stream bacterial community during a storm event and highlight the potential of high-throughput sequencing approaches for assessing the microbiological quality of our environment. PMID:27060115

Mesoscopic Community Structure of Financial Markets Revealed by Price and Sign Fluctuations

PubMed Central

Almog, Assaf; Besamusca, Ferry; MacMahon, Mel; Garlaschelli, Diego

2015-01-01

The mesoscopic organization of complex systems, from financial markets to the brain, is an intermediate between the microscopic dynamics of individual units (stocks or neurons, in the mentioned cases), and the macroscopic dynamics of the system as a whole. The organization is determined by “communities” of units whose dynamics, represented by time series of activity, is more strongly correlated internally than with the rest of the system. Recent studies have shown that the binary projections of various financial and neural time series exhibit nontrivial dynamical features that resemble those of the original data. This implies that a significant piece of information is encoded into the binary projection (i.e. the sign) of such increments. Here, we explore whether the binary signatures of multiple time series can replicate the same complex community organization of the financial market, as the original weighted time series. We adopt a method that has been specifically designed to detect communities from cross-correlation matrices of time series data. Our analysis shows that the simpler binary representation leads to a community structure that is almost identical with that obtained using the full weighted representation. These results confirm that binary projections of financial time series contain significant structural information. PMID:26226226

Stability in a changing world - palm community dynamics in the hyperdiverse western Amazon over 17 years.

PubMed

Olivares, Ingrid; Svenning, Jens-Christian; van Bodegom, Peter M; Valencia, Renato; Balslev, Henrik

2017-03-01

Are the hyperdiverse local forests of the western Amazon undergoing changes linked to global and local drivers such as climate change, or successional dynamics? We analyzed local climatic records to assess potential climatic changes in Yasuní National Park, Ecuador, and compared two censuses (1995, 2012) of a palm community to assess changes in community structure and composition. Over 17 years, the structure and composition of this palm community remained remarkably stable. Soil humidity was significantly lower and canopy conditions were significantly more open in 2012 compared to 1995, but local climatic records showed that no significant changes in precipitation, temperature or river level have occurred during the last decade. Thus, we found no evidence of recent directional shifts in climate or the palm community in Yasuní. The absence of changes in local climate and plant community dynamics in Yasuní contrasts with recent findings from eastern Amazon, where environmental change is driving significant changes in ecosystem dynamics. Our findings suggest that until now, local forests in the northwest Amazon may have escaped pressure from climate change. The stability of this rich palm community embedded in the hyperdiverse Yasuní National Park underlines its uniqueness as a sanctuary for the protection of Amazonian diversity from global change impacts. © 2016 John Wiley & Sons Ltd.

Water regime history drives responses of soil Namib Desert microbial communities to wetting events

NASA Astrophysics Data System (ADS)

Frossard, Aline; Ramond, Jean-Baptiste; Seely, Mary; Cowan, Don A.

2015-07-01

Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel “dry condition” control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities.

Water regime history drives responses of soil Namib Desert microbial communities to wetting events.

PubMed

Frossard, Aline; Ramond, Jean-Baptiste; Seely, Mary; Cowan, Don A

2015-07-21

Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel "dry condition" control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities.

Influence of oak woodland composition and structure on infection by Phytophthora ramorum

Treesearch

Nathan Rank; Hall Cushman; Brian Anacker; David Rizzo; Ross Meentemeyer

2008-01-01

Introduced plant pathogens have major ecological impacts in many parts of the world. While the spread of pathogens can be strongly mediated by the composition and structure of local host plant communities, little is known about effects of plant community structure on invasion dynamics of introduced pathogens. The progress of infection by the invasive pathogen ...

Detection of communities with Naming Game-based methods

PubMed Central

Ribeiro, Carlos Henrique Costa

2017-01-01

Complex networks are often organized in groups or communities of agents that share the same features and/or functions, and this structural organization is built naturally with the formation of the system. In social networks, we argue that the dynamic of linguistic interactions of agreement among people can be a crucial factor in generating this community structure, given that sharing opinions with another person bounds them together, and disagreeing constantly would probably weaken the relationship. We present here a computational model of opinion exchange that uncovers the community structure of a network. Our aim is not to present a new community detection method proper, but to show how a model of social communication dynamics can reveal the (simple and overlapping) community structure in an emergent way. Our model is based on a standard Naming Game, but takes into consideration three social features: trust, uncertainty and opinion preference, that are built over time as agents communicate among themselves. We show that the separate addition of each social feature in the Naming Game results in gradual improvements with respect to community detection. In addition, the resulting uncertainty and trust values classify nodes and edges according to role and position in the network. Also, our model has shown a degree of accuracy both for non-overlapping and overlapping communities that are comparable with most algorithms specifically designed for topological community detection. PMID:28797097

Microbial community dynamics in the rhizosphere of a cadmium hyper-accumulator

NASA Astrophysics Data System (ADS)

Wood, J. L.; Zhang, C.; Mathews, E. R.; Tang, C.; Franks, A. E.

2016-11-01

Phytoextraction is influenced by the indigenous soil microbial communities during the remediation of heavy metal contaminated soils. Soil microbial communities can affect plant growth, metal availability and the performance of phytoextraction-assisting inocula. Understanding the basic ecology of indigenous soil communities associated with the phytoextraction process, including the interplay between selective pressures upon the communities, is an important step towards phytoextraction optimization. This study investigated the impact of cadmium (Cd), and the presence of a Cd-accumulating plant, Carpobrotus rossii (Haw.) Schwantes, on the structure of soil-bacterial and fungal communities using automated ribosomal intergenic spacer analysis (ARISA) and quantitative PCR (qPCR). Whilst Cd had no detectable influence upon fungal communities, bacterial communities underwent significant structural changes with no reduction in 16S rRNA copy number. The presence of C. rossii influenced the structure of all communities and increased ITS copy number. Suites of operational taxonomic units (OTUs) changed in abundance in response to either Cd or C. rossii, however we found little evidence to suggest that the two selective pressures were acting synergistically. The Cd-induced turnover in bacterial OTUs suggests that Cd alters competition dynamics within the community. Further work to understand how competition is altered could provide a deeper understanding of the microbiome-plant-environment and aid phytoextraction optimization.

Microbial community dynamics in the rhizosphere of a cadmium hyper-accumulator

PubMed Central

Wood, J. L.; Zhang, C.; Mathews, E. R.; Tang, C.; Franks, A. E.

2016-01-01

Phytoextraction is influenced by the indigenous soil microbial communities during the remediation of heavy metal contaminated soils. Soil microbial communities can affect plant growth, metal availability and the performance of phytoextraction-assisting inocula. Understanding the basic ecology of indigenous soil communities associated with the phytoextraction process, including the interplay between selective pressures upon the communities, is an important step towards phytoextraction optimization. This study investigated the impact of cadmium (Cd), and the presence of a Cd-accumulating plant, Carpobrotus rossii (Haw.) Schwantes, on the structure of soil-bacterial and fungal communities using automated ribosomal intergenic spacer analysis (ARISA) and quantitative PCR (qPCR). Whilst Cd had no detectable influence upon fungal communities, bacterial communities underwent significant structural changes with no reduction in 16S rRNA copy number. The presence of C. rossii influenced the structure of all communities and increased ITS copy number. Suites of operational taxonomic units (OTUs) changed in abundance in response to either Cd or C. rossii, however we found little evidence to suggest that the two selective pressures were acting synergistically. The Cd-induced turnover in bacterial OTUs suggests that Cd alters competition dynamics within the community. Further work to understand how competition is altered could provide a deeper understanding of the microbiome-plant-environment and aid phytoextraction optimization. PMID:27805014

Think locally, act locally: detection of small, medium-sized, and large communities in large networks.

PubMed

Jeub, Lucas G S; Balachandran, Prakash; Porter, Mason A; Mucha, Peter J; Mahoney, Michael W

2015-01-01

It is common in the study of networks to investigate intermediate-sized (or "meso-scale") features to try to gain an understanding of network structure and function. For example, numerous algorithms have been developed to try to identify "communities," which are typically construed as sets of nodes with denser connections internally than with the remainder of a network. In this paper, we adopt a complementary perspective that communities are associated with bottlenecks of locally biased dynamical processes that begin at seed sets of nodes, and we employ several different community-identification procedures (using diffusion-based and geodesic-based dynamics) to investigate community quality as a function of community size. Using several empirical and synthetic networks, we identify several distinct scenarios for "size-resolved community structure" that can arise in real (and realistic) networks: (1) the best small groups of nodes can be better than the best large groups (for a given formulation of the idea of a good community); (2) the best small groups can have a quality that is comparable to the best medium-sized and large groups; and (3) the best small groups of nodes can be worse than the best large groups. As we discuss in detail, which of these three cases holds for a given network can make an enormous difference when investigating and making claims about network community structure, and it is important to take this into account to obtain reliable downstream conclusions. Depending on which scenario holds, one may or may not be able to successfully identify "good" communities in a given network (and good communities might not even exist for a given community quality measure), the manner in which different small communities fit together to form meso-scale network structures can be very different, and processes such as viral propagation and information diffusion can exhibit very different dynamics. In addition, our results suggest that, for many large realistic networks, the output of locally biased methods that focus on communities that are centered around a given seed node (or set of seed nodes) might have better conceptual grounding and greater practical utility than the output of global community-detection methods. They also illustrate structural properties that are important to consider in the development of better benchmark networks to test methods for community detection.

Think locally, act locally: Detection of small, medium-sized, and large communities in large networks

NASA Astrophysics Data System (ADS)

Jeub, Lucas G. S.; Balachandran, Prakash; Porter, Mason A.; Mucha, Peter J.; Mahoney, Michael W.

2015-01-01

It is common in the study of networks to investigate intermediate-sized (or "meso-scale") features to try to gain an understanding of network structure and function. For example, numerous algorithms have been developed to try to identify "communities," which are typically construed as sets of nodes with denser connections internally than with the remainder of a network. In this paper, we adopt a complementary perspective that communities are associated with bottlenecks of locally biased dynamical processes that begin at seed sets of nodes, and we employ several different community-identification procedures (using diffusion-based and geodesic-based dynamics) to investigate community quality as a function of community size. Using several empirical and synthetic networks, we identify several distinct scenarios for "size-resolved community structure" that can arise in real (and realistic) networks: (1) the best small groups of nodes can be better than the best large groups (for a given formulation of the idea of a good community); (2) the best small groups can have a quality that is comparable to the best medium-sized and large groups; and (3) the best small groups of nodes can be worse than the best large groups. As we discuss in detail, which of these three cases holds for a given network can make an enormous difference when investigating and making claims about network community structure, and it is important to take this into account to obtain reliable downstream conclusions. Depending on which scenario holds, one may or may not be able to successfully identify "good" communities in a given network (and good communities might not even exist for a given community quality measure), the manner in which different small communities fit together to form meso-scale network structures can be very different, and processes such as viral propagation and information diffusion can exhibit very different dynamics. In addition, our results suggest that, for many large realistic networks, the output of locally biased methods that focus on communities that are centered around a given seed node (or set of seed nodes) might have better conceptual grounding and greater practical utility than the output of global community-detection methods. They also illustrate structural properties that are important to consider in the development of better benchmark networks to test methods for community detection.

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.

Microbial community dynamics and biogas production from manure fractions in sludge bed anaerobic digestion.

PubMed

Nordgård, A S R; Bergland, W H; Bakke, R; Vadstein, O; Østgaard, K; Bakke, I

2015-12-01

To elucidate how granular sludge inoculum and particle-rich organic loading affect the structure of the microbial communities and process performance in upflow anaerobic sludge bed (UASB) reactors. We investigated four reactors run on dairy manure filtrate and four on pig manure supernatant for three months achieving similar methane yields. The reactors fed with less particle rich pig manure stabilized faster and had highest capacity. Microbial community dynamics analysed by a PCR/denaturing gradient gel electrophoresis approach showed that influent was a major determinant for the composition of the reactor communities. Comparisons of pre- and non-adapted inoculum in the reactors run on pig manure supernatant showed that the community structure of the nonadapted inoculum adapted in approximately two months. Microbiota variance partitioning analysis revealed that running time, organic loading rate and inoculum together explained 26 and 31% of the variance in bacterial and archaeal communities respectively. The microbial communities of UASBs adapted to the reactor conditions in treatment of particle rich manure fractions, obtaining high capacity, especially on pig manure supernatant. These findings provide relevant insight into the microbial community dynamics in startup and operation of sludge bed reactors for methane production from slurry fractions, a major potential source of biogas. © 2015 The Society for Applied Microbiology.

Atlantic Salmon (Salmo salar L.) Gastrointestinal Microbial Community Dynamics in Relation to Digesta Properties and Diet.

PubMed

Zarkasi, Kamarul Zaman; Taylor, Richard S; Abell, Guy C J; Tamplin, Mark L; Glencross, Brett D; Bowman, John P

2016-04-01

To better understand salmon GI tract microbial community dynamics in relation to diet, a feeding trial was performed utilising diets with different proportions of fish meal, protein, lipid and energy levels. Salmon gut dysfunction has been associated with the occurrence of casts, or an empty hind gut. A categorical scoring system describing expressed digesta consistency was evaluated in relation to GI tract community structure. Faster growing fish generally had lower faecal scores while the diet cohorts showed minor differences in faecal score though the overall lowest scores were observed with a low protein, low energy diet. The GI tract bacterial communities were highly dynamic over time with the low protein, low energy diet associated with the most divergent community structure. This included transiently increased abundance of anaerobic (Bacteroidia and Clostridia) during January and February, and facultatively anaerobic (lactic acid bacteria) taxa from February onwards. The digesta had enriched populations of these groups in relation to faecal cast samples. The majority of samples (60-86 %) across all diet cohorts were eventually dominated by the genus Aliivibrio. The results suggest that an interaction between time of sampling and diet is most strongly related to community structure. Digesta categorization revealed microbes involved with metabolism of diet components change progressively over time and could be a useful system to assess feeding responses.

Compensatory dynamics are rare in natural ecological communities.

Treesearch

J.E. Houlahan; D.J. Currie; K. Cottenie; G.S. Cumming; S.K.M. Ernest; C.S. Findlay; S.D. Fuhlendorf; R.D. Stevens; T.J. Willis; I.P. Woiwod; S.M. Wondzell

2007-01-01

Hubbell recently presented a theoretical framework, neutral models, for explaining large-scale patterns of community structure. This theory rests on the foundation of zero-sum ecological communities, that is, the assumption that the number of individuals in a community stays constant over time. If community abundances stay relatively constant, (i.e. approximating the...

Spatiotemporal model of barley and cereal yellow dwarf virus transmission dynamics with seasonality and plant competition

Treesearch

S.M. Moore; C.A. Manore; V.A. Bokil; E.T. Borer; P.R. Hosseini

2011-01-01

Many generalist pathogens are influenced by the spatial distributions and relative abundances of susceptible host species. The spatial structure of host populations can influence patterns of infection incidence (or disease outbreaks), and the effects of a generalist pathogen on host community dynamics in a spatially heterogeneous community may differ from predictions...

Lewis Structures Technology, 1988. Volume 2: Structural Mechanics

NASA Technical Reports Server (NTRS)

1988-01-01

Lewis Structures Div. performs and disseminates results of research conducted in support of aerospace engine structures. These results have a wide range of applicability to practitioners of structural engineering mechanics beyond the aerospace arena. The engineering community was familiarized with the depth and range of research performed by the division and its academic and industrial partners. Sessions covered vibration control, fracture mechanics, ceramic component reliability, parallel computing, nondestructive evaluation, constitutive models and experimental capabilities, dynamic systems, fatigue and damage, wind turbines, hot section technology (HOST), aeroelasticity, structural mechanics codes, computational methods for dynamics, structural optimization, and applications of structural dynamics, and structural mechanics computer codes.

Modeling microbial community structure and functional diversity across time and space.

PubMed

Larsen, Peter E; Gibbons, Sean M; Gilbert, Jack A

2012-07-01

Microbial communities exhibit exquisitely complex structure. Many aspects of this complexity, from the number of species to the total number of interactions, are currently very difficult to examine directly. However, extraordinary efforts are being made to make these systems accessible to scientific investigation. While recent advances in high-throughput sequencing technologies have improved accessibility to the taxonomic and functional diversity of complex communities, monitoring the dynamics of these systems over time and space - using appropriate experimental design - is still expensive. Fortunately, modeling can be used as a lens to focus low-resolution observations of community dynamics to enable mathematical abstractions of functional and taxonomic dynamics across space and time. Here, we review the approaches for modeling bacterial diversity at both the very large and the very small scales at which microbial systems interact with their environments. We show that modeling can help to connect biogeochemical processes to specific microbial metabolic pathways. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Temperature-Dependent Conformational Properties of Human Neuronal Calcium Sensor-1 Protein Revealed by All-Atom Simulations.

PubMed

Zhu, Yuzhen; Ma, Buyong; Qi, Ruxi; Nussinov, Ruth; Zhang, Qingwen

2016-04-14

Neuronal calcium sensor-1 (NCS-1) protein has orthologues from Saccharomyces cerevisiae to human with highly conserved amino acid sequences. NCS-1 is an important factor controlling the animal's response to temperature change. This leads us to investigate the temperature effects on the conformational dynamics of human NCS-1 at 310 and 316 K by all-atom molecular dynamics (MD) simulations and dynamic community network analysis. Four independent 500 ns MD simulations show that secondary structure content at 316 K is similar to that at 310 K, whereas the global protein structure is expanded. Loop 3 (L3) adopts an extended state occuping the hydrophobic crevice, and the number of suboptimal communication paths between residue D176 and V190 is reduced at 316 K. The dynamic community network analysis suggests that the interdomain correlation is weakened, and the intradomain coupling is strengthened at 316 K. The elevated temperature reduces the number of the salt bridges, especially in C-domain. This study suggests that the elevated temperature affects the conformational dynamics of human NCS-1 protein. Comparison of the structural dynamics of R102Q mutant and Δ176-190 truncated NCS-1 suggests that the structural and dynamical response of NCS-1 protein to elevated temperature may be one of its intrinsic functional properties.

Constructing financial network based on PMFG and threshold method

NASA Astrophysics Data System (ADS)

Nie, Chun-Xiao; Song, Fu-Tie

2018-04-01

Based on planar maximally filtered graph (PMFG) and threshold method, we introduced a correlation-based network named PMFG-based threshold network (PTN). We studied the community structure of PTN and applied ISOMAP algorithm to represent PTN in low-dimensional Euclidean space. The results show that the community corresponds well to the cluster in the Euclidean space. Further, we studied the dynamics of the community structure and constructed the normalized mutual information (NMI) matrix. Based on the real data in the market, we found that the volatility of the market can lead to dramatic changes in the community structure, and the structure is more stable during the financial crisis.

Improving resolution of dynamic communities in human brain networks through targeted node removal

PubMed Central

Turner, Benjamin O.; Miller, Michael B.; Carlson, Jean M.

2017-01-01

Current approaches to dynamic community detection in complex networks can fail to identify multi-scale community structure, or to resolve key features of community dynamics. We propose a targeted node removal technique to improve the resolution of community detection. Using synthetic oscillator networks with well-defined “ground truth” communities, we quantify the community detection performance of a common modularity maximization algorithm. We show that the performance of the algorithm on communities of a given size deteriorates when these communities are embedded in multi-scale networks with communities of different sizes, compared to the performance in a single-scale network. We demonstrate that targeted node removal during community detection improves performance on multi-scale networks, particularly when removing the most functionally cohesive nodes. Applying this approach to network neuroscience, we compare dynamic functional brain networks derived from fMRI data taken during both repetitive single-task and varied multi-task experiments. After the removal of regions in visual cortex, the most coherent functional brain area during the tasks, community detection is better able to resolve known functional brain systems into communities. In addition, node removal enables the algorithm to distinguish clear differences in brain network dynamics between these experiments, revealing task-switching behavior that was not identified with the visual regions present in the network. These results indicate that targeted node removal can improve spatial and temporal resolution in community detection, and they demonstrate a promising approach for comparison of network dynamics between neuroscientific data sets with different resolution parameters. PMID:29261662

Markov Dynamics as a Zooming Lens for Multiscale Community Detection: Non Clique-Like Communities and the Field-of-View Limit

PubMed Central

Schaub, Michael T.; Delvenne, Jean-Charles; Yaliraki, Sophia N.; Barahona, Mauricio

2012-01-01

In recent years, there has been a surge of interest in community detection algorithms for complex networks. A variety of computational heuristics, some with a long history, have been proposed for the identification of communities or, alternatively, of good graph partitions. In most cases, the algorithms maximize a particular objective function, thereby finding the ‘right’ split into communities. Although a thorough comparison of algorithms is still lacking, there has been an effort to design benchmarks, i.e., random graph models with known community structure against which algorithms can be evaluated. However, popular community detection methods and benchmarks normally assume an implicit notion of community based on clique-like subgraphs, a form of community structure that is not always characteristic of real networks. Specifically, networks that emerge from geometric constraints can have natural non clique-like substructures with large effective diameters, which can be interpreted as long-range communities. In this work, we show that long-range communities escape detection by popular methods, which are blinded by a restricted ‘field-of-view’ limit, an intrinsic upper scale on the communities they can detect. The field-of-view limit means that long-range communities tend to be overpartitioned. We show how by adopting a dynamical perspective towards community detection [1], [2], in which the evolution of a Markov process on the graph is used as a zooming lens over the structure of the network at all scales, one can detect both clique- or non clique-like communities without imposing an upper scale to the detection. Consequently, the performance of algorithms on inherently low-diameter, clique-like benchmarks may not always be indicative of equally good results in real networks with local, sparser connectivity. We illustrate our ideas with constructive examples and through the analysis of real-world networks from imaging, protein structures and the power grid, where a multiscale structure of non clique-like communities is revealed. PMID:22384178

Potential link between plant and fungal distributions in a dipterocarp rainforest: community and phylogenetic structure of tropical ectomycorrhizal fungi across a plant and soil ecotone.

PubMed

Peay, Kabir G; Kennedy, Peter G; Davies, Stuart J; Tan, Sylvester; Bruns, Thomas D

2010-01-01

*Relatively little is known about diversity or structure of tropical ectomycorrhizal communities or their roles in tropical ecosystem dynamics. In this study, we present one of the largest molecular studies to date of an ectomycorrhizal community in lowland dipterocarp rainforest. *We sampled roots from two 0.4 ha sites located across an ecotone within a 52 ha forest dynamics plot. Our plots contained > 500 tree species and > 40 species of ectomycorrhizal host plants. Fungi were identified by sequencing ribosomal RNA genes. *The community was dominated by the Russulales (30 species), Boletales (17), Agaricales (18), Thelephorales (13) and Cantharellales (12). Total species richness appeared comparable to molecular studies of temperate forests. Community structure changed across the ecotone, although it was not possible to separate the role of environmental factors vs host plant preferences. Phylogenetic analyses were consistent with a model of community assembly where habitat associations are influenced by evolutionary conservatism of functional traits within ectomycorrhizal lineages. *Because changes in the ectomycorrhizal fungal community parallel those of the tree community at this site, this study demonstrates the potential link between the distribution of tropical tree diversity and the distribution of tropical ectomycorrhizal diversity in relation to local-scale edaphic variation.

Dynamic Effects of Biochar on the Bacterial Community Structure in Soil Contaminated with Polycyclic Aromatic Hydrocarbons.

PubMed

Song, Yang; Bian, Yongrong; Wang, Fang; Xu, Min; Ni, Ni; Yang, Xinglun; Gu, Chenggang; Jiang, Xin

2017-08-16

Amending soil with biochar is an effective soil remediation strategy for organic contaminants. This study investigated the dynamic effects of wheat straw biochar on the bacterial community structure during remediation by high-throughput sequencing. The wheat straw biochar amended into the soil significantly reduced the bioavailability and toxicity of polycyclic aromatic hydrocarbons (PAHs). Biochar amendment helped to maintain the bacterial diversity in the PAH-contaminated soil. The relationship between the immobilization of PAHs and the soil bacterial diversity fit a quadratic model. Before week 12 of the incubation, the incubation time was the main factor contributing to the changes in the soil bacterial community structure. However, biochar greatly affected the bacterial community structure after 12 weeks of amendment, and the effects were dependent upon the biochar type. Amendment with biochar mainly facilitated the growth of rare bacterial genera (relative abundance of 0.01-1%) in the studied soil. Therefore, the application of wheat straw biochar into PAH-contaminated soil can reduce the environmental risks of PAHs and benefit the soil microbial ecology.

Interactions between Snow Chemistry, Mercury Inputs and Microbial Population Dynamics in an Arctic Snowpack

PubMed Central

Larose, Catherine; Prestat, Emmanuel; Cecillon, Sébastien; Berger, Sibel; Malandain, Cédric; Lyon, Delina; Ferrari, Christophe; Schneider, Dominique; Dommergue, Aurélien; Vogel, Timothy M.

2013-01-01

We investigated the interactions between snowpack chemistry, mercury (Hg) contamination and microbial community structure and function in Arctic snow. Snowpack chemistry (inorganic and organic ions) including mercury (Hg) speciation was studied in samples collected during a two-month field study in a high Arctic site, Svalbard, Norway (79°N). Shifts in microbial community structure were determined by using a 16S rRNA gene phylogenetic microarray. We linked snowpack and meltwater chemistry to changes in microbial community structure by using co-inertia analyses (CIA) and explored changes in community function due to Hg contamination by q-PCR quantification of Hg-resistance genes in metagenomic samples. Based on the CIA, chemical and microbial data were linked (p = 0.006) with bioavailable Hg (BioHg) and methylmercury (MeHg) contributing significantly to the ordination of samples. Mercury was shown to influence community function with increases in merA gene copy numbers at low BioHg levels. Our results show that snowpacks can be considered as dynamic habitats with microbial and chemical components responding rapidly to environmental changes. PMID:24282515

Dynamics of the microbial community during continuous methane fermentation in continuously stirred tank reactors.

PubMed

Tang, Yue-Qin; Shigematsu, Toru; Morimura, Shigeru; Kida, Kenji

2015-04-01

Methane fermentation is an attractive technology for the treatment of organic wastes and wastewaters. However, the process is difficult to control, and treatment rates and digestion efficiency require further optimization. Understanding the microbiology mechanisms of methane fermentation is of fundamental importance to improving this process. In this review, we summarize the dynamics of microbial communities in methane fermentation chemostats that are operated using completely stirred tank reactors (CSTRs). Each chemostat was supplied with one substrate as the sole carbon source. The substrates include acetate, propionate, butyrate, long-chain fatty acids, glycerol, protein, glucose, and starch. These carbon sources are general substrates and intermediates of methane fermentation. The factors that affect the structure of the microbial community are discussed. The carbon source, the final product, and the operation conditions appear to be the main factors that affect methane fermentation and determine the structure of the microbial community. Understanding the structure of the microbial community during methane fermentation will guide the design and operation of practical wastewater treatments. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

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.

Epidemic Wave Dynamics Attributable to Urban Community Structure: A Theoretical Characterization of Disease Transmission in a Large Network

PubMed Central

Eggo, Rosalind M; Lenczner, Michael

2015-01-01

Background Multiple waves of transmission during infectious disease epidemics represent a major public health challenge, but the ecological and behavioral drivers of epidemic resurgence are poorly understood. In theory, community structure—aggregation into highly intraconnected and loosely interconnected social groups—within human populations may lead to punctuated outbreaks as diseases progress from one community to the next. However, this explanation has been largely overlooked in favor of temporal shifts in environmental conditions and human behavior and because of the difficulties associated with estimating large-scale contact patterns. Objective The aim was to characterize naturally arising patterns of human contact that are capable of producing simulated epidemics with multiple wave structures. Methods We used an extensive dataset of proximal physical contacts between users of a public Wi-Fi Internet system to evaluate the epidemiological implications of an empirical urban contact network. We characterized the modularity (community structure) of the network and then estimated epidemic dynamics under a percolation-based model of infectious disease spread on the network. We classified simulated epidemics as multiwave using a novel metric and we identified network structures that were critical to the network’s ability to produce multiwave epidemics. Results We identified robust community structure in a large, empirical urban contact network from which multiwave epidemics may emerge naturally. This pattern was fueled by a special kind of insularity in which locally popular individuals were not the ones forging contacts with more distant social groups. Conclusions Our results suggest that ordinary contact patterns can produce multiwave epidemics at the scale of a single urban area without the temporal shifts that are usually assumed to be responsible. Understanding the role of community structure in epidemic dynamics allows officials to anticipate epidemic resurgence without having to forecast future changes in hosts, pathogens, or the environment. PMID:26156032

Living in the branches: population dynamics and ecological processes in dendritic networks

USGS Publications Warehouse

Grant, E.H.C.; Lowe, W.H.; Fagan, W.F.

2007-01-01

Spatial structure regulates and modifies processes at several levels of ecological organization (e.g. individual/genetic, population and community) and is thus a key component of complex systems, where knowledge at a small scale can be insufficient for understanding system behaviour at a larger scale. Recent syntheses outline potential applications of network theory to ecological systems, but do not address the implications of physical structure for network dynamics. There is a specific need to examine how dendritic habitat structure, such as that found in stream, hedgerow and cave networks, influences ecological processes. Although dendritic networks are one type of ecological network, they are distinguished by two fundamental characteristics: (1) both the branches and the nodes serve as habitat, and (2) the specific spatial arrangement and hierarchical organization of these elements interacts with a species' movement behaviour to alter patterns of population distribution and abundance, and community interactions. Here, we summarize existing theory relating to ecological dynamics in dendritic networks, review empirical studies examining the population- and community-level consequences of these networks, and suggest future research integrating spatial pattern and processes in dendritic systems.

The interaction of cannibalism and omnivory: consequences for community dynamics.

PubMed

Rudolf, Volker H W

2007-11-01

Although cannibalism is ubiquitous in food webs and frequent in systems where a predator and its prey also share a common resource (intraguild predation, IGP), its impacts on species interactions and the dynamics and structure of communities are still poorly understood. In addition, the few existing studies on cannibalism have generally focused on cannibalism in the top-predator, ignoring that it is frequent at intermediate trophic levels. A set of structured models shows that cannibalism can completely alter the dynamics and structure of three-species IGP systems depending on the trophic position where cannibalism occurs. Contrary to the expectations of simple models, the IG predator can exploit the resources more efficiently when it is cannibalistic, enabling the predator to persist at lower resource densities than the IG prey. Cannibalism in the IG predator can also alter the effect of enrichment, preventing predator-mediated extinction of the IG prey at high productivities predicted by simple models. Cannibalism in the IG prey can reverse the effect of top-down cascades, leading to an increase in the resource with decreasing IG predator density. These predictions are consistent with current data. Overall, cannibalism promotes the coexistence of the IG predator and IG prey. These results indicate that including cannibalism in current models can overcome the discrepancy between theory and empirical data. Thus, we need to measure and account for cannibalistic interactions to reliably predict the structure and dynamics of communities.

Complex, Dynamic Combination of Physical, Chemical and Nutritional Variables Controls Spatio-Temporal Variation of Sandy Beach Community Structure

PubMed Central

Ortega Cisneros, Kelly; Smit, Albertus J.; Laudien, Jürgen; Schoeman, David S.

2011-01-01

Sandy beach ecological theory states that physical features of the beach control macrobenthic community structure on all but the most dissipative beaches. However, few studies have simultaneously evaluated the relative importance of physical, chemical and biological factors as potential explanatory variables for meso-scale spatio-temporal patterns of intertidal community structure in these systems. Here, we investigate macroinfaunal community structure of a micro-tidal sandy beach that is located on an oligotrophic subtropical coast and is influenced by seasonal estuarine input. We repeatedly sampled biological and environmental variables at a series of beach transects arranged at increasing distances from the estuary mouth. Sampling took place over a period of five months, corresponding with the transition between the dry and wet season. This allowed assessment of biological-physical relationships across chemical and nutritional gradients associated with a range of estuarine inputs. Physical, chemical, and biological response variables, as well as measures of community structure, showed significant spatio-temporal patterns. In general, bivariate relationships between biological and environmental variables were rare and weak. However, multivariate correlation approaches identified a variety of environmental variables (i.e., sampling session, the C∶N ratio of particulate organic matter, dissolved inorganic nutrient concentrations, various size fractions of photopigment concentrations, salinity and, to a lesser extent, beach width and sediment kurtosis) that either alone or combined provided significant explanatory power for spatio-temporal patterns of macroinfaunal community structure. Overall, these results showed that the macrobenthic community on Mtunzini Beach was not structured primarily by physical factors, but instead by a complex and dynamic blend of nutritional, chemical and physical drivers. This emphasises the need to recognise ocean-exposed sandy beaches as functional ecosystems in their own right. PMID:21858213

Complex, dynamic combination of physical, chemical and nutritional variables controls spatio-temporal variation of sandy beach community structure.

PubMed

Ortega Cisneros, Kelly; Smit, Albertus J; Laudien, Jürgen; Schoeman, David S

2011-01-01

Sandy beach ecological theory states that physical features of the beach control macrobenthic community structure on all but the most dissipative beaches. However, few studies have simultaneously evaluated the relative importance of physical, chemical and biological factors as potential explanatory variables for meso-scale spatio-temporal patterns of intertidal community structure in these systems. Here, we investigate macroinfaunal community structure of a micro-tidal sandy beach that is located on an oligotrophic subtropical coast and is influenced by seasonal estuarine input. We repeatedly sampled biological and environmental variables at a series of beach transects arranged at increasing distances from the estuary mouth. Sampling took place over a period of five months, corresponding with the transition between the dry and wet season. This allowed assessment of biological-physical relationships across chemical and nutritional gradients associated with a range of estuarine inputs. Physical, chemical, and biological response variables, as well as measures of community structure, showed significant spatio-temporal patterns. In general, bivariate relationships between biological and environmental variables were rare and weak. However, multivariate correlation approaches identified a variety of environmental variables (i.e., sampling session, the C∶N ratio of particulate organic matter, dissolved inorganic nutrient concentrations, various size fractions of photopigment concentrations, salinity and, to a lesser extent, beach width and sediment kurtosis) that either alone or combined provided significant explanatory power for spatio-temporal patterns of macroinfaunal community structure. Overall, these results showed that the macrobenthic community on Mtunzini Beach was not structured primarily by physical factors, but instead by a complex and dynamic blend of nutritional, chemical and physical drivers. This emphasises the need to recognise ocean-exposed sandy beaches as functional ecosystems in their own right.

Think Locally, Act Locally: The Detection of Small, Medium-Sized, and Large Communities in Large Networks

PubMed Central

Jeub, Lucas G. S.; Balachandran, Prakash; Porter, Mason A.; Mucha, Peter J.; Mahoney, Michael W.

2016-01-01

It is common in the study of networks to investigate intermediate-sized (or “meso-scale”) features to try to gain an understanding of network structure and function. For example, numerous algorithms have been developed to try to identify “communities,” which are typically construed as sets of nodes with denser connections internally than with the remainder of a network. In this paper, we adopt a complementary perspective that “communities” are associated with bottlenecks of locally-biased dynamical processes that begin at seed sets of nodes, and we employ several different community-identification procedures (using diffusion-based and geodesic-based dynamics) to investigate community quality as a function of community size. Using several empirical and synthetic networks, we identify several distinct scenarios for “size-resolved community structure” that can arise in real (and realistic) networks: (i) the best small groups of nodes can be better than the best large groups (for a given formulation of the idea of a good community); (ii) the best small groups can have a quality that is comparable to the best medium-sized and large groups; and (iii) the best small groups of nodes can be worse than the best large groups. As we discuss in detail, which of these three cases holds for a given network can make an enormous difference when investigating and making claims about network community structure, and it is important to take this into account to obtain reliable downstream conclusions. Depending on which scenario holds, one may or may not be able to successfully identify “good” communities in a given network (and good communities might not even exist for a given community quality measure), the manner in which different small communities fit together to form meso-scale network structures can be very different, and processes such as viral propagation and information diffusion can exhibit very different dynamics. In addition, our results suggest that, for many large realistic networks, the output of locally-biased methods that focus on communities that are centered around a given seed node might have better conceptual grounding and greater practical utility than the output of global community-detection methods. They also illustrate subtler structural properties that are important to consider in the development of better benchmark networks to test methods for community detection. PMID:25679670

PLFA profiling of microbial community structure and seasonal shifts in soils of a Douglas-fir chronosequence

Treesearch

Jennifer Moore-Kucera; Richard P. Dick

2008-01-01

The impact and frequency of forest harvesting could significantly affect soil microbial community (SMC) structure and functioning. The ability of soil microorganisms to perform biogeochemical processes is critical for sustaining forest productivity and has a direct impact on decomposition dynamics and carbon storage potential. The Wind River Canopy Crane Research...

Urban ecological stewardship: understanding the structure, function and network of community-based urban land management

Treesearch

Erika s. Svendsen; Lindsay K. Campbell

2008-01-01

Urban environmental stewardship activities are on the rise in cities throughout the Northeast. Groups participating in stewardship activities range in age, size, and geography and represent an increasingly complex and dynamic arrangement of civil society, government and business sectors. To better understand the structure, function and network of these community-based...

Lewis Structures Technology, 1988. Volume 3: Structural Integrity Fatigue and Fracture Wind Turbines HOST

NASA Technical Reports Server (NTRS)

1988-01-01

The charter of the Structures Division is to perform and disseminate results of research conducted in support of aerospace engine structures. These results have a wide range of applicability to practioners of structural engineering mechanics beyond the aerospace arena. The specific purpose of the symposium was to familiarize the engineering structures community with the depth and range of research performed by the division and its academic and industrial partners. Sessions covered vibration control, fracture mechanics, ceramic component reliability, parallel computing, nondestructive evaluation, constitutive models and experimental capabilities, dynamic systems, fatigue and damage, wind turbines, hot section technology (HOST), aeroelasticity, structural mechanics codes, computational methods for dynamics, structural optimization, and applications of structural dynamics, and structural mechanics computer codes.

Predicted Bacterial Interactions Affect in Vivo Microbial Colonization Dynamics in Nematostella

PubMed Central

Domin, Hanna; Zurita-Gutiérrez, Yazmín H.; Scotti, Marco; Buttlar, Jann; Hentschel Humeida, Ute; Fraune, Sebastian

2018-01-01

The maintenance and resilience of host-associated microbiota during development is a fundamental process influencing the fitness of many organisms. Several host properties were identified as influencing factors on bacterial colonization, including the innate immune system, mucus composition, and diet. In contrast, the importance of bacteria–bacteria interactions on host colonization is less understood. Here, we use bacterial abundance data of the marine model organism Nematostella vectensis to reconstruct potential bacteria–bacteria interactions through co-occurrence networks. The analysis indicates that bacteria–bacteria interactions are dynamic during host colonization and change according to the host’s developmental stage. To assess the predictive power of inferred interactions, we tested bacterial isolates with predicted cooperative or competitive behavior for their ability to influence bacterial recolonization dynamics. Within 3 days of recolonization, all tested bacterial isolates affected bacterial community structure, while only competitive bacteria increased bacterial diversity. Only 1 week after recolonization, almost no differences in bacterial community structure could be observed between control and treatments. These results show that predicted competitive bacteria can influence community structure for a short period of time, verifying the in silico predictions. However, within 1 week, the effects of the bacterial isolates are neutralized, indicating a high degree of resilience of the bacterial community. PMID:29740401

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.

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.

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.

From individuals to populations to communities: a dynamic energy budget model of marine ecosystem size-spectrum including life history diversity.

PubMed

Maury, Olivier; Poggiale, Jean-Christophe

2013-05-07

Individual metabolism, predator-prey relationships, and the role of biodiversity are major factors underlying the dynamics of food webs and their response to environmental variability. Despite their crucial, complementary and interacting influences, they are usually not considered simultaneously in current marine ecosystem models. In an attempt to fill this gap and determine if these factors and their interaction are sufficient to allow realistic community structure and dynamics to emerge, we formulate a mathematical model of the size-structured dynamics of marine communities which integrates mechanistically individual, population and community levels. The model represents the transfer of energy generated in both time and size by an infinite number of interacting fish species spanning from very small to very large species. It is based on standard individual level assumptions of the Dynamic Energy Budget theory (DEB) as well as important ecological processes such as opportunistic size-based predation and competition for food. Resting on the inter-specific body-size scaling relationships of the DEB theory, the diversity of life-history traits (i.e. biodiversity) is explicitly integrated. The stationary solutions of the model as well as the transient solutions arising when environmental signals (e.g. variability of primary production and temperature) propagate through the ecosystem are studied using numerical simulations. It is shown that in the absence of density-dependent feedback processes, the model exhibits unstable oscillations. Density-dependent schooling probability and schooling-dependent predatory and disease mortalities are proposed to be important stabilizing factors allowing stationary solutions to be reached. At the community level, the shape and slope of the obtained quasi-linear stationary spectrum matches well with empirical studies. When oscillations of primary production are simulated, the model predicts that the variability propagates along the spectrum in a given frequency-dependent size range before decreasing for larger sizes. At the species level, the simulations show that small and large species dominate the community successively (small species being more abundant at small sizes and large species being more abundant at large sizes) and that the total biomass of a species decreases with its maximal size which again corroborates empirical studies. Our results indicate that the simultaneous consideration of individual growth and reproduction, size-structured trophic interactions, the diversity of life-history traits and a density-dependent stabilizing process allow realistic community structure and dynamics to emerge without any arbitrary prescription. As a logical consequence of our model construction and a basis for future studies, we define the function Φ as the relative contribution of each species to the total biomass of the ecosystem, for any given size. We argue that this function is a measure of the functional role of biodiversity characterizing the impact of the structure of the community (its species composition) on its function (the relative proportions of losses, dissipation and biological work). Copyright © 2013 Elsevier Ltd. All rights reserved.

Composition, structure, and dynamics of the Illinois Ozark Hills Forest

Treesearch

Lisa M. Helmig; James S. Fralish

2011-01-01

In the mature oak-hickory ecosystem of the Illinois Ozark Hills, forest community composition, dynamics, and structure were studied to examine the extent of conversion to mesophytic species and eventually predict the broad threshold time of complete conversion. Tree, sapling, and seedling data were collected from 87 plots distributed throughout the region. Data for the...

Microbial community dynamics during assays of harbour oil spill bioremediation: a microscale simulation study.

PubMed

Cappello, S; Caruso, G; Zampino, D; Monticelli, L S; Maimone, G; Denaro, R; Tripodo, B; Troussellier, M; Yakimov, M; Giuliano, L

2007-01-01

Microcosm experiments simulating an oil spill event were performed to evaluate the response of the natural microbial community structure of Messina harbour seawater following the accidental load of petroleum. An experimental harbour seawater microcosm, supplemented with nutrients and crude oil, was monitored above 15 days in comparison with unpolluted ones (control microcosms). Bacterial cells were counted with a Live/Dead BacLight viability kit; leucine aminopeptidase, beta-glucosidase, alkaline phosphatase, lipase and esterase enzymes were measured using fluorogenic substrates. The microbial community dynamic was monitored by isolation of total RNA, RT-PCR amplification of 16S rRNA, cloning and sequencing. Oil addition stimulated an increase of the total bacterial abundance, leucine aminopeptidase and phosphatase activity rates, as well as a change in the community structure. This suggested a prompt response of micro-organisms to the load of petroleum hydrocarbons. The present study on the viability, specific composition and metabolic characteristics of the microbial community allows a more precise assessment of oil pollution. Both structural and functional parameters offer interesting perspectives as indicators to monitor changes caused by petroleum hydrocarbons. A better knowledge of microbial structural successions at oil-polluted sites is essential for environmental bioremediation. Data obtained in microcosm studies improve our understanding of natural processes occurring during oil spills.

Composition and Dynamics of Bacterial Communities of a Drinking Water Supply System as Assessed by RNA- and DNA-Based 16S rRNA Gene Fingerprinting

PubMed Central

Eichler, Stefan; Christen, Richard; Höltje, Claudia; Westphal, Petra; Bötel, Julia; Brettar, Ingrid; Mehling, Arndt; Höfle, Manfred G.

2006-01-01

Bacterial community dynamics of a whole drinking water supply system (DWSS) were studied from source to tap. Raw water for this DWSS is provided by two reservoirs with different water characteristics in the Harz mountains of Northern Germany. Samples were taken after different steps of treatment of raw water (i.e., flocculation, sand filtration, and chlorination) and at different points along the supply system to the tap. RNA and DNA were extracted from the sampled water. The 16S rRNA or its genes were partially amplified by reverse transcription-PCR or PCR and analyzed by single-strand conformation polymorphism community fingerprints. The bacterial community structures of the raw water samples from the two reservoirs were very different, but no major changes of these structures occurred after flocculation and sand filtration. Chlorination of the processed raw water strongly affected bacterial community structure, as reflected by the RNA-based fingerprints. This effect was less pronounced for the DNA-based fingerprints. After chlorination, the bacterial community remained rather constant from the storage containers to the tap. Furthermore, the community structure of the tap water did not change substantially for several months. Community composition was assessed by sequencing of abundant bands and phylogenetic analysis of the sequences obtained. The taxonomic compositions of the bacterial communities from both reservoirs were very different at the species level due to their different limnologies. On the other hand, major taxonomic groups, well known to occur in freshwater, such as Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes, were found in both reservoirs. Significant differences in the detection of the major groups were observed between DNA-based and RNA-based fingerprints irrespective of the reservoir. Chlorination of the drinking water seemed to promote growth of nitrifying bacteria. Detailed analysis of the community dynamics of the whole DWSS revealed a significant influence of both source waters on the overall composition of the drinking water microflora and demonstrated the relevance of the raw water microflora for the drinking water microflora provided to the end user. PMID:16517632

Temporal variations in a phytoplankton community in a subtropical reservoir: An interplay of extrinsic and intrinsic community effects.

PubMed

Yang, Wen; Zheng, Zhongming; Zheng, Cheng; Lu, Kaihong; Ding, Dewen; Zhu, Jinyong

2018-01-15

The phytoplankton community structure is potentially influenced by both extrinsic effects originating from the surrounding environment and intrinsic effects relying on interspecific interactions between two species. However, few studies have simultaneously considered both types of effects and assessed the relative importance of these factors. In this study, we used data collected over nine months (August 2012-May 2013) from a typical subtropical reservoir in southeast China to analyze the temporal variation of its phytoplankton community structure and develop a quantitative understanding of the extrinsic and intrinsic effects on phytoplankton community dynamics. Significant temporal variations were observed in environmental variables as well as the phytoplankton and zooplankton communities, whereas their variational trajectories and directions were entirely different. Variance partitioning analysis showed that extrinsic factors significantly explained only 31% of the variation in the phytoplankton community, thus suggesting that these factors were incomplete predictors of the community structure. Random forest-based models showed that 48% of qualified responsible phytoplankton species were more accurately predicted by phytoplankton-only models, which revealed clear effects of interspecific species-to-species interactions. Furthermore, we used association networks to model the interactions among phytoplankton, zooplankton and the environment. Network comparisons indicated that interspecific interactions were widely present in the phytoplankton community and dominated the network rather than those between phytoplankton and extrinsic factors. These findings expand the current understanding of the underlying mechanisms that govern phytoplankton community dynamics. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

Mnemonic convergence in social networks: The emergent properties of cognition at a collective level.

PubMed

Coman, Alin; Momennejad, Ida; Drach, Rae D; Geana, Andra

2016-07-19

The development of shared memories, beliefs, and norms is a fundamental characteristic of human communities. These emergent outcomes are thought to occur owing to a dynamic system of information sharing and memory updating, which fundamentally depends on communication. Here we report results on the formation of collective memories in laboratory-created communities. We manipulated conversational network structure in a series of real-time, computer-mediated interactions in fourteen 10-member communities. The results show that mnemonic convergence, measured as the degree of overlap among community members' memories, is influenced by both individual-level information-processing phenomena and by the conversational social network structure created during conversational recall. By studying laboratory-created social networks, we show how large-scale social phenomena (i.e., collective memory) can emerge out of microlevel local dynamics (i.e., mnemonic reinforcement and suppression effects). The social-interactionist approach proposed herein points to optimal strategies for spreading information in social networks and provides a framework for measuring and forging collective memories in communities of individuals.

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.

Exploring the dynamic links between microbial ecology and redox state of the hyporheic zone: insight from flume experiments

NASA Astrophysics Data System (ADS)

Kaufman, M.; Cardenas, M. B.; Stegen, J.; Graham, E.; Cook, P. L. M.; Kessler, A. J.

2016-12-01

The hyporheic zone (HZ) provides key ecosystem services such as heavy metal sequestration, nutrient uptake and consumption, and habitat for a diverse collection of ecologically and commercially important species. Microbes are responsible for many of the chemical transformations in the HZ. These microbe populations are intimately linked to redox conditions, and recent work has shown that redox conditions in the HZ can be highly dynamic. Here we investigate the dynamic coupling between surface flow conditions, hyporheic redox conditions, and the hyporheic microbiome. Our window into this world is a large experimental flume (5m x 0.7m x 0.3m), prepared and incubated in a way that is relatively common to hyporheic zone research, without a strong attempt to impose a specific microbial community structure. We use computer-controlled flow combined with sand bedforms within the flume to generate a pattern of oxic and anoxic sediment zones, from which we collected sediment and water samples. Dissolved oxygen was mapped with a large planar optode. The samples were analyzed for microbial community composition through 16S rRNA gene sequencing. We compare the population structure between oxic and anoxic zones, showing that the presence of oxygen in the HZ is a strong predictor of microbial composition. Additionally, we compare both the oxic and anoxic community structure from the flume to those of samples taken from natural environments, showing both interesting similarities and differences. In the future, we plan to use time-series sampling to observe the response times of microbial communities subjected to dynamic surface channel flow and redox conditions. This work will yield greater understanding of the role that dynamic rivers play in microbe-provided ecosystem services.

Exploring the dynamic links between microbial ecology and redox state of the hyporheic zone: insight from flume experiments

NASA Astrophysics Data System (ADS)

Kaufman, M.; Cardenas, M. B.; Stegen, J.; Graham, E.; Cook, P. L. M.; Kessler, A. J.

2017-12-01

The hyporheic zone (HZ) provides key ecosystem services such as heavy metal sequestration, nutrient uptake and consumption, and habitat for a diverse collection of ecologically and commercially important species. Microbes are responsible for many of the chemical transformations in the HZ. These microbe populations are intimately linked to redox conditions, and recent work has shown that redox conditions in the HZ can be highly dynamic. Here we investigate the dynamic coupling between surface flow conditions, hyporheic redox conditions, and the hyporheic microbiome. Our window into this world is a large experimental flume (5m x 0.7m x 0.3m), prepared and incubated in a way that is relatively common to hyporheic zone research, without a strong attempt to impose a specific microbial community structure. We use computer-controlled flow combined with sand bedforms within the flume to generate a pattern of oxic and anoxic sediment zones, from which we collected sediment and water samples. Dissolved oxygen was mapped with a large planar optode. The samples were analyzed for microbial community composition through 16S rRNA gene sequencing. We compare the population structure between oxic and anoxic zones, showing that the presence of oxygen in the HZ is a strong predictor of microbial composition. Additionally, we compare both the oxic and anoxic community structure from the flume to those of samples taken from natural environments, showing both interesting similarities and differences. In the future, we plan to use time-series sampling to observe the response times of microbial communities subjected to dynamic surface channel flow and redox conditions. This work will yield greater understanding of the role that dynamic rivers play in microbe-provided ecosystem services.

Bacterial Community Dynamics in Full-Scale Activated Sludge Bioreactors: Operational and Ecological Factors Driving Community Assembly and Performance

PubMed Central

Valentín-Vargas, Alexis; Toro-Labrador, Gladys; Massol-Deyá, Arturo A.

2012-01-01

The assembling of bacterial communities in conventional activated sludge (CAS) bioreactors was thought, until recently, to be chaotic and mostly unpredictable. Studies done over the last decade have shown that specific, and often, predictable random and non-random factors could be responsible for that process. These studies have also motivated a “structure–function” paradigm that is yet to be resolved. Thus, elucidating the factors that affect community assembly in the bioreactors is necessary for predicting fluctuations in community structure and function. For this study activated sludge samples were collected during a one-year period from two geographically distant CAS bioreactors of different size. Combining community fingerprinting analysis and operational parameters data with a robust statistical analysis, we aimed to identify relevant links between system performance and bacterial community diversity and dynamics. In addition to revealing a significant β-diversity between the bioreactors’ communities, results showed that the largest bioreactor had a less dynamic but more efficient and diverse bacterial community throughout the study. The statistical analysis also suggests that deterministic factors, as opposed to stochastic factors, may have a bigger impact on the community structure in the largest bioreactor. Furthermore, the community seems to rely mainly on mechanisms of resistance and functional redundancy to maintain functional stability. We suggest that the ecological theories behind the Island Biogeography model and the species-area relationship were appropriate to predict the assembly of bacterial communities in these CAS bioreactors. These results are of great importance for engineers and ecologists as they reveal critical aspects of CAS systems that could be applied towards improving bioreactor design and operation. PMID:22880016

A preliminary riparian/wetland vegetation community classification of the Upper and Middle Rio Grande watersheds in New Mexico

Treesearch

Paula Durkin; Esteban Muldavin; Mike Bradley; Stacey E. Carr

1996-01-01

The riparian wetland vegetation communities of the upper and middle Rio Grande watersheds in New Mexico were surveyed in 1992 through 1994. The communities are hierarchically classified in terms of species composition and vegetation structure. The resulting Community Types are related to soil conditions, hydrological regime, and temporal dynamics. The classification is...

A mathematical programming approach for sequential clustering of dynamic networks

NASA Astrophysics Data System (ADS)

Silva, Jonathan C.; Bennett, Laura; Papageorgiou, Lazaros G.; Tsoka, Sophia

2016-02-01

A common analysis performed on dynamic networks is community structure detection, a challenging problem that aims to track the temporal evolution of network modules. An emerging area in this field is evolutionary clustering, where the community structure of a network snapshot is identified by taking into account both its current state as well as previous time points. Based on this concept, we have developed a mixed integer non-linear programming (MINLP) model, SeqMod, that sequentially clusters each snapshot of a dynamic network. The modularity metric is used to determine the quality of community structure of the current snapshot and the historical cost is accounted for by optimising the number of node pairs co-clustered at the previous time point that remain so in the current snapshot partition. Our method is tested on social networks of interactions among high school students, college students and members of the Brazilian Congress. We show that, for an adequate parameter setting, our algorithm detects the classes that these students belong more accurately than partitioning each time step individually or by partitioning the aggregated snapshots. Our method also detects drastic discontinuities in interaction patterns across network snapshots. Finally, we present comparative results with similar community detection methods for time-dependent networks from the literature. Overall, we illustrate the applicability of mathematical programming as a flexible, adaptable and systematic approach for these community detection problems. Contribution to the Topical Issue "Temporal Network Theory and Applications", edited by Petter Holme.

Microbial Community Structures and Dynamics in the O3/BAC Drinking Water Treatment Process

PubMed Central

Tian, Jian; Lu, Jun; Zhang, Yu; Li, Jian-Cheng; Sun, Li-Chen; Hu, Zhang-Li

2014-01-01

Effectiveness of drinking water treatment, in particular pathogen control during the water treatment process, is always a major public health concern. In this investigation, the application of PCR-DGGE technology to the analysis of microbial community structures and dynamics in the drinking water treatment process revealed several dominant microbial populations including: α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Bacteroidetes, Actinobacteria Firmicutes and Cyanobacteria. α-Proteobacteria and β-Proteobacteria were the dominant bacteria during the whole process. Bacteroidetes and Firmicutes were the dominant bacteria before and after treatment, respectively. Firmicutes showed season-dependent changes in population dynamics. Importantly, γ-Proteobacteria, which is a class of medically important bacteria, was well controlled by the O3/biological activated carbon (BAC) treatment, resulting in improved effluent water bio-safety. PMID:24937529

Temporal and Spatial Dynamics of Sediment Anaerobic Ammonium Oxidation (Anammox) Bacteria in Freshwater Lakes.

PubMed

Yang, Yuyin; Dai, Yu; Li, Ningning; Li, Bingxin; Xie, Shuguang; Liu, Yong

2017-02-01

Anaerobic ammonium-oxidizing (anammox) process can play an important role in freshwater nitrogen cycle. However, the distribution of anammox bacteria in freshwater lake and the associated environmental factors remain essentially unclear. The present study investigated the temporal and spatial dynamics of sediment anammox bacterial populations in eutrotrophic Dianchi Lake and mesotrophic Erhai Lake on the Yunnan Plateau (southwestern China). The remarkable spatial change of anammox bacterial abundance was found in Dianchi Lake, while the relatively slight spatial shift occurred in Erhai Lake. Dianchi Lake had greater anammox bacterial abundance than Erhai Lake. In both Dianchi Lake and Erhai Lake, anammox bacteria were much more abundant in summer than in spring. Anammox bacterial community richness, diversity, and structure in these two freshwater lakes were subjected to temporal and spatial variations. Sediment anammox bacterial communities in Dianchi Lake and Erhai Lake were dominated by Candidatus Brocadia and a novel phylotype followed by Candidatus Kuenenia; however, these two lakes had distinct anammox bacterial community structure. In addition, trophic status determined sediment anammox bacterial community structure.

The community ecology of pathogens: coinfection, coexistence and community composition.

PubMed

Seabloom, Eric W; Borer, Elizabeth T; Gross, Kevin; Kendig, Amy E; Lacroix, Christelle; Mitchell, Charles E; Mordecai, Erin A; Power, Alison G

2015-04-01

Disease and community ecology share conceptual and theoretical lineages, and there has been a resurgence of interest in strengthening links between these fields. Building on recent syntheses focused on the effects of host community composition on single pathogen systems, we examine pathogen (microparasite) communities using a stochastic metacommunity model as a starting point to bridge community and disease ecology perspectives. Such models incorporate the effects of core community processes, such as ecological drift, selection and dispersal, but have not been extended to incorporate host-pathogen interactions, such as immunosuppression or synergistic mortality, that are central to disease ecology. We use a two-pathogen susceptible-infected (SI) model to fill these gaps in the metacommunity approach; however, SI models can be intractable for examining species-diverse, spatially structured systems. By placing disease into a framework developed for community ecology, our synthesis highlights areas ripe for progress, including a theoretical framework that incorporates host dynamics, spatial structuring and evolutionary processes, as well as the data needed to test the predictions of such a model. Our synthesis points the way for this framework and demonstrates that a deeper understanding of pathogen community dynamics will emerge from approaches working at the interface of disease and community ecology. © 2015 John Wiley & Sons Ltd/CNRS.

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.

Hydrological drivers of wetland vegetational biodiversity patterns within Everglades National Park, Florida

NASA Astrophysics Data System (ADS)

Todd, J.; Pumo, D.; Azaele, S.; Muneepeerakul, R.; Miralles-Wilhelm, F. R.; Rinaldo, A.; Rodriguez-Iturbe, I.

2009-12-01

The influence of hydrological dynamics on vegetational biodiversity and structuring of wetland environments is of growing interest as wetlands are modified by human alteration and the increasing threat from climate change. Hydrology has long been considered a driving force in shaping wetland communities as the frequency of inundation along with the duration and depth of flooding are key determinants of wetland structure. We attempt to link hydrological dynamics with vegetational distribution and species richness across Everglades National Park (ENP) using two publicly available datasets. The first, the Everglades Depth Estimation Network (EDEN),is a water-surface model which determines the median daily measure of water level across a 400mX400m grid over seven years of measurement. The second is a vegetation map and classification system at the 1:15,000 scale which categorizes vegetation within the Everglades into 79 community types. From these data, we have studied the probabilistic structure of the frequency, duration, and depth of hydroperiods. Preliminary results indicate that the percentage of time a location is inundated is a principal structuring variable with individual communities responding differently. For example, sawgrass appears to be more of a generalist community as it is found across a wide range of time inundated percentages while spike rush has a more restricted distribution and favors wetter environments disproportionately more than predicted at random. Further, the diversity of vegetation communities (e.g. a measure of biodiversity) found across a hydrologic variable does not necessarily match the distribution function for that variable on the landscape. For instance, the number of communities does not differ across the percentage of time inundated. Different measures of vegetation biodiversity such as the local number of community types are also studied at different spatial scales with some characteristics, like the slope of the semi-logarithmic relation between rank and occupancy, found to be robust to scale changes. The ENP offers an expansive natural environment in which to study how vegetational dynamics and community composition are affected by hydrologic variables from the small scale (at the individual community level) to the large (biodiversity measures at differing spatial scales).

Temporal and spatial constraints on community assembly during microbial colonization of wood in seawater.

PubMed

Kalenitchenko, Dimitri; Fagervold, Sonja K; Pruski, Audrey M; Vétion, Gilles; Yücel, Mustafa; Le Bris, Nadine; Galand, Pierre E

2015-12-01

Wood falls on the ocean floor form chemosynthetic ecosystems that remain poorly studied compared with features such as hydrothermal vents or whale falls. In particular, the microbes forming the base of this unique ecosystem are not well characterized and the ecology of communities is not known. Here we use wood as a model to study microorganisms that establish and maintain a chemosynthetic ecosystem. We conducted both aquaria and in situ deep-sea experiments to test how different environmental constraints structure the assembly of bacterial, archaeal and fungal communities. We also measured changes in wood lipid concentrations and monitored sulfide production as a way to detect potential microbial activity. We show that wood falls are dynamic ecosystems with high spatial and temporal community turnover, and that the patterns of microbial colonization change depending on the scale of observation. The most illustrative example was the difference observed between pine and oak wood community dynamics. In pine, communities changed spatially, with strong differences in community composition between wood microhabitats, whereas in oak, communities changed more significantly with time of incubation. Changes in community assembly were reflected by changes in phylogenetic diversity that could be interpreted as shifts between assemblies ruled by species sorting to assemblies structured by competitive exclusion. These ecological interactions followed the dynamics of the potential microbial metabolisms accompanying wood degradation in the sea. Our work showed that wood is a good model for creating and manipulating chemosynthetic ecosystems in the laboratory, and attracting not only typical chemosynthetic microbes but also emblematic macrofaunal species.

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.

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

Dynamic changes of bacterial community under bioremediation with Sphingobium sp. LY-6 in buprofezin-contaminated soil.

PubMed

Liu, Yuan; Hou, Qianqian; Liu, Wanru; Meng, Yawen; Wang, Guangli

2015-08-01

Buprofezin is a commonly used chemical with satisfactory biological activity against sucking insect pests, but its disposal can cause serious environmental problems. To study the feasibility of remedying contamination by buprofezin, microcosm experiments were carried out to study the effects of various concentrations of buprofezin and Sphingobium sp. LY-6 on soil bacterial communities in soils collected from vegetable fields. In this experiment, the results showed that buprofezin was effectively degraded by Sphingobium sp. LY-6 in incubation soils. Comparing to non-incubated soils, the cumulative degradation ratio of buprofezin was significantly increased, up to the extent of 85 and 51%, in the initial concentration of 10 and 100 mg kg(-1). The abundance and community structure of the bacterial communities were analysed by real-time PCR (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP). The findings suggest that buprofezin had a negative effect on soil bacterial community, and decreases in bacterial abundance were observed in the later part of the incubation period. The bacterial community structure and diversity shifted significantly at each sampling time. In conclusion, the buprofezin-degrading strain LY-6 played a major role in the bioremediation of the buprofezin-contaminated soil and influenced the dynamics and structure of the bacterial community, demonstrating the great potential of exogenous microorganisms for soil remediation.

Examination of the relationship between host worm community structure on transmission of the parasite, Myxobolus cerebralis by developing taxon-specific probes for multiplex qPCR to identify worm taxa in stream communities

NASA Astrophysics Data System (ADS)

Fytilis, N.; Lamb, R.; Kerans, B.; Stevens, L.; Rizzo, D. M.

2011-12-01

Fish diseases are often caused by waterborne parasites, making them ideal systems for modeling the non-linear relationships between disease dynamics, stream dwelling oligochaete communities and geochemical features. Myxobolus cerebralis, the causative agent of whirling disease in salmonid fishes, has been a major contributor to the loss of wild rainbow trout populations in numerous streams within the Intermountain West. The parasite alternates between an invertebrate and vertebrate host, being transmitted between the sediment feeding worm Tubifex tubifex (T.tubifex) and salmonid fishes. Worm community biodiversity and abundance are influenced by biogeochemical features and have been linked to disease severity in fish. The worm (T.tubifex) lives in communities with 3-4 other types of worms in stream sediments. Unfortunately, taxonomic identification of oligochaetes is largely dependent on morphological characteristics of sexually mature adults. We have collected and identified ~700 worms from eight sites using molecular genetic probes and a taxonomic key. Additionally, ~1700 worms were identified using only molecular genetic probes. To facilitate distinguishing among tubificids, we developed two multiplex molecular genetic probe-based quantitative polymerase reaction (qPCR) assays to assess tubificid communities in the study area. Similar qPCR techniques specific for M.cerebralis used to determine if individual worms were infected with the parasite. We show how simple Bayesian analysis of the qPCR data can predict the worm community structure and reveal relationships between biodiversity of host communities and host-parasite dynamics. To our knowledge, this is the first study that combines molecular data of both the host and the parasite to examine the effects of host community structure on the transmission of a parasite. Our work can be extended to examine the links between worm community structure and biogeochemical features using molecular genetics and Bayesian statistics to assist in identifying new nonlinear relationships and suggest new subsets of input parameters. Future work includes the development of a new complex systems tool capable of assimilating biological DNA sequence data and biogeochemical features using artificial neural networks and Bayesian analysis. The methodologies developed here helped mine the relationships between biodiversity of host communities and host-parasite dynamics. The results from our study will be useful to managers and researchers for assessing the risk of whirling disease in drainages where tubificid community composition data are needed. This collaboration between modelers, field ecologists and geneticists will prove useful in modeling efforts and will enable more effective, high-volume hypothesis generation. The ability to characterize areas of high whirling disease risk is essential for improving our understanding of the dynamics of M.cerebralis such that appropriate management strategies can be implemented.

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

Dynamic Modeling of the Economic Impacts of a Terrorist Attack using a Radiological Dispersion Device

DTIC Science & Technology

2009-03-01

Coverage to Loss Ratio Increasing Indiv idual Losses f rom Contamination Daining Recovery Decreasing Losses Through Community Recov ery Community...Localized Stimulus Plan Switch Noname 1 Daining Recov ery Converter Business Loss Structure 64 were never directly refunded by federal...Incentiv es Revitalization Plan Legislative Financial Backing of Localized Stimulus Plan Switch Daining Recovery Converter Tax Rev enue Loss Structure

Trophic network models explain instability of Early Triassic terrestrial communities

PubMed Central

Roopnarine, Peter D; Angielczyk, Kenneth D; Wang, Steve C; Hertog, Rachel

2007-01-01

Studies of the end-Permian mass extinction have emphasized potential abiotic causes and their direct biotic effects. Less attention has been devoted to secondary extinctions resulting from ecological crises and the effect of community structure on such extinctions. Here we use a trophic network model that combines topological and dynamic approaches to simulate disruptions of primary productivity in palaeocommunities. We apply the model to Permian and Triassic communities of the Karoo Basin, South Africa, and show that while Permian communities bear no evidence of being especially susceptible to extinction, Early Triassic communities appear to have been inherently less stable. Much of the instability results from the faster post-extinction diversification of amphibian guilds relative to amniotes. The resulting communities differed fundamentally in structure from their Permian predecessors. Additionally, our results imply that changing community structures over time may explain long-term trends like declining rates of Phanerozoic background extinction PMID:17609191

Diversity and Dynamics of Microbial Community Structure in Different Mangrove, Marine and Freshwater Sediments During Anaerobic Debromination of PBDEs

PubMed Central

Wang, Ya Fen; Zhu, Hao Wen; Wang, Ying; Zhang, Xiang Ling; Tam, Nora Fung Yee

2018-01-01

Little is known about the diversity and succession of indigenous microbial community during debromination of polybrominated diphenyl ethers (PBDEs). This study examined the diversity and dynamics of microbial community structure in eight saline (mangrove and marine) and freshwater sediment microcosms exhibiting different debrominating capabilities for hexa-BDE 153, a common congener in sediments, using terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses. The results showed that microbial community structure greatly differed between the saline and freshwater microcosms, likely leading to distinct variations in their debrominating capabilities and pathways. Higher relative abundances of Chloroflexi and Deltaproteobacteria succeed by Alphaproteobacteria and Betaproteobacteria were detected in the two mangrove microcosms with the fastest debrominating capabilities mainly via para pathway, respectively; the dominance of Alphaproteobacteria resulted in less accumulation of tetra-BDEs and more complete debromination of lower brominated congeners (from di- to tetra-BDEs). Meanwhile, the shifts in both microbial community structure and PBDE profiles were relatively small in the less efficient freshwater microcosms, with relatively more ortho and meta brominated products of BDE-153 resulted. Coincidently, one of the freshwater microcosms showed sudden increases of Chloroflexi and Deltaproteobacteria by the end of incubation, which synchronized with the increase in the removal rate of BDE-153. The significant relationship between microbial community structure and PBDEs was confirmed by redundancy analysis (18.7% of total variance explained, P = 0.002). However, the relative abundance of the well-known dechlorinator Dehalococcoides showed no clear correlation with the debrominating capability across different microcosms. These findings shed light in the significance of microbial community network in different saline environments on enhancement of PBDE intrinsic debromination. PMID:29867858

Diversity and Dynamics of Microbial Community Structure in Different Mangrove, Marine and Freshwater Sediments During Anaerobic Debromination of PBDEs.

PubMed

Wang, Ya Fen; Zhu, Hao Wen; Wang, Ying; Zhang, Xiang Ling; Tam, Nora Fung Yee

2018-01-01

Little is known about the diversity and succession of indigenous microbial community during debromination of polybrominated diphenyl ethers (PBDEs). This study examined the diversity and dynamics of microbial community structure in eight saline (mangrove and marine) and freshwater sediment microcosms exhibiting different debrominating capabilities for hexa-BDE 153, a common congener in sediments, using terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses. The results showed that microbial community structure greatly differed between the saline and freshwater microcosms, likely leading to distinct variations in their debrominating capabilities and pathways. Higher relative abundances of Chloroflexi and Deltaproteobacteria succeed by Alphaproteobacteria and Betaproteobacteria were detected in the two mangrove microcosms with the fastest debrominating capabilities mainly via para pathway, respectively; the dominance of Alphaproteobacteria resulted in less accumulation of tetra-BDEs and more complete debromination of lower brominated congeners (from di- to tetra-BDEs). Meanwhile, the shifts in both microbial community structure and PBDE profiles were relatively small in the less efficient freshwater microcosms, with relatively more ortho and meta brominated products of BDE-153 resulted. Coincidently, one of the freshwater microcosms showed sudden increases of Chloroflexi and Deltaproteobacteria by the end of incubation, which synchronized with the increase in the removal rate of BDE-153. The significant relationship between microbial community structure and PBDEs was confirmed by redundancy analysis (18.7% of total variance explained, P = 0.002). However, the relative abundance of the well-known dechlorinator Dehalococcoides showed no clear correlation with the debrominating capability across different microcosms. These findings shed light in the significance of microbial community network in different saline environments on enhancement of PBDE intrinsic debromination.

Interactive effects of warming, eutrophication and size structure: impacts on biodiversity and food-web structure.

PubMed

Binzer, Amrei; Guill, Christian; Rall, Björn C; Brose, Ulrich

2016-01-01

Warming and eutrophication are two of the most important global change stressors for natural ecosystems, but their interaction is poorly understood. We used a dynamic model of complex, size-structured food webs to assess interactive effects on diversity and network structure. We found antagonistic impacts: Warming increases diversity in eutrophic systems and decreases it in oligotrophic systems. These effects interact with the community size structure: Communities of similarly sized species such as parasitoid-host systems are stabilized by warming and destabilized by eutrophication, whereas the diversity of size-structured predator-prey networks decreases strongly with warming, but decreases only weakly with eutrophication. Nonrandom extinction risks for generalists and specialists lead to higher connectance in networks without size structure and lower connectance in size-structured communities. Overall, our results unravel interactive impacts of warming and eutrophication and suggest that size structure may serve as an important proxy for predicting the community sensitivity to these global change stressors. © 2015 John Wiley & Sons Ltd.

A fast community detection method in bipartite networks by distance dynamics

NASA Astrophysics Data System (ADS)

Sun, Hong-liang; Ch'ng, Eugene; Yong, Xi; Garibaldi, Jonathan M.; See, Simon; Chen, Duan-bing

2018-04-01

Many real bipartite networks are found to be divided into two-mode communities. In this paper, we formulate a new two-mode community detection algorithm BiAttractor. It is based on distance dynamics model Attractor proposed by Shao et al. with extension from unipartite to bipartite networks. Since Jaccard coefficient of distance dynamics model is incapable to measure distances of different types of vertices in bipartite networks, our main contribution is to extend distance dynamics model from unipartite to bipartite networks using a novel measure Local Jaccard Distance (LJD). Furthermore, distances between different types of vertices are not affected by common neighbors in the original method. This new idea makes clear assumptions and yields interpretable results in linear time complexity O(| E |) in sparse networks, where | E | is the number of edges. Experiments on synthetic networks demonstrate it is capable to overcome resolution limit compared with existing other methods. Further research on real networks shows that this model can accurately detect interpretable community structures in a short time.

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

Hierarchical spatial structure of stream fish colonization and extinction

USGS Publications Warehouse

Hitt, N.P.; Roberts, J.H.

2012-01-01

Spatial variation in extinction and colonization is expected to influence community composition over time. In stream fish communities, local species richness (alpha diversity) and species turnover (beta diversity) are thought to be regulated by high extinction rates in headwater streams and high colonization rates in downstream areas. We evaluated the spatiotemporal structure of fish communities in streams originally surveyed by Burton and Odum 1945 (Ecology 26: 182-194) in Virginia, USA and explored the effects of species traits on extinction and colonization dynamics. We documented dramatic changes in fish community structure at both the site and stream scales. Of the 34 fish species observed, 20 (59%) were present in both time periods, but 11 (32%) colonized the study area and three (9%) were extirpated over time. Within streams, alpha diversity increased in two of three streams but beta diversity decreased dramatically in all streams due to fish community homogenization caused by colonization of common species and extirpation of rare species. Among streams, however, fish communities differentiated over time. Regression trees indicated that reproductive life-history traits such as spawning mound construction, associations with mound-building species, and high fecundity were important predictors of species persistence or colonization. Conversely, native fishes not associated with mound-building exhibited the highest rates of extirpation from streams. Our results demonstrate that stream fish colonization and extinction dynamics exhibit hierarchical spatial structure and suggest that mound-building fishes serve as keystone species for colonization of headwater streams.

Towards a Dialogical Pedagogy: Some Characteristics of a Community of Mathematical Inquiry

ERIC Educational Resources Information Center

Kennedy, Nadia Stoyanova

2009-01-01

This paper discusses a teaching model called community of mathematical inquiry (CMI), characterized by dialogical and inquiry-driven communication and a dynamic structure of intertwined cognitive processes including distributed thinking, mathematical argumentation, integrated reasoning, conceptual transformation, internalization of critical…

Microbial community structures in algae cultivation ponds for bioconversion of agricultural wastes from livestock industry for feed production

USDA-ARS?s Scientific Manuscript database

Dynamics of seasonal microbial community compositions in algae cultivation ponds are complex. There is very limited knowledge on community compositions that may play significant roles in the bioconversion of manure nu¬trients to animal feed. Algae production is an alternative where land area for pro...

Organizing for Change: A Case Study of Grassroots Leadership at a Kentucky Community College

ERIC Educational Resources Information Center

Borregard, Andrea Rae

2016-01-01

Community colleges constitute a special type of higher education organization: their complex mission, dynamics, personnel structures, and values require a distinct set of understandings and skills to lead and manage them well. Most of the research on leadership in community colleges focuses on leaders in positions of power (presidents, provosts,…

Money circulation networks reveal emerging geographical communities

NASA Astrophysics Data System (ADS)

Brockmann, D.; Theis, F.; David, V.

2008-03-01

Geographical communities and their boundaries are key determinants of various spatially extended dynamical phenomena. Examples are migration dynamics of species, the spread of infectious diseases, bioinvasive processes, and the spatial evolution of language. We address the question to what extend multiscale human transportation networks encode geographical community structures, how they differ from geopolitical classifications, whether they are spatially coherent, and analyse their structure as a function of length scale. Our analysis is based on a proxy network for human transportation obtained from the geographic circulation of more than 10 million dollar bills in the United States recorded at the bill tracking website www.wheresgeorge.com. The data extends that of a previous study (Brockmann et al., Nature 2006) on the discovery of scaling laws of human travel by an order of magnitude and permits an approach to multiscale human transportation from a network perspective.

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.

NETWORK STRUCTURE, MULTIPLEXITY, AND EVOLUTION AS INFLUENCES ON COMMUNITY-BASED PARTICIPATORY INTERVENTIONS.

PubMed

Wang, Rong; Tanjasiri, Sora Park; Palmer, Paula; Valente, Thomas W

2016-08-01

This study applies an ecological perspective to the context of community-based participatory research (CBPR). Specifically, it examines how endogenous and exogenous factors influence the dynamics of CBPR partnerships, including the tendency toward reciprocity and transitivity, the organizational type, the level of resource sufficiency, the level of organizational influence, and the perceived CBPR effect on organizations. The results demonstrate that network structure is related to the selection and retention of interorganizational networks over time, and organizations of the same type are more likely to form partnerships with each other. It shows that the dynamics of the CBPR initiative presented in this article were driven by the structure of the interorganizational networks rather than their individual organizational attributes. Implications for sustaining CBPR partnerships are drawn from the findings.

NETWORK STRUCTURE, MULTIPLEXITY, AND EVOLUTION AS INFLUENCES ON COMMUNITY-BASED PARTICIPATORY INTERVENTIONS

PubMed Central

Wang, Rong; Tanjasiri, Sora Park; Palmer, Paula; Valente, Thomas W.

2017-01-01

This study applies an ecological perspective to the context of community-based participatory research (CBPR). Specifically, it examines how endogenous and exogenous factors influence the dynamics of CBPR partnerships, including the tendency toward reciprocity and transitivity, the organizational type, the level of resource sufficiency, the level of organizational influence, and the perceived CBPR effect on organizations. The results demonstrate that network structure is related to the selection and retention of interorganizational networks over time, and organizations of the same type are more likely to form partnerships with each other. It shows that the dynamics of the CBPR initiative presented in this article were driven by the structure of the interorganizational networks rather than their individual organizational attributes. Implications for sustaining CBPR partnerships are drawn from the findings. PMID:29430067

Mnemonic convergence in social networks: The emergent properties of cognition at a collective level

PubMed Central

Coman, Alin; Momennejad, Ida; Drach, Rae D.; Geana, Andra

2016-01-01

The development of shared memories, beliefs, and norms is a fundamental characteristic of human communities. These emergent outcomes are thought to occur owing to a dynamic system of information sharing and memory updating, which fundamentally depends on communication. Here we report results on the formation of collective memories in laboratory-created communities. We manipulated conversational network structure in a series of real-time, computer-mediated interactions in fourteen 10-member communities. The results show that mnemonic convergence, measured as the degree of overlap among community members’ memories, is influenced by both individual-level information-processing phenomena and by the conversational social network structure created during conversational recall. By studying laboratory-created social networks, we show how large-scale social phenomena (i.e., collective memory) can emerge out of microlevel local dynamics (i.e., mnemonic reinforcement and suppression effects). The social-interactionist approach proposed herein points to optimal strategies for spreading information in social networks and provides a framework for measuring and forging collective memories in communities of individuals. PMID:27357678

Integrating succession and community assembly perspectives

PubMed Central

Chang, Cynthia; HilleRisLambers, Janneke

2016-01-01

Succession and community assembly research overlap in many respects, such as through their focus on how ecological processes like dispersal, environmental filters, and biotic interactions influence community structure. Indeed, many recent advances have been made by successional studies that draw on modern analytical techniques introduced by contemporary community assembly studies. However, community assembly studies generally lack a temporal perspective, both on how the forces structuring communities might change over time and on how historical contingency (e.g. priority effects and legacy effects) and complex transitions (e.g. threshold effects) might alter community trajectories. We believe a full understanding of the complex interacting processes that shape community dynamics across large temporal scales can best be achieved by combining concepts, tools, and study systems into an integrated conceptual framework that draws upon both succession and community assembly theory. PMID:27785355

Mathematical Modeling of Microbial Community Dynamics: A Methodological Review

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

Song, Hyun-Seob; Cannon, William R.; Beliaev, Alex S.

Microorganisms in nature form diverse communities that dynamically change in structure and function in response to environmental variations. As a complex adaptive system, microbial communities show higher-order properties that are not present in individual microbes, but arise from their interactions. Predictive mathematical models not only help to understand the underlying principles of the dynamics and emergent properties of natural and synthetic microbial communities, but also provide key knowledge required for engineering them. In this article, we provide an overview of mathematical tools that include not only current mainstream approaches, but also less traditional approaches that, in our opinion, can bemore » potentially useful. We discuss a broad range of methods ranging from low-resolution supra-organismal to high-resolution individual-based modeling. Particularly, we highlight the integrative approaches that synergistically combine disparate methods. In conclusion, we provide our outlook for the key aspects that should be further developed to move microbial community modeling towards greater predictive power.« less

Network community-based model reduction for vortical flows

NASA Astrophysics Data System (ADS)

Gopalakrishnan Meena, Muralikrishnan; Nair, Aditya G.; Taira, Kunihiko

2018-06-01

A network community-based reduced-order model is developed to capture key interactions among coherent structures in high-dimensional unsteady vortical flows. The present approach is data-inspired and founded on network-theoretic techniques to identify important vortical communities that are comprised of vortical elements that share similar dynamical behavior. The overall interaction-based physics of the high-dimensional flow field is distilled into the vortical community centroids, considerably reducing the system dimension. Taking advantage of these vortical interactions, the proposed methodology is applied to formulate reduced-order models for the inter-community dynamics of vortical flows, and predict lift and drag forces on bodies in wake flows. We demonstrate the capabilities of these models by accurately capturing the macroscopic dynamics of a collection of discrete point vortices, and the complex unsteady aerodynamic forces on a circular cylinder and an airfoil with a Gurney flap. The present formulation is found to be robust against simulated experimental noise and turbulence due to its integrating nature of the system reduction.

Emergence of structured communities through evolutionary dynamics.

PubMed

Shtilerman, Elad; Kessler, David A; Shnerb, Nadav M

2015-10-21

Species-rich communities, in which many competing species coexist in a single trophic level, are quite frequent in nature, but pose a formidable theoretical challenge. In particular, it is known that complex competitive systems become unstable and unfeasible when the number of species is large. Recently, many studies have attributed the stability of natural communities to the structure of the interspecific interaction network, yet the nature of such structures and the underlying mechanisms responsible for them remain open questions. Here we introduce an evolutionary model, based on the generic Lotka-Volterra competitive framework, from which a stable, structured, diverse community emerges spontaneously. The modular structure of the competition matrix reflects the phylogeny of the community, in agreement with the hierarchial taxonomic classification. Closely related species tend to have stronger niche overlap and weaker fitness differences, as opposed to pairs of species from different modules. The competitive-relatedness hypothesis and the idea of emergent neutrality are discussed in the context of this evolutionary model. Copyright © 2015 Elsevier Ltd. All rights reserved.

Reclaiming respectability? The class-cultural dynamics of crime, community and governance in inner-city Dublin.

PubMed

Ilan, Jonathan

2011-01-01

This paper critically examines developments in Irish urban governance through an ethnographic account of one community's historical memory and contemporary structure. During an era of rapid economic growth, the Irish state has courted previously excluded communities, offering them greater "inclusion" as "partners" in responding to urban decay and crime. The micro-governance structures this creates, however, become sites of contest between competing community factions and class-cultural imperatives. Tensions emerge between aspirational community leaders championing the aesthetics (if not the values) of "respectability" and residual residents who are presented as "rough". The paper demonstrates that nuances of class-cultural identity dictate the character of partnership governance at the community level with particular implications for local regeneration and crime control agendas.

nirS-Encoding denitrifier community composition, distribution, and abundance along the coastal wetlands of China.

PubMed

Gao, Juan; Hou, Lijun; Zheng, Yanling; Liu, Min; Yin, Guoyu; Li, Xiaofei; Lin, Xianbiao; Yu, Chendi; Wang, Rong; Jiang, Xiaofen; Sun, Xiuru

2016-10-01

For the past few decades, human activities have intensively increased the reactive nitrogen enrichment in China's coastal wetlands. Although denitrification is a critical pathway of nitrogen removal, the understanding of denitrifier community dynamics driving denitrification remains limited in the coastal wetlands. In this study, the diversity, abundance, and community composition of nirS-encoding denitrifiers were analyzed to reveal their variations in China's coastal wetlands. Diverse nirS sequences were obtained and more than 98 % of them shared considerable phylogenetic similarity with sequences obtained from aquatic systems (marine/estuarine/coastal sediments and hypoxia sea water). Clone library analysis revealed that the distribution and composition of nirS-harboring denitrifiers had a significant latitudinal differentiation, but without a seasonal shift. Canonical correspondence analysis showed that the community structure of nirS-encoding denitrifiers was significantly related to temperature and ammonium concentration. The nirS gene abundance ranged from 4.3 × 10(5) to 3.7 × 10(7) copies g(-1) dry sediment, with a significant spatial heterogeneity. Among all detected environmental factors, temperature was a key factor affecting not only the nirS gene abundance but also the community structure of nirS-type denitrifiers. Overall, this study significantly enhances our understanding of the structure and dynamics of denitrifying communities in the coastal wetlands of China.

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.

Cameras on the NEPTUNE Canada seafloor observatory: Towards monitoring hydrothermal vent ecosystem dynamics

NASA Astrophysics Data System (ADS)

Robert, K.; Matabos, M.; Sarrazin, J.; Sarradin, P.; Lee, R. W.; Juniper, K.

2010-12-01

Hydrothermal vent environments are among the most dynamic benthic habitats in the ocean. The relative roles of physical and biological factors in shaping vent community structure remain unclear. Undersea cabled observatories offer the power and bandwidth required for high-resolution, time-series study of the dynamics of vent communities and the physico-chemical forces that influence them. The NEPTUNE Canada cabled instrument array at the Endeavour hydrothermal vents provides a unique laboratory for researchers to conduct long-term, integrated studies of hydrothermal vent ecosystem dynamics in relation to environmental variability. Beginning in September-October 2010, NEPTUNE Canada (NC) will be deploying a multi-disciplinary suite of instruments on the Endeavour Segment of the Juan de Fuca Ridge. Two camera and sensor systems will be used to study ecosystem dynamics in relation to hydrothermal discharge. These studies will make use of new experimental protocols for time-series observations that we have been developing since 2008 at other observatory sites connected to the VENUS and NC networks. These protocols include sampling design, camera calibration (i.e. structure, position, light, settings) and image analysis methodologies (see communication by Aron et al.). The camera systems to be deployed in the Main Endeavour vent field include a Sidus high definition video camera (2010) and the TEMPO-mini system (2011), designed by IFREMER (France). Real-time data from three sensors (O2, dissolved Fe, temperature) integrated with the TEMPO-mini system will enhance interpretation of imagery. For the first year of observations, a suite of internally recording temperature probes will be strategically placed in the field of view of the Sidus camera. These installations aim at monitoring variations in vent community structure and dynamics (species composition and abundances, interactions within and among species) in response to changes in environmental conditions at different temporal scales. High-resolution time-series studies also provide a mean of studying population dynamics, biological rhythms, organism growth and faunal succession. In addition to programmed time-series monitoring, the NC infrastructure will also permit manual and automated modification of observational protocols in response to natural events. This will enhance our ability to document potentially critical but short-lived environmental forces affecting vent communities.

Dynamics in cyanobacterial communities from a relatively stable environment in an urbanised area (ambient springs in Central Poland).

PubMed

Nowicka-Krawczyk, Paulina; Żelazna-Wieczorek, Joanna

2017-02-01

Ambient springs are often cited as an example of an ecosystem with stable environmental conditions. A static biotope fosters the development of constant communities with a stable qualitative and relatively stable quantitative structure. Two years of studying cyanobacteria in different microhabitats of the rheocrenic and limnocrenic ambient springs located in urban areas showed that there is a high degree of cyanobacterial diversity and spatial and seasonal dynamics in communities. Spatial heterogeneity in relation to the type of spring and the type of microhabitat is reflected not only by a change in the quantitative structure (the number of species and their biomass), but also by a change in the composition of species. Seasonal changes depended on the type of spring and the type of microhabitat, where weather conditions influenced the communities by different degrees. Cyanobacterial communities of limnocrenes were more diverse in terms of composition and biomass, but they revealed a low seasonal dynamic in contrast to the communities of rheocrenes. The classification of springs based on their environmental conditions revealed that some springs were similar. The resemblance stemmed from the origin of human impact, which was reflected to a high degree in changes in the natural hydrochemical conditions of the springs. For the purpose of understanding which environmental factors had the greatest influence on cyanobacterial communities, a BIO-ENV procedure was performed. The procedure revealed that of most importance was a group of ions not related to the nature of the spring environment - NH 4 + , NO 2 - , NO 3 - , and PO 4 3- . The presence of these ions in groundwater was a result of direct and indirect human activity in the area of aquifers. The dynamics in communities in the studied springs were accelerated by human impact and weather conditions. Copyright © 2016 Elsevier B.V. All rights reserved.

Climatic warming destabilizes forest ant communities

PubMed Central

Diamond, Sarah E.; Nichols, Lauren M.; Pelini, Shannon L.; Penick, Clint A.; Barber, Grace W.; Cahan, Sara Helms; Dunn, Robert R.; Ellison, Aaron M.; Sanders, Nathan J.; Gotelli, Nicholas J.

2016-01-01

How will ecological communities change in response to climate warming? Direct effects of temperature and indirect cascading effects of species interactions are already altering the structure of local communities, but the dynamics of community change are still poorly understood. We explore the cumulative effects of warming on the dynamics and turnover of forest ant communities that were warmed as part of a 5-year climate manipulation experiment at two sites in eastern North America. At the community level, warming consistently increased occupancy of nests and decreased extinction and nest abandonment. This consistency was largely driven by strong responses of a subset of thermophilic species at each site. As colonies of thermophilic species persisted in nests for longer periods of time under warmer temperatures, turnover was diminished, and species interactions were likely altered. We found that dynamical (Lyapunov) community stability decreased with warming both within and between sites. These results refute null expectations of simple temperature-driven increases in the activity and movement of thermophilic ectotherms. The reduction in stability under warming contrasts with the findings of previous studies that suggest resilience of species interactions to experimental and natural warming. In the face of warmer, no-analog climates, communities of the future may become increasingly fragile and unstable. PMID:27819044

Climatic warming destabilizes forest ant communities.

PubMed

Diamond, Sarah E; Nichols, Lauren M; Pelini, Shannon L; Penick, Clint A; Barber, Grace W; Cahan, Sara Helms; Dunn, Robert R; Ellison, Aaron M; Sanders, Nathan J; Gotelli, Nicholas J

2016-10-01

How will ecological communities change in response to climate warming? Direct effects of temperature and indirect cascading effects of species interactions are already altering the structure of local communities, but the dynamics of community change are still poorly understood. We explore the cumulative effects of warming on the dynamics and turnover of forest ant communities that were warmed as part of a 5-year climate manipulation experiment at two sites in eastern North America. At the community level, warming consistently increased occupancy of nests and decreased extinction and nest abandonment. This consistency was largely driven by strong responses of a subset of thermophilic species at each site. As colonies of thermophilic species persisted in nests for longer periods of time under warmer temperatures, turnover was diminished, and species interactions were likely altered. We found that dynamical (Lyapunov) community stability decreased with warming both within and between sites. These results refute null expectations of simple temperature-driven increases in the activity and movement of thermophilic ectotherms. The reduction in stability under warming contrasts with the findings of previous studies that suggest resilience of species interactions to experimental and natural warming. In the face of warmer, no-analog climates, communities of the future may become increasingly fragile and unstable.

SCOUT: simultaneous time segmentation and community detection in dynamic networks

PubMed Central

Hulovatyy, Yuriy; Milenković, Tijana

2016-01-01

Many evolving complex real-world systems can be modeled via dynamic networks. An important problem in dynamic network research is community detection, which finds groups of topologically related nodes. Typically, this problem is approached by assuming either that each time point has a distinct community organization or that all time points share a single community organization. The reality likely lies between these two extremes. To find the compromise, we consider community detection in the context of the problem of segment detection, which identifies contiguous time periods with consistent network structure. Consequently, we formulate a combined problem of segment community detection (SCD), which simultaneously partitions the network into contiguous time segments with consistent community organization and finds this community organization for each segment. To solve SCD, we introduce SCOUT, an optimization framework that explicitly considers both segmentation quality and partition quality. SCOUT addresses limitations of existing methods that can be adapted to solve SCD, which consider only one of segmentation quality or partition quality. In a thorough evaluation, SCOUT outperforms the existing methods in terms of both accuracy and computational complexity. We apply SCOUT to biological network data to study human aging. PMID:27881879

Microbial community dynamics in Inferno Crater Lake, a thermally fluctuating geothermal spring

PubMed Central

Ward, Laura; Taylor, Michael W; Power, Jean F; Scott, Bradley J; McDonald, Ian R; Stott, Matthew B

2017-01-01

Understanding how microbial communities respond and adjust to ecosystem perturbation is often difficult to interpret due to multiple and often simultaneous variations in observed conditions. In this research, we investigated the microbial community dynamics of Inferno Crater Lake, an acidic geothermal spring in New Zealand with a unique thermal cycle that varies between 30 and 80 °C over a period of 40–60 days. Using a combination of next-generation sequencing, geochemical analysis and quantitative PCR we found that the microbial community composition was predominantly chemolithotrophic and strongly associated with the thermal cycle. At temperatures >65 °C, the microbial community was dominated almost exclusively by sulphur-oxidising archaea (Sulfolobus-like spp.). By contrast, at mesophilic temperatures the community structure was more mixed, comprising both archaea and bacteria but dominated primarily by chemolithotrophic sulphur and hydrogen oxidisers. Multivariate analysis of physicochemical data confirmed that temperature was the only significant variable associated with community turnover. This research contributes to our understanding of microbial community dynamics in variable environments, using a naturally alternating system as a model and extends our limited knowledge of acidophile ecology in geothermal habitats. PMID:28072418

Microbial community dynamics in Inferno Crater Lake, a thermally fluctuating geothermal spring.

PubMed

Ward, Laura; Taylor, Michael W; Power, Jean F; Scott, Bradley J; McDonald, Ian R; Stott, Matthew B

2017-05-01

Understanding how microbial communities respond and adjust to ecosystem perturbation is often difficult to interpret due to multiple and often simultaneous variations in observed conditions. In this research, we investigated the microbial community dynamics of Inferno Crater Lake, an acidic geothermal spring in New Zealand with a unique thermal cycle that varies between 30 and 80 °C over a period of 40-60 days. Using a combination of next-generation sequencing, geochemical analysis and quantitative PCR we found that the microbial community composition was predominantly chemolithotrophic and strongly associated with the thermal cycle. At temperatures >65 °C, the microbial community was dominated almost exclusively by sulphur-oxidising archaea (Sulfolobus-like spp.). By contrast, at mesophilic temperatures the community structure was more mixed, comprising both archaea and bacteria but dominated primarily by chemolithotrophic sulphur and hydrogen oxidisers. Multivariate analysis of physicochemical data confirmed that temperature was the only significant variable associated with community turnover. This research contributes to our understanding of microbial community dynamics in variable environments, using a naturally alternating system as a model and extends our limited knowledge of acidophile ecology in geothermal habitats.

Vegetation dynamics

Treesearch

Sammy L. King; Terry J. Antrobus; Sarah Billups

2000-01-01

A disturbance can be defined as "any relatively discrete event in time that disrupts ecosystem, community, or population structure and changes resources, substrate availability, or the physical environment" (Pickett and White 1985). Vegetation dynamics are a function of the temporal and spatial patterns of the disturbance regime. Natural disturbance regimes...

Understanding Microbial Communities: Function, Structure and Dynamics

DTIC Science & Technology

2015-02-11

allow us to characterise the species composition of these communities from a variety of environmentally and medically-relevant habitats. Despite this...ecology. The primary purpose of this program was to facilitate the building a scientific community around using and developing mathematical...biology and advancement of new biotechnologies and medical applications. Summary of results (a) Activities Over the course of the 4 months of

Hierarchical modeling and inference in ecology: The analysis of data from populations, metapopulations and communities

USGS Publications Warehouse

Royle, J. Andrew; Dorazio, Robert M.

2008-01-01

A guide to data collection, modeling and inference strategies for biological survey data using Bayesian and classical statistical methods. This book describes a general and flexible framework for modeling and inference in ecological systems based on hierarchical models, with a strict focus on the use of probability models and parametric inference. Hierarchical models represent a paradigm shift in the application of statistics to ecological inference problems because they combine explicit models of ecological system structure or dynamics with models of how ecological systems are observed. The principles of hierarchical modeling are developed and applied to problems in population, metapopulation, community, and metacommunity systems. The book provides the first synthetic treatment of many recent methodological advances in ecological modeling and unifies disparate methods and procedures. The authors apply principles of hierarchical modeling to ecological problems, including * occurrence or occupancy models for estimating species distribution * abundance models based on many sampling protocols, including distance sampling * capture-recapture models with individual effects * spatial capture-recapture models based on camera trapping and related methods * population and metapopulation dynamic models * models of biodiversity, community structure and dynamics.

Opinion dynamics in a group-based society

NASA Astrophysics Data System (ADS)

Gargiulo, F.; Huet, S.

2010-09-01

Many models have been proposed to analyze the evolution of opinion structure due to the interaction of individuals in their social environment. Such models analyze the spreading of ideas both in completely interacting backgrounds and on social networks, where each person has a finite set of interlocutors. In this paper we analyze the reciprocal feedback between the opinions of the individuals and the structure of the interpersonal relationships at the level of community structures. For this purpose we define a group-based random network and we study how this structure co-evolves with opinion dynamics processes. We observe that the adaptive network structure affects the opinion dynamics process helping the consensus formation. The results also show interesting behaviors in regards to the size distribution of the groups and their correlation with opinion structure.

GENETIC STRUCTURE OF TRIATOMA INFESTANS POPULATIONS IN RURAL COMMUNITIES OF SANTIAGO DEL ESTERO, NORTHERN ARGENTINA

PubMed Central

Marcet, PL; Mora, MS; Cutrera, AP; Jones, L; Gürtler, RE; Kitron, U; Dotson, EM

2008-01-01

To gain an understanding of the genetic structure and dispersal dynamics of T. infestans populations, we analyzed the multilocus genotype of 10 microsatellite loci for 352 T. infestans collected in 21 houses of 11 rural communities in October 2002. Genetic structure was analyzed at the community and house compound levels. Analysis revealed that vector control actions affected the genetic structure of T. infestans populations. Bug populations from communities under sustained vector control (core area) were highly structured and genetic differentiation between neighboring house compounds was significant. In contrast, bug populations from communities with sporadic vector control actions were more homogeneous and lacked defined genetic clusters. Genetic differentiation between population pairs did not fit a model of isolation by distance at the microgeographical level. Evidence consistent with flight or walking bug dispersal was detected within and among communities, dispersal was more female-biased in the core area and results suggested that houses received immigrants from more than one source. Putative sources and mechanisms of re-infestation are described. These data may be use to design improved vector control strategies PMID:18773972

Synchronous dynamics of zooplankton competitors prevail in temperate lake ecosystems.

PubMed

Vasseur, David A; Fox, Jeremy W; Gonzalez, Andrew; Adrian, Rita; Beisner, Beatrix E; Helmus, Matthew R; Johnson, Catherine; Kratina, Pavel; Kremer, Colin; de Mazancourt, Claire; Miller, Elizabeth; Nelson, William A; Paterson, Michael; Rusak, James A; Shurin, Jonathan B; Steiner, Christopher F

2014-08-07

Although competing species are expected to exhibit compensatory dynamics (negative temporal covariation), empirical work has demonstrated that competitive communities often exhibit synchronous dynamics (positive temporal covariation). This has led to the suggestion that environmental forcing dominates species dynamics; however, synchronous and compensatory dynamics may appear at different length scales and/or at different times, making it challenging to identify their relative importance. We compiled 58 long-term datasets of zooplankton abundance in north-temperate and sub-tropical lakes and used wavelet analysis to quantify general patterns in the times and scales at which synchronous/compensatory dynamics dominated zooplankton communities in different regions and across the entire dataset. Synchronous dynamics were far more prevalent at all scales and times and were ubiquitous at the annual scale. Although we found compensatory dynamics in approximately 14% of all combinations of time period/scale/lake, there were no consistent scales or time periods during which compensatory dynamics were apparent across different regions. Our results suggest that the processes driving compensatory dynamics may be local in their extent, while those generating synchronous dynamics operate at much larger scales. This highlights an important gap in our understanding of the interaction between environmental and biotic forces that structure communities. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Seasonal Variation on Microbial Community and Methane Production during Anaerobic Digestion of Cattle Manure in Brazil.

PubMed

Resende, Juliana Alves; Godon, Jean-Jacques; Bonnafous, Anaïs; Arcuri, Pedro Braga; Silva, Vânia Lúcia; Otenio, Marcelo Henrique; Diniz, Cláudio Galuppo

2016-04-01

Anaerobic digestion is an alternative method for the treatment of animal manure and wastewater. The anaerobic bioconversion of biomass requires a multi-step biological process, including microorganisms with distinct roles. The diversity and composition of microbial structure in pilot-scale anaerobic digestion operating at ambient temperature in Brazil were studied. Influence of the seasonal and temporal patterns on bacterial and archaeal communities were assessed by studying the variations in density, dynamic and diversity and structure. The average daily biogas produced in the summer and winter months was 18.7 and 16 L day(-1), respectively, and there was no difference in the average methane yield. Quantitative PCR analysis revealed that no differences in abundances and dynamics were found for bacterial communities and the total number of Archaea in different seasons. Analysis of bacterial clone libraries revealed a predominance of Firmicutes (54.5 %/summer and 46.7 %/winter) and Bacteroidetes (31.4 %/summer and 44.4 %/winter). Within the Archaea, the phylum Euryarchaeota was predominant in both digesters. Phylogenetic distribution showed changes in percentage between the phyla identified, but no alterations were recorded in the quality and amount of produced methane or community dynamics. The results may suggest that redundancy of microbial groups may have occurred, pointing to a more complex microbial community in the ecosystem related to this ambient temperature system.

An Adaptive Complex Network Model for Brain Functional Networks

PubMed Central

Gomez Portillo, Ignacio J.; Gleiser, Pablo M.

2009-01-01

Brain functional networks are graph representations of activity in the brain, where the vertices represent anatomical regions and the edges their functional connectivity. These networks present a robust small world topological structure, characterized by highly integrated modules connected sparsely by long range links. Recent studies showed that other topological properties such as the degree distribution and the presence (or absence) of a hierarchical structure are not robust, and show different intriguing behaviors. In order to understand the basic ingredients necessary for the emergence of these complex network structures we present an adaptive complex network model for human brain functional networks. The microscopic units of the model are dynamical nodes that represent active regions of the brain, whose interaction gives rise to complex network structures. The links between the nodes are chosen following an adaptive algorithm that establishes connections between dynamical elements with similar internal states. We show that the model is able to describe topological characteristics of human brain networks obtained from functional magnetic resonance imaging studies. In particular, when the dynamical rules of the model allow for integrated processing over the entire network scale-free non-hierarchical networks with well defined communities emerge. On the other hand, when the dynamical rules restrict the information to a local neighborhood, communities cluster together into larger ones, giving rise to a hierarchical structure, with a truncated power law degree distribution. PMID:19738902

Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut

PubMed Central

Reese, Aspen T; Cho, Eugenia H; Klitzman, Bruce; Nichols, Scott P; Wisniewski, Natalie A; Villa, Max M; Durand, Heather K; Jiang, Sharon; Midani, Firas S; Nimmagadda, Sai N; O'Connell, Thomas M; Wright, Justin P; Deshusses, Marc A

2018-01-01

How host and microbial factors combine to structure gut microbial communities remains incompletely understood. Redox potential is an important environmental feature affected by both host and microbial actions. We assessed how antibiotics, which can impact host and microbial function, change redox state and how this contributes to post-antibiotic succession. We showed gut redox potential increased within hours of an antibiotic dose in mice. Host and microbial functioning changed under treatment, but shifts in redox potentials could be attributed specifically to bacterial suppression in a host-free ex vivo human gut microbiota model. Redox dynamics were linked to blooms of the bacterial family Enterobacteriaceae. Ecological succession to pre-treatment composition was associated with recovery of gut redox, but also required dispersal from unaffected gut communities. As bacterial competition for electron acceptors can be a key ecological factor structuring gut communities, these results support the potential for manipulating gut microbiota through managing bacterial respiration. PMID:29916366

Response of bird community structure to habitat management in piñon-juniper woodland-sagebrush ecotones

USGS Publications Warehouse

Knick, Steven T.; Hanser, Steven E.; Grace, James B.; Hollenbeck, Jeff P.; Leu, Matthias

2017-01-01

Piñon (Pinus spp.) and juniper (Juniperus spp.) woodlands have been expanding their range across the intermountain western United States into landscapes dominated by sagebrush (Artemisia spp.) shrublands. Management actions using prescribed fire and mechanical cutting to reduce woodland cover and control expansion provided opportunities to understand how environmental structure and changes due to these treatments influence bird communities in piñon-juniper systems. We surveyed 43 species of birds and measured vegetation for 1–3 years prior to treatment and 6–7 years post-treatment at 13 locations across Oregon, California, Idaho, Nevada, and Utah. We used structural equation modeling to develop and statistically test our conceptual model that the current bird assembly at a site is structured primarily by the previous bird community with additional drivers from current and surrounding habitat conditions as well as external regional bird dynamics. Treatment reduced woodland cover by >5% at 80 of 378 survey sites. However, habitat change achieved by treatment was highly variable because actual disturbance differed widely in extent and intensity. Biological inertia in the bird community was the strongest single driver; 72% of the variation in the bird assemblage was explained by the community that existed seven years earlier. Greater net reduction in woodlands resulted in slight shifts in the bird community to one having ecotone or shrubland affinities. However, the overall influence of woodland changes from treatment were relatively small and were buffered by other extrinsic factors. Regional bird dynamics did not significantly influence the structure of local bird communities at our sites. Our results suggest that bird communities in piñon-juniper woodlands can be highly stable when management treatments are conducted in areas with more advanced woodland development and at the level of disturbance measured in our study.

Robustness of the bacterial community in the cabbage white butterfly larval midgut.

PubMed

Robinson, Courtney J; Schloss, Patrick; Ramos, Yolied; Raffa, Kenneth; Handelsman, Jo

2010-02-01

Microbial communities typically vary in composition and structure over space and time. Little is known about the inherent characteristics of communities that govern various drivers of these changes, such as random variation, changes in response to perturbation, or susceptibility to invasion. In this study, we use 16S ribosomal RNA gene sequences to describe variation among bacterial communities in the midguts of cabbage white butterfly (Pieris rapae) larvae and examine the influence of community structure on susceptibility to invasion. We compared communities in larvae experiencing the same conditions at different times (temporal variation) or fed different diets (perturbation). The most highly represented phylum was Proteobacteria, which was present in all midgut communities. The observed species richness ranged from six to 15, and the most abundant members affiliated with the genera Methylobacteria, Asaia, Acinetobacter, Enterobacter, and Pantoea. Individual larvae subjected to the same conditions at the same time harbored communities that were highly similar in structure and membership, whereas the communities observed within larval populations changed with diet and over time. In addition, structural changes due to perturbation coincided with enhanced susceptibility to invasion by Enterobacter sp. NAB3R and Pantoea stewartii CWB600, suggesting that resistance to invasion is in part governed by community structure. These findings along with the observed conservation of membership at the phylum level, variation in structure and membership at lower taxonomic levels, and its relative simplicity make the cabbage white butterfly larval community an attractive model for studying community dynamics and robustness.

Complexity of Bacterial Communities in a River-Floodplain System (Danube, Austria)

PubMed Central

Besemer, Katharina; Moeseneder, Markus M.; Arrieta, Jesus M.; Herndl, Gerhard J.; Peduzzi, Peter

2005-01-01

Natural floodplains play an essential role in the processing and decomposition of organic matter and in the self-purification ability of rivers, largely due to the activity of bacteria. Knowledge about the composition of bacterial communities and its impact on organic-matter cycling is crucial for the understanding of ecological processes in river-floodplain systems. Particle-associated and free-living bacterial assemblages from the Danube River and various floodplain pools with different hydrological characteristics were investigated using terminal restriction fragment length polymorphism analysis. The particle-associated bacterial community exhibited a higher number of operational taxonomic units (OTUs) and was more heterogeneous in time and space than the free-living community. The temporal dynamics of the community structure were generally higher in isolated floodplain pools. The community structures of the river and the various floodplain pools, as well as those of the particle-associated and free-living bacteria, differed significantly. The compositional dynamics of the planktonic bacterial communities were related to changes in the algal biomass, temperature, and concentrations of organic and inorganic nutrients. The OTU richness of the free-living community was correlated with the concentration and origin of organic matter and the concentration of inorganic nutrients, while no correlation with the OTU richness of the particle-associated assemblage was found. Our results demonstrate the importance of the river-floodplain interactions and the influence of damming and regulation on the bacterial-community composition. PMID:15691909

THR ROLE OF SEABED DYNAMICS IN STRUCTURING A MESOHALINE MACROBENTIC INFAUNAL COMMUNITY

EPA Science Inventory

Estuaries are dynamic physical environments. The stability of the sediment-water interface is influenced by sources and rates of sediment delivery and reworking of sediments by currents, tides, waves and biology, but effects of disruption of this interface on benthic biology are...

Organisms as cooperative ecosystem engineers in intertidal flats

NASA Astrophysics Data System (ADS)

Passarelli, Claire; Olivier, Frédéric; Paterson, David M.; Meziane, Tarik; Hubas, Cédric

2014-09-01

The importance of facilitative interactions and organismal ecosystem engineering for establishing the structure of communities is increasingly being recognised for many different ecosystems. For example, soft-bottom tidal flats host a wide range of ecosystem engineers, probably because the harsh physico-chemical environmental conditions render these species of particular importance for community structure and function. These environments are therefore interesting when focusing on how ecosystem engineers interact and the consequences of these interactions on community dynamics. In this review, we initially detail the influence on benthic systems of two kinds of ecosystem engineers that are particularly common in tidal flats. Firstly, we examine species providing biogenic structures, which are often the only source of habitat complexity in these environments. Secondly, we focus on species whose activities alter sediment stability, which is a crucial feature structuring the dynamics of communities in tidal flats. The impacts of these engineers on both environment and communities were assessed but in addition the interaction between ecosystem engineers was examined. Habitat cascades occur when one engineer favours the development of another, which in turn creates or modifies and improves habitat for other species. Non-hierarchical interactions have often been shown to display non-additive effects, so that the effects of the association cannot be predicted from the effects of individual organisms. Here we propose the term of “cooperative ecosystem engineering” when two species interact in a way which enhances habitat suitability as a result of a combined engineering effect. Finally, we conclude by describing the potential threats for ecosystem engineers in intertidal areas, potential effects on their interactions and their influence on communities and ecosystem function.

Towards an eco-phylogenetic framework for infectious disease ecology.

PubMed

Fountain-Jones, Nicholas M; Pearse, William D; Escobar, Luis E; Alba-Casals, Ana; Carver, Scott; Davies, T Jonathan; Kraberger, Simona; Papeş, Monica; Vandegrift, Kurt; Worsley-Tonks, Katherine; Craft, Meggan E

2018-05-01

Identifying patterns and drivers of infectious disease dynamics across multiple scales is a fundamental challenge for modern science. There is growing awareness that it is necessary to incorporate multi-host and/or multi-parasite interactions to understand and predict current and future disease threats better, and new tools are needed to help address this task. Eco-phylogenetics (phylogenetic community ecology) provides one avenue for exploring multi-host multi-parasite systems, yet the incorporation of eco-phylogenetic concepts and methods into studies of host pathogen dynamics has lagged behind. Eco-phylogenetics is a transformative approach that uses evolutionary history to infer present-day dynamics. Here, we present an eco-phylogenetic framework to reveal insights into parasite communities and infectious disease dynamics across spatial and temporal scales. We illustrate how eco-phylogenetic methods can help untangle the mechanisms of host-parasite dynamics from individual (e.g. co-infection) to landscape scales (e.g. parasite/host community structure). An improved ecological understanding of multi-host and multi-pathogen dynamics across scales will increase our ability to predict disease threats. © 2017 Cambridge Philosophical Society.

Seasonal Dynamics of the Airborne Bacterial Community and Selected Viruses in a Children's Daycare Center.

PubMed

Prussin, Aaron J; Vikram, Amit; Bibby, Kyle J; Marr, Linsey C

2016-01-01

Children's daycare centers appear to be hubs of respiratory infectious disease transmission, yet there is only limited information about the airborne microbial communities that are present in daycare centers. We have investigated the microbial community of the air in a daycare center, including seasonal dynamics in the bacterial community and the presence of specific viral pathogens. We collected filters from the heating, ventilation, and air conditioning (HVAC) system of a daycare center every two weeks over the course of a year. Amplifying and sequencing the 16S rRNA gene revealed that the air was dominated by Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes that are commonly associated with the human skin flora. Clear seasonal differences in the microbial community were not evident; however, the community structure differed when the daycare center was closed and unoccupied for a 13-day period. These results suggest that human occupancy, rather than the environment, is the major driver in shaping the microbial community structure in the air of the daycare center. Using PCR for targeted viruses, we detected a seasonal pattern in the presence of respiratory syncytial virus that included the period of typical occurrence of the disease related to the virus; however, we did not detect the presence of adenovirus or rotavirus at any time.

Seasonal Dynamics of the Airborne Bacterial Community and Selected Viruses in a Children’s Daycare Center

PubMed Central

Prussin, Aaron J.; Vikram, Amit; Bibby, Kyle J.; Marr, Linsey C.

2016-01-01

Children’s daycare centers appear to be hubs of respiratory infectious disease transmission, yet there is only limited information about the airborne microbial communities that are present in daycare centers. We have investigated the microbial community of the air in a daycare center, including seasonal dynamics in the bacterial community and the presence of specific viral pathogens. We collected filters from the heating, ventilation, and air conditioning (HVAC) system of a daycare center every two weeks over the course of a year. Amplifying and sequencing the 16S rRNA gene revealed that the air was dominated by Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes that are commonly associated with the human skin flora. Clear seasonal differences in the microbial community were not evident; however, the community structure differed when the daycare center was closed and unoccupied for a 13-day period. These results suggest that human occupancy, rather than the environment, is the major driver in shaping the microbial community structure in the air of the daycare center. Using PCR for targeted viruses, we detected a seasonal pattern in the presence of respiratory syncytial virus that included the period of typical occurrence of the disease related to the virus; however, we did not detect the presence of adenovirus or rotavirus at any time. PMID:26942410

Seasonal patterns in microbial communities inhabiting the hot springs of Tengchong, Yunnan Province, China.

PubMed

Briggs, Brandon R; Brodie, Eoin L; Tom, Lauren M; Dong, Hailiang; Jiang, Hongchen; Huang, Qiuyuan; Wang, Shang; Hou, Weiguo; Wu, Geng; Huang, Liuquin; Hedlund, Brian P; Zhang, Chuanlun; Dijkstra, Paul; Hungate, Bruce A

2014-06-01

Studies focusing on seasonal dynamics of microbial communities in terrestrial and marine environments are common; however, little is known about seasonal dynamics in high-temperature environments. Thus, our objective was to document the seasonal dynamics of both the physicochemical conditions and the microbial communities inhabiting hot springs in Tengchong County, Yunnan Province, China. The PhyloChip microarray detected 4882 operational taxonomic units (OTUs) within 79 bacterial phylum-level groups and 113 OTUs within 20 archaeal phylum-level groups, which are additional 54 bacterial phyla and 11 archaeal phyla to those that were previously described using pyrosequencing. Monsoon samples (June 2011) showed increased concentrations of potassium, total organic carbon, ammonium, calcium, sodium and total nitrogen, and decreased ferrous iron relative to the dry season (January 2011). At the same time, the highly ordered microbial communities present in January gave way to poorly ordered communities in June, characterized by higher richness of Bacteria, including microbes related to mesophiles. These seasonal changes in geochemistry and community structure are likely due to high rainfall influx during the monsoon season and indicate that seasonal dynamics occurs in high-temperature environments experiencing significant changes in seasonal recharge. Thus, geothermal environments are not isolated from the surrounding environment and seasonality affects microbial ecology. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Drivers of Macrofungi Community Structure Differ between Soil and Rotten-Wood Substrates in a Temperate Mountain Forest in China

PubMed Central

Chen, Yun; Svenning, Jens-Christian; Wang, Xueying; Cao, Ruofan; Yuan, Zhiliang; Ye, Yongzhong

2018-01-01

The effects of environmental and dispersal processes on macrofungi community assembly remain unclear. Further, it is not well understood if community assembly differs for different functional guilds of macrofungi, e.g., soil and rotten-wood macrofungi. In this study, using 2433 macrofungi sporocarps belonging to 217 species located within a forest dynamics plot in temperate mountain forest (China), we examined the explanatory power of topography, spatial eigenvectors (representing unknown spatial processes, e.g., dispersal), plant community, and light availability for local spatial variation in the macrofungi community through variance partitioning and partial least squares path modeling. We found spatial eigenvectors and light as the most important factors for explaining species richness and composition of macrofungi. Light was negatively correlated with species richness of macrofungi. Furthermore, species richness and composition of soil macrofungi were best explained by light, and species richness and composition of rotten-wood macrofungi were best explained by spatial eigenvectors. Woody plant community structure was not an important factor for species richness and composition of macrofungi. Our findings suggest that spatial processes, perhaps dispersal limitation, and light availability were the most important factors affecting macrofungi community in temperate deciduous broad-leaved forest. Major differences in influencing factors between soil and rotten-wood macrofungi were observed, with light as the major driver for soil macrofungi and unknown spatial processes as the major driver for rotten-wood macrofungi. These findings shed new light to the processes shaping community assembly in macrofungi in temperate deciduous broad-leaved forest and point to the potential importance of both intrinsic dynamics, such as dispersal, and external forcing, such as forest dynamics, via its effect on light availability. PMID:29410660

Microbial Communities in Cerrado Soils under Native Vegetation Subjected to Prescribed Fires and Under Pasture

EPA Science Inventory

The objective of this work was to evaluate the effects of fire regimes and vegetation cover on the structure and dynamics of soil microbial communities, through phospholipid fatty acid (PLFA) analysis. Comparisons were made between native areas with different woody covers ("cerra...

Productivity and community structure of ectomycorrhizal fungal sporocarps under increased atmospheric CO2 and O3

Treesearch

Carrie Andrew; Erik A. Lilleskov

2009-01-01

Sporocarp production is essential for ectomycorrhizal fungal recombination and dispersal, which influences fungal community dynamics. Increasing atmospheric carbon dioxide (CO2) and ozone (O3) affect host plant carbon gain and allocation, which may in turn influence ectomycorrhizal sporocarp production if the carbon...

Co-existence of Anaerobic Ammonium Oxidation Bacteria and Denitrifying Anaerobic Methane Oxidation Bacteria in Sewage Sludge: Community Diversity and Seasonal Dynamics.

PubMed

Xu, Sai; Lu, Wenjing; Mustafa, Muhammad Farooq; Caicedo, Luis Miguel; Guo, Hanwen; Fu, Xindi; Wang, Hongtao

2017-11-01

Anaerobic ammonium oxidation (ANAMMOX) and denitrifying anaerobic methane oxidation (DAMO) have been recently discovered as relevant processes in the carbon and nitrogen cycles of wastewater treatment plants. In this study, the seasonal dynamics of ANAMMOX and DAMO bacterial community structures and their abundance in sewage sludge collected from wastewater treatment plants were analysed. Results indicated that ANAMMOX and DAMO bacteria co-existed in sewage sludge in different seasons and their abundance was positively correlated (P < 0.05). The high abundance of ANAMMOX and DAMO bacteria in autumn and winter indicated that these seasons were the preferred time to favour the growth of ANAMMOX and DAMO bacteria. The community structure of ANNAMOX and DAMO bacteria could also shift with seasonal changes. The "Candidatus Brocadia" genus of ANAMMOX bacteria was mainly recovered in spring and summer, and an unknown cluster was primarily detected in autumn and winter. Similar patterns of seasonal variation in the community structure of DAMO bacteria were also observed. Group B was the dominant in spring and summer, whereas in autumn and winter, group A and group B presented almost the same proportion. The redundancy analysis revealed that pH and nitrate were the most significant factors affecting community structures of these two groups (P < 0.01). This study reported the diversity of ANAMMOX and DAMO in wastewater treatment plants that may be the basis for new nitrogen removal technologies.

Patterns of rare and abundant marine microbial eukaryotes.

PubMed

Logares, Ramiro; Audic, Stéphane; Bass, David; Bittner, Lucie; Boutte, Christophe; Christen, Richard; Claverie, Jean-Michel; Decelle, Johan; Dolan, John R; Dunthorn, Micah; Edvardsen, Bente; Gobet, Angélique; Kooistra, Wiebe H C F; Mahé, Frédéric; Not, Fabrice; Ogata, Hiroyuki; Pawlowski, Jan; Pernice, Massimo C; Romac, Sarah; Shalchian-Tabrizi, Kamran; Simon, Nathalie; Stoeck, Thorsten; Santini, Sébastien; Siano, Raffaele; Wincker, Patrick; Zingone, Adriana; Richards, Thomas A; de Vargas, Colomban; Massana, Ramon

2014-04-14

Biological communities are normally composed of a few abundant and many rare species. This pattern is particularly prominent in microbial communities, in which most constituent taxa are usually extremely rare. Although abundant and rare subcommunities may present intrinsic characteristics that could be crucial for understanding community dynamics and ecosystem functioning, microbiologists normally do not differentiate between them. Here, we investigate abundant and rare subcommunities of marine microbial eukaryotes, a crucial group of organisms that remains among the least-explored biodiversity components of the biosphere. We surveyed surface waters of six separate coastal locations in Europe, independently considering the picoplankton, nanoplankton, and microplankton/mesoplankton organismal size fractions. Deep Illumina sequencing of the 18S rRNA indicated that the abundant regional community was mostly structured by organismal size fraction, whereas the rare regional community was mainly structured by geographic origin. However, some abundant and rare taxa presented similar biogeography, pointing to spatiotemporal structure in the rare microeukaryote biosphere. Abundant and rare subcommunities presented regular proportions across samples, indicating similar species-abundance distributions despite taxonomic compositional variation. Several taxa were abundant in one location and rare in other locations, suggesting large oscillations in abundance. The substantial amount of metabolically active lineages found in the rare biosphere suggests that this subcommunity constitutes a diversity reservoir that can respond rapidly to environmental change. We propose that marine planktonic microeukaryote assemblages incorporate dynamic and metabolically active abundant and rare subcommunities, with contrasting structuring patterns but fairly regular proportions, across space and time. Copyright © 2014 Elsevier Ltd. All rights reserved.

Predation risk suppresses the positive feedback between size structure and cannibalism.

PubMed

Kishida, Osamu; Trussell, Geoffrey C; Ohno, Ayaka; Kuwano, Shinya; Ikawa, Takuya; Nishimura, Kinya

2011-11-01

1. Cannibalism can play a prominent role in the structuring and dynamics of ecological communities. Previous studies have emphasized the importance of size structure and density of cannibalistic species in shaping short- and long-term cannibalism dynamics, but our understanding of how predators influence cannibalism dynamics is limited. This is despite widespread evidence that many prey species exhibit behavioural and morphological adaptations in response to predation risk. 2. This study examined how the presence and absence of predation risk from larval dragonflies Aeshna nigroflava affected cannibalism dynamics in its prey larval salamanders Hynobius retardatus. 3. We found that feedback dynamics between size structure and cannibalism depended on whether dragonfly predation risk was present. In the absence of dragonfly risk cues, a positive feedback between salamander size structure and cannibalism through time occurred because most of the replicates in this treatment contained at least one salamander larvae having an enlarged gape (i.e. cannibal). In contrast, this feedback and the emergence of cannibalism were rarely observed in the presence of the dragonfly risk cues. Once salamander size divergence occurred, experimental reversals of the presence or absence of dragonfly risk cues did not alter existing cannibalism dynamics as the experiment progressed. Thus, the effects of risk on the mechanisms driving cannibalism dynamics likely operated during the early developmental period of the salamander larvae. 4. The effects of dragonfly predation risk on behavioural aspects of cannibalistic interactions among hatchlings may prohibit the initiation of dynamics between size structure and cannibalism. Our predation trials clearly showed that encounter rates among hatchlings and biting and ingestion rates of prospective prey by prospective cannibals were significantly lower in the presence vs. absence of dragonfly predation risk even though the size asymmetry between cannibals and victims was similar in both risk treatments. These results suggest that dragonfly risk cues first suppress cannibalism among hatchlings and then prevent size variation from increasing through time. 5. We suggest that the positive feedback dynamics between size structure and cannibalism and their modification by predation risk may also operate in other systems to shape the population dynamics of cannibalistic prey species as well as overall community dynamics. © 2011 The Authors. Journal of Animal Ecology © 2011 British Ecological Society.

Emergence of evolutionary cycles in size-structured food webs.

PubMed

Ritterskamp, Daniel; Bearup, Daniel; Blasius, Bernd

2016-11-07

The interplay of population dynamics and evolution within ecological communities has been of long-standing interest for ecologists and can give rise to evolutionary cycles, e.g. taxon cycles. Evolutionary cycling was intensely studied in small communities with asymmetric competition; the latter drives the evolutionary processes. Here we demonstrate that evolutionary cycling arises naturally in larger communities if trophic interactions are present, since these are intrinsically asymmetric. To investigate the evolutionary dynamics of a trophic community, we use an allometric food web model. We find that evolutionary cycles emerge naturally for a large parameter ranges. The origin of the evolutionary dynamics is an intrinsic asymmetry in the feeding kernel which creates an evolutionary ratchet, driving species towards larger bodysize. We reveal different kinds of cycles: single morph cycles, and coevolutionary and mixed cycling of complete food webs. The latter refers to the case where each trophic level can have different evolutionary dynamics. We discuss the generality of our findings and conclude that ongoing evolution in food webs may be more frequent than commonly believed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Animal diversity and ecosystem functioning in dynamic food webs

NASA Astrophysics Data System (ADS)

Schneider, Florian D.; Brose, Ulrich; Rall, Björn C.; Guill, Christian

2016-10-01

Species diversity is changing globally and locally, but the complexity of ecological communities hampers a general understanding of the consequences of animal species loss on ecosystem functioning. High animal diversity increases complementarity of herbivores but also increases feeding rates within the consumer guild. Depending on the balance of these counteracting mechanisms, species-rich animal communities may put plants under top-down control or may release them from grazing pressure. Using a dynamic food-web model with body-mass constraints, we simulate ecosystem functions of 20,000 communities of varying animal diversity. We show that diverse animal communities accumulate more biomass and are more exploitative on plants, despite their higher rates of intra-guild predation. However, they do not reduce plant biomass because the communities are composed of larger, and thus energetically more efficient, plant and animal species. This plasticity of community body-size structure reconciles the debate on the consequences of animal species loss for primary productivity.

Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes.

PubMed

Zhang, Yuanchen; Kastman, Erik K; Guasto, Jeffrey S; Wolfe, Benjamin E

2018-01-23

Most studies of bacterial motility have examined small-scale (micrometer-centimeter) cell dispersal in monocultures. However, bacteria live in multispecies communities, where interactions with other microbes may inhibit or facilitate dispersal. Here, we demonstrate that motile bacteria in cheese rind microbiomes use physical networks created by filamentous fungi for dispersal, and that these interactions can shape microbial community structure. Serratia proteamaculans and other motile cheese rind bacteria disperse on fungal networks by swimming in the liquid layers formed on fungal hyphae. RNA-sequencing, transposon mutagenesis, and comparative genomics identify potential genetic mechanisms, including flagella-mediated motility, that control bacterial dispersal on hyphae. By manipulating fungal networks in experimental communities, we demonstrate that fungal-mediated bacterial dispersal can shift cheese rind microbiome composition by promoting the growth of motile over non-motile community members. Our single-cell to whole-community systems approach highlights the interactive dynamics of bacterial motility in multispecies microbiomes.

Modeling species-abundance relationships in multi-species collections

USGS Publications Warehouse

Peng, S.; Yin, Z.; Ren, H.; Guo, Q.

2003-01-01

Species-abundance relationship is one of the most fundamental aspects of community ecology. Since Motomura first developed the geometric series model to describe the feature of community structure, ecologists have developed many other models to fit the species-abundance data in communities. These models can be classified into empirical and theoretical ones, including (1) statistical models, i.e., negative binomial distribution (and its extension), log-series distribution (and its extension), geometric distribution, lognormal distribution, Poisson-lognormal distribution, (2) niche models, i.e., geometric series, broken stick, overlapping niche, particulate niche, random assortment, dominance pre-emption, dominance decay, random fraction, weighted random fraction, composite niche, Zipf or Zipf-Mandelbrot model, and (3) dynamic models describing community dynamics and restrictive function of environment on community. These models have different characteristics and fit species-abundance data in various communities or collections. Among them, log-series distribution, lognormal distribution, geometric series, and broken stick model have been most widely used.

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.

Responding to rural social care needs: older people empowering themselves, others and their community.

PubMed

Walsh, Kieran; O'Shea, Eamon

2008-12-01

Older adult active retirement groups encompass health promotion, social and community psychological potential. However, little is known about the internal dynamics of these groups or their contribution to individual well-being and the community. This paper examines the Third Age Foundation as an example of one such group operating in a rural area in Ireland and explores the various relationships at work internally and externally. Methodology included: structured and semi-structured interviews, focus groups and a postal survey. A substantial contribution to members' well-being and community competence and cohesion was found. Findings are discussed in reference to the importance of individual and community empowerment, sustainability, social entrepreneurship/leadership and the potential of such models to support community-based living in older age.

Incarceration, Prisoner Reentry, and Communities

PubMed Central

Morenoff, Jeffrey D.; Harding, David J.

2014-01-01

Since the mid-1970s the United States has experienced an enormous rise in incarceration and accompanying increases in returning prisoners and in post-release community correctional supervision. Poor urban communities are disproportionately impacted by these phenomena. This review focuses on two complementary questions regarding incarceration, prisoner reentry, and communities:(1) whether and how mass incarceration has affected the social and economic structure of American communities, and (2) how residential neighborhoods affect the social and economic reintegration of returning prisoners. These two questions can be seen as part of a dynamic process involving a pernicious “feedback” loop, in which mass incarceration undermines the structure and social organization of some communities, thus creating more criminogenic environments for returning prisoners and further diminishing their prospects for successful reentry and reintegration. PMID:25400321

CEAS/AIAA/ICASE/NASA Langley International Forum on Aeroelasticity and Structural Dynamics 1999. Pt. 2

NASA Technical Reports Server (NTRS)

Whitlow, Jr., Woodrow (Editor); Todd, Emily N. (Editor)

1999-01-01

The proceedings of a workshop sponsored by the Confederation of European Aerospace Societies (CEAS), the American Institute of Aeronautics and Astronautics (AIAA), the National Aeronautics and Space Administration (NASA), Washington, D.C., and the Institute for Computer Applications in Science and Engineering (ICASE), Hampton, Virginia, and held in Williamsburg, Virginia June 22-25, 1999 represent a collection of the latest advances in aeroelasticity and structural dynamics from the world community. Research in the areas of unsteady aerodynamics and aeroelasticity, structural modeling and optimization, active control and adaptive structures, landing dynamics, certification and qualification, and validation testing are highlighted in the collection of papers. The wide range of results will lead to advances in the prediction and control of the structural response of aircraft and spacecraft.

Forest dynamics following eastern hemlock mortality in the southern Appalachians

Treesearch

Chelcy R. Ford; Katherine J. Elliott; Barton D. Clinton; Brian D. Kloeppel; James M. Vose

2011-01-01

Understanding changes in community composition caused by invasive species is critical for predicting effects on ecosystem function, particularly when the invasive threatens a foundation species. Here we focus on dynamics of forest structure, composition and microclimate, and how these interact in southern Appalachian riparian forests following invasion by hemlock...

The influence of historical climate on the population dynamics of three dominant sagebrush steppe plants.

USDA-ARS?s Scientific Manuscript database

Climate change could alter the population growth of dominant species, leading to profound effects on community structure and ecosystem dynamics. Understanding the links between historical variation in climate and population vital rates (survival, growth, recruitment) is one way to predict the impact...

Virulence and biodegradation potential of dynamic microbial communities associated with decaying Cladophora in Great Lakes

USGS Publications Warehouse

Chun, Chan Lan; Peller, Julie R.; Shively, Dawn; Byappanahalli, Muruleedhara N.; Whitman, Richard L.; Staley, Christopher; Zhang, Qian; Ishii, Satoshi; Sadowsky, Michael J.

2017-01-01

Cladophora mats that accumulate and decompose along shorelines of the Great Lakes create potential threats to the health of humans and wildlife. The decaying algae create a low oxygen and redox potential environment favoring growth and persistence of anaerobic microbial populations, including Clostridium botulinum, the causal agent of botulism in humans, birds, and other wildlife. In addition to the diverse population of microbes, a dynamic chemical environment is generated, which involves production of numerous organic and inorganic substances, many of which are believed to be toxic to the sand and aquatic biotic communities. In this study, we used 16S-rDNA-based-amplicon sequencing and microfluidic-based quantitative PCR approaches to characterize the bacterial community structure and the abundances of human pathogens associated with Cladophora at different stages (up to 90 days) of algal decay in laboratory microcosms. Oxygen levels were largely depleted after a few hours of incubation. As Cladophora decayed, the algal microbial biodiversity decreased within 24 h, and the mat transitioned from an aerobic to anaerobic environment. There were increasing abundances of enteric and pathogenic bacteria during decomposition of Cladophora, including Acinetobacter, Enterobacter, Kluyvera, Cedecea, and others. In contrast, there were no or very few sequences (< 0.07%) assigned to such groups in fresh Cladophora samples. Principal coordinate analysis indicated that the bacterial community structure was dynamic and changed significantly with decay time. Knowledge of microbial communities and chemical composition of decaying algal mats is critical to our further understanding of the role that Cladophora plays in a beach ecosystem's structure and function, including the algal role in trophic interactions. Based on these findings, public and environmental health concerns should be considered when decaying Cladophora mats accumulate Great Lakes shorelines.

Virulence and biodegradation potential of dynamic microbial communities associated with decaying Cladophora in Great Lakes.

PubMed

Chun, Chan Lan; Peller, Julie R; Shively, Dawn; Byappanahalli, Muruleedhara N; Whitman, Richard L; Staley, Christopher; Zhang, Qian; Ishii, Satoshi; Sadowsky, Michael J

2017-01-01

Cladophora mats that accumulate and decompose along shorelines of the Great Lakes create potential threats to the health of humans and wildlife. The decaying algae create a low oxygen and redox potential environment favoring growth and persistence of anaerobic microbial populations, including Clostridium botulinum, the causal agent of botulism in humans, birds, and other wildlife. In addition to the diverse population of microbes, a dynamic chemical environment is generated, which involves production of numerous organic and inorganic substances, many of which are believed to be toxic to the sand and aquatic biotic communities. In this study, we used 16S-rDNA-based-amplicon sequencing and microfluidic-based quantitative PCR approaches to characterize the bacterial community structure and the abundances of human pathogens associated with Cladophora at different stages (up to 90days) of algal decay in laboratory microcosms. Oxygen levels were largely depleted after a few hours of incubation. As Cladophora decayed, the algal microbial biodiversity decreased within 24h, and the mat transitioned from an aerobic to anaerobic environment. There were increasing abundances of enteric and pathogenic bacteria during decomposition of Cladophora, including Acinetobacter, Enterobacter, Kluyvera, Cedecea, and others. In contrast, there were no or very few sequences (<0.07%) assigned to such groups in fresh Cladophora samples. Principal coordinate analysis indicated that the bacterial community structure was dynamic and changed significantly with decay time. Knowledge of microbial communities and chemical composition of decaying algal mats is critical to our further understanding of the role that Cladophora plays in a beach ecosystem's structure and function, including the algal role in trophic interactions. Based on these findings, public and environmental health concerns should be considered when decaying Cladophora mats accumulate Great Lakes shorelines. Copyright © 2016 Elsevier B.V. All rights reserved.

Community-level consequences of cannibalism.

PubMed

Ohlberger, Jan; Langangen, Oystein; Stenseth, Nils C; Vøllestad, L Asbjørn

2012-12-01

Ecological interactions determine the structure and dynamics of communities and their responses to the environment. Understanding the community-level effects of ecological interactions, such as intra- and interspecifc competition, predation, and cannibalism, is therefore central to ecological theory and ecosystem management. Here, we investigate the community-level consequences of cannibalism in populations with density-dependent maturation and reproduction. We model a stage-structured consumer population with an ontogenetic diet shift to analyze how cannibalism alters the conditions for the invasion and persistence of stage-specific predators and competitors. Our results demonstrate that cannibalistic interactions can facilitate coexistence with other species at both trophic levels. This effect of cannibalism critically depends on the food dependence of the demographic processes. The underlying mechanism is a cannibalism-induced shift in the biomass distribution between the consumer life stages. These findings suggest that cannibalism may alter the structure of ecological communities through its effects on species coexistence.

Antagonistic interactions are sufficient to explain self-assemblage of bacterial communities in a homogeneous environment: a computational modeling approach

PubMed Central

Zapién-Campos, Román; Olmedo-Álvarez, Gabriela; Santillán, Moisés

2015-01-01

Most of the studies in Ecology have been devoted to analyzing the effects the environment has on individuals, populations, and communities, thus neglecting the effects of biotic interactions on the system dynamics. In the present work we study the structure of bacterial communities in the oligotrophic shallow water system of Churince, Cuatro Cienegas, Mexico. Since the physicochemical conditions of this water system are homogeneous and quite stable in time, it is an excellent candidate to study how biotic factors influence the structure of bacterial communities. In a previous study, the binary antagonistic interactions of 78 bacterial strains, isolated from Churince, were experimentally determined. We employ these data to develop a computer algorithm to simulate growth experiments in a cellular grid representing the pond. Remarkably, in our model, the dynamics of all the simulated bacterial populations is determined solely by antagonistic interactions. Our results indicate that all bacterial strains (even those that are antagonized by many other bacteria) survive in the long term, and that the underlying mechanism is the formation of bacterial community patches. Patches corresponding to less antagonistic and highly susceptible strains are consistently isolated from the highly-antagonistic bacterial colonies by patches of neutral strains. These results concur with the observed features of the bacterial community structure previously reported. Finally, we study how our findings depend on factors like initial population size, differential population growth rates, homogeneous population death rates, and enhanced bacterial diffusion. PMID:26052318

[What to do to avoid death by starvation? Domestic dynamics and childhood feeding practices in a rural area of extreme poverty in Mexico].

PubMed

Pelcastre-Villafuerte, Blanca; Riquer-Fernández, Florinda; de León-Reyes, Verónica; Reyes-Morales, Hortensia; Gutiérrez-Trujillo, Gonzalo; Bronfman, Mario

2006-01-01

To describe and compare household dynamics in terms of structure, beliefs and nutrition-related behavior in the homes of malnourished and well-nourished children less than five years of age. The authors carried out a qualitative ethnographic study using participant observation, and in depth interviews. Interviews were conducted with the child's caretaker or key informants, prior oral informed consent. Child care and childhood feeding practices at home and in the community were the focus of observations. The study included two periods of field work conducted in 2001, in three rural municipalities from the Río Balsas region, in Guerrero state, Mexico. The study's ethical and methodological aspects were approved by the National Research Commission of the Mexican Institute of Social Security. Households were differentially characterized by number of members, composition, type of relationship, source of income, and interactions among household members and with the community. Monoparental structures, in an early stage of the household cycle, give rise to conditions that render the child prone to malnutrition. Extended family structure represented more favorable household dynamics.

Primer selection impacts specific population abundances but not community dynamics in a monthly time-series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton.

PubMed

Wear, Emma K; Wilbanks, Elizabeth G; Nelson, Craig E; Carlson, Craig A

2018-03-09

Primers targeting the 16S small subunit ribosomal RNA marker gene, used to characterize bacterial and archaeal communities, have recently been re-evaluated for marine planktonic habitats. To investigate whether primer selection affects the ecological interpretation of bacterioplankton populations and community dynamics, amplicon sequencing with four primer sets targeting several hypervariable regions of the 16S rRNA gene was conducted on both mock communities constructed from cloned 16S rRNA genes and a time-series of DNA samples from the temperate coastal Santa Barbara Channel. Ecological interpretations of community structure (delineation of depth and seasonality, correlations with environmental factors) were similar across primer sets, while population dynamics varied. We observed substantial differences in relative abundances of taxa known to be poorly resolved by some primer sets, such as Thaumarchaeota and SAR11, and unexpected taxa including Roseobacter clades. Though the magnitude of relative abundances of common OTUs differed between primer sets, the relative abundances of the OTUs were nonetheless strongly correlated. We do not endorse one primer set but rather enumerate strengths and weaknesses to facilitate selection appropriate to a system or experimental goal. While 16S rRNA gene primer bias suggests caution in assessing quantitative population dynamics, community dynamics appear robust across studies using different primers. © 2018 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters

PubMed Central

Vanwonterghem, Inka; Jensen, Paul D; Dennis, Paul G; Hugenholtz, Philip; Rabaey, Korneel; Tyson, Gene W

2014-01-01

A replicate long-term experiment was conducted using anaerobic digestion (AD) as a model process to determine the relative role of niche and neutral theory on microbial community assembly, and to link community dynamics to system performance. AD is performed by a complex network of microorganisms and process stability relies entirely on the synergistic interactions between populations belonging to different functional guilds. In this study, three independent replicate anaerobic digesters were seeded with the same diverse inoculum, supplied with a model substrate, α-cellulose, and operated for 362 days at a 10-day hydraulic residence time under mesophilic conditions. Selective pressure imposed by the operational conditions and model substrate caused large reproducible changes in community composition including an overall decrease in richness in the first month of operation, followed by synchronised population dynamics that correlated with changes in reactor performance. This included the synchronised emergence and decline of distinct Ruminococcus phylotypes at day 148, and emergence of a Clostridium and Methanosaeta phylotype at day 178, when performance became stable in all reactors. These data suggest that many dynamic functional niches are predictably filled by phylogenetically coherent populations over long time scales. Neutral theory would predict that a complex community with a high degree of recognised functional redundancy would lead to stochastic changes in populations and community divergence over time. We conclude that deterministic processes may play a larger role in microbial community dynamics than currently appreciated, and under controlled conditions it may be possible to reliably predict community structural and functional changes over time. PMID:24739627

Plant-plant competition outcomes are modulated by plant effects on the soil bacterial community.

PubMed

Hortal, S; Lozano, Y M; Bastida, F; Armas, C; Moreno, J L; Garcia, C; Pugnaire, F I

2017-12-19

Competition is a key process that determines plant community structure and dynamics, often mediated by nutrients and water availability. However, the role of soil microorganisms on plant competition, and the links between above- and belowground processes, are not well understood. Here we show that the effects of interspecific plant competition on plant performance are mediated by feedbacks between plants and soil bacterial communities. Each plant species selects a singular community of soil microorganisms in its rhizosphere with a specific species composition, abundance and activity. When two plant species interact, the resulting soil bacterial community matches that of the most competitive plant species, suggesting strong competitive interactions between soil bacterial communities as well. We propose a novel mechanism by which changes in belowground bacterial communities promoted by the most competitive plant species influence plant performance and competition outcome. These findings emphasise the strong links between plant and soil communities, paving the way to a better understanding of plant community dynamics and the effects of soil bacterial communities on ecosystem functioning and services.

Microbial community structure is affected by cropping sequences and poultry litter under long-term no-tillage

USDA-ARS?s Scientific Manuscript database

Soil microorganisms play essential roles in soil organic matter dynamics and nutrient cycling in agroecosystems and have been used as soil quality indicators. The response of soil microbial communities to land management is complex and the long-term impacts of cropping systems on soil microbes is l...

An evaluation of the impact of multi-walled carbon nanotubes on soil microbial community structure and functional diversity

USDA-ARS?s Scientific Manuscript database

Increasing application of carbon nanotubes (CNTs) triggers the need for an assessment of their effects on organisms in the environment. Soil microbial communities play a significant role in soil organic matter dynamics and nutrient cycling. This study evaluated the impacts of multi-walled carbon nan...

Social Dynamics in Adult and Community Education Networks: Insights from a Case Study

ERIC Educational Resources Information Center

Dollhausen, Karin; Alke, Matthias

2014-01-01

Implementing network type structures has become a widely appreciated strategy to promote actor-relationships in the field of adult and community education and to coordinate them purposefully. However, there is still a lack of knowledge on how a "successful" coordination of actor-relationships can actually be achieved. This paper offers…

Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics

PubMed Central

Harcombe, William R.; Riehl, William J.; Dukovski, Ilija; Granger, Brian R.; Betts, Alex; Lang, Alex H.; Bonilla, Gracia; Kar, Amrita; Leiby, Nicholas; Mehta, Pankaj; Marx, Christopher J.; Segrè, Daniel

2014-01-01

Summary The inter-species exchange of metabolites plays a key role in the spatio-temporal dynamics of microbial communities. This raises the question whether ecosystem-level behavior of structured communities can be predicted using genome-scale models of metabolism for multiple organisms. We developed a modeling framework that integrates dynamic flux balance analysis with diffusion on a lattice, and applied it to engineered consortia. First, we predicted, and experimentally confirmed, the species-ratio to which a 2-species mutualistic consortium converges, and the equilibrium composition of a newly engineered 3-member community. We next identified a specific spatial arrangement of colonies, which gives rise to what we term the “eclipse dilemma”: does a competitor placed between a colony and its cross-feeding partner benefit or hurt growth of the original colony? Our experimentally validated finding, that the net outcome is beneficial, highlights the complex nature of metabolic interactions in microbial communities, while at the same time demonstrating their predictability. PMID:24794435

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

A trait based dynamic energy budget approach to explore emergent microalgal community structure

NASA Astrophysics Data System (ADS)

Cheng, Y.; Bouskill, N.; Karaoz, U.; Geng, H.; Lane, T.; Pett-Ridge, J.; Mayali, X.; Brodie, E.

2015-12-01

Microalgae play important roles in the global carbon budget. Phytoplankton, including microalgae, are responsible for around 50% of global primary production, and also hold promise as a viable renewable biofuel source. Research has been underway for decades to realize the full potential of algal biofuels at the commercial scale, however, uni-algal ponds are typically threatened by collapse due to microalgal grazing and parasite invasions. Recently, it has been proposed that functionally diverse microalgal-bacterial communities can achieve high biomass and/or lipid yields, and are more stable (less susceptible to invasion) than a monoculture. Similar positive diversity-productivity relationships have been observed in a wide range of ecosystem studies, but the purposeful maintenance of a diverse microbiome is less common in managed systems. In our work, a trait based dynamic energy budget model was developed to explore emergent microalgal community structure under various environmental (e.g. light, temperature, nutrient availability) conditions. The complex algal community can be reduced into functional groups (guilds). Each guild (algae or bacteria) is characterized by distinct physiological traits (e.g. nutrient requirement, growth rate, substrate affinity, lipid production) constrained by biochemical trade-offs. These trait values are derived from literature and information encoded in genomic data. Metabolism of the algae and the bacterial species (symbiotic or non-symbiotic) are described within a dynamic energy budget framework. The model offers a mechanistic framework to predict the optimal microalgal community assemblage towards high productivity and resistance to invasion under prevailing environmental conditions.

Floral colour versus phylogeny in structuring subalpine flowering communities.

PubMed

McEwen, Jamie R; Vamosi, Jana C

2010-10-07

The relative number of seeds produced by competing species can influence the community structure; yet, traits that influence seed production, such as pollinator attraction and floral colour, have received little attention in community ecology. Here, we analyse floral colour using reflectance spectra that include near-UV and examined the phylogenetic signal of floral colour. We found that coflowering species within communities tended to be more divergent in floral colour than expected by chance. However, coflowering species were not phylogenetically dispersed, in part due to our finding that floral colour is a labile trait with a weak phylogenetic signal. Furthermore, while we found that locally rare and common species exhibited equivalent floral colour distances from their coflowering neighbours, frequent species (those found in more communities) exhibited higher colour distances from their coflowering neighbours. Our findings support recent studies, which have found that (i) plant lineages exhibit frequent floral colour transitions; and (ii) traits that influence local population dynamics contribute to community structure.

[Dynamics of bacterial community during the bloom caused by Skeletonema costatum and Akashiwo sanguinea in Xiamen sea area].

PubMed

Li, Yi; Yang, Caiyun; Li, Dong; Tian, Yun; Zheng, Tianling

2012-10-04

To investigate the dynamics of bacterial community in Xiamen sea during the bloom mainly caused by Skeletonema costatum and Akashiwo sanguine in August 2011. Bacterial community structures of samples from two bloom sites and one non-bloom site were evaluated by PCR-DGGE (Denaturing gradient gel electrophoresis, DGGE). The genetic diversity of bacterial community was analyzed based on the DGGE fingerprint. The correlation between bacterial community and environmental parameters was studied by Canoco. The bacterial community was largely related to pH and N/P during the start-up stage of the bloom; while in the demise stage, it was mostly correlated to salinity and temperature. According to the results of sequence analysis of DGGE dominant bands, Gammaproteobacteria accounted for 47.7% during the bloom and Pseudoalteromonas, Pseudomonas, Alteromonas, Hydrogenophaga, Actibacter and Oleibacter were dominant genus in bacterial community. The Shannon-Weaver diversity index showed that the diversity of bacterial community in bloom site increased firstly and then decreased during this bloom. Hydrogenophaga was dominant in the start-up stage of bloom, while Pseudomonas and Pseudoalteromonas were dominant in the demise stage of bloom. The diversity of attached bacteria and free-living bacteria in bloom sites reached maximum in the same day (the concentration of algae was high) , both of them changed greatly during the bloom while the environment factors which correlated with the two communities were different. It is the first report about dynamics of bacterial community during the bloom caused by several algae together. This work is helpful to understand the dynamics of bacterial community during the bloom, and provides a theoretical basis for bloom's control in the future.

An experimental analysis of granivory in a desert ecosystem: Progress report

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

Brown, J.H.

1987-03-01

Controlled, replicated experiments are revealing the network of interactions that determine structure, dynamics, and energy transfer in a desert community that is functionally interconnected by the consumption of seeds (granivory). This community includes seed-eating rodents, ants, and birds, seed-producing annual and perennial plants, and other kinds of organisms that interact with these. The experiments entail removal of important species or functional groups of granivores or plants and supplementation of seed resources. The results demonstrate a large number of direct and indirect interactions that have important effects on the abundance of species and functional groups, the structure of the community, andmore » the dynamics of energy flow. The results suggest that networks of interaction are structured with sufficient overlap in resource requirements and interconnections through indirect pathways that community- and ecosystem-level processes, such as energy flow, are relatively insensitive to major perturbations in the abundance of particular species or functional groups. This preliminary finding has important implications for understanding the response of ecosystems to natural and human-caused perturbations, for the management of agricultural and other human-modified ecosystems, and for the design of perturbation-resistant networks for acquisition and distribution of human resources such energy and information. 44 refs.« less

Predicting taxonomic and functional structure of microbial communities in acid mine drainage

PubMed Central

Kuang, Jialiang; Huang, Linan; He, Zhili; Chen, Linxing; Hua, Zhengshuang; Jia, Pu; Li, Shengjin; Liu, Jun; Li, Jintian; Zhou, Jizhong; Shu, Wensheng

2016-01-01

Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray–Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural acidophilic microbial communities. PMID:26943622

Predicting taxonomic and functional structure of microbial communities in acid mine drainage.

PubMed

Kuang, Jialiang; Huang, Linan; He, Zhili; Chen, Linxing; Hua, Zhengshuang; Jia, Pu; Li, Shengjin; Liu, Jun; Li, Jintian; Zhou, Jizhong; Shu, Wensheng

2016-06-01

Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray-Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural acidophilic microbial communities.

Dynamics of the Fouling Layer Microbial Community in a Membrane Bioreactor

PubMed Central

Ziegler, Anja S.; McIlroy, Simon J.; Larsen, Poul; Albertsen, Mads; Hansen, Aviaja A.; Heinen, Nicolas; Nielsen, Per Halkjær

2016-01-01

Membrane fouling presents the greatest challenge to the application of membrane bioreactor (MBR) technology. Formation of biofilms on the membrane surface is the suggested cause, yet little is known of the composition or dynamics of the microbial community responsible. To gain an insight into this important question, we applied 16S rRNA gene amplicon sequencing with a curated taxonomy and fluorescent in situ hybridization to monitor the community of a pilot-scale MBR carrying out enhanced biological nitrogen and phosphorus removal with municipal wastewater. In order to track the dynamics of the fouling process, we concurrently investigated the communities of the biofilm, MBR bulk sludge, and the conventional activated sludge system used to seed the MBR system over several weeks from start-up. As the biofilm matured the initially abundant betaproteobacterial genera Limnohabitans, Hydrogenophaga and Malikia were succeeded by filamentous Chloroflexi and Gordonia as the abundant species. This study indicates that, although putative pioneer species appear, the biofilm became increasingly similar to the bulk community with time. This suggests that the microbial population in bulk water will largely determine the community structure of the mature biofilm. PMID:27399199

Soil fungi colony growth and community dynamics

NASA Astrophysics Data System (ADS)

Falconer, Ruth E.; Kravchenko, Alexandra; Otten, Wilfred

2010-05-01

Fungi are a major player in soil functioning, they contribute to soil structure formation and shaping of plant communities through their role in nutrient cycling, pathogenesis and symbiosis. Theoretical approaches which have emerged over the years and improved considerably our understanding of above ground plant communities are still lacking below ground. A theoretical framework is needed, such that links soil physics, fungal biology and mathematical biology in order to understand fungal community dynamics and diversity in undisturbed soils. Such a framework is essential if we are to understand how environmental change or soil manipulation impacts biodiversity. Different land use and management practices significantly affect soil environmental characteristics crucial for fungal communities by contributing different quantities and qualities of biomass inputs, generating different levels of soil disturbance, influencing soil temperature and moisture regimes, and affecting structure and geometry of soil pore space. Differences in pore structures generated by long-term differences in land use and management are reflected in notable changes in soil physical and hydraulic properties, including soil porosity, hydraulic conductivity and water retention (Brye and Pirani, 2005). Changes in numbers, shapes, and distributions of soil macropores have been often observed (e.g., Pachepsky et al., 1996; Giménez et al., 1997; Udawatta et al., 2008). However, specific implications of these differences in pore structure and geometries for ability of pathogenic as well as non-pathogenic fungi to colonize soil have not yet been addressed. Recent advances in computed tomography and microscopy facilitate detailed examination of the inner pore structures of undisturbed soil samples as well as visualization of fungal mycelia. Such tools together with modelling generate a new level of understanding of the mechanisms governing fungal behaviour at microscopic scales, and for the first time allow us to examine species interactions in a 3D soil environment.

[Effect of flooding time on community structure and abundance of Geobacteraceae in paddy soil].

PubMed

You, Jiaohua; Xia, Shuhong; Wang, Baoli; Qu, Dong

2011-06-01

The dynamic characteristics of community structure and relative abundance of Geobacteraceae were investigated to understand their response to microbial iron (III) reducing in flooded paddy soil. The paddy soil was incubated anaerobically and the amount of Fe(II) was determined during the flooding incubation. We retrieved Geobacteraceae sequences from clone libraries constructed for different time points (1 h and day 1, 5, 10, 20 and 30) after flooding of the paddy soil. The diversity and community structure were analyzed by using RFLP method, and the relative abundance of Geobacteraceae was detected by real-time PCR. Microbial reduction of iron (III) changed greatly in early time and was stable after incubated for 20 d in paddy soil. The largest iron reduction potential was 10.16 mg/g with a Vmax of 1.064 mg/(g x d) at the time of 4.84 d whereas this process achieved plateau after 20 days flooding. Diversity of Geobacteraceae, given by alpha indices, fluctuated during the flooding incubation. Two peaks of diversity were observed in treatments of 5 d and 20 d respectively, while significant low diversity appeared in samples of 10 d and 30 d. Beta indices described the differences between community structures of Geobacteraceae and hence reflected the variation of the flooding situation over time. In all samples, 10 RFLP-based preponderant types were found, which fell into clade 1 and clade 2 of Geobacteraceae. The relative abundance of Geobacteraceae was the lowest in 1 d (1.20% ) and the highest in 20 d (4.54%). The dynamic variation of Geobacteraceae diversity, community structure and abundance are closely related to microbial iron (III) reducing in flooding paddy soil.

Gastropod diversification and community structuring processes in ancient Lake Ohrid: a metacommunity speciation perspective

NASA Astrophysics Data System (ADS)

Hauffe, T.; Albrecht, C.; Wilke, T.

2015-09-01

The Balkan Lake Ohrid is the oldest and most speciose freshwater lacustrine system in Europe. However, it remains unclear whether the diversification of its endemic taxa is mainly driven by neutral processes, environmental factors, or species interactions. This calls for a holistic perspective involving both evolutionary processes and ecological dynamics. Such a unifying framework - the metacommunity speciation model - considers how community assembly affects diversification and vice versa by assessing the relative contribution of the three main community assembly processes, dispersal limitation, environmental filtering, and species interaction. The current study therefore used the species-rich model taxon Gastropoda to assess how extant communities in Lake Ohrid are structured by performing process based metacommunity analyses. Specifically, the study aimed at (i) identifying the relative importance of the three community assembly processes and (ii) to test whether the importance of these individual processes changes gradually with lake depth or whether they are distinctively related to eco-zones. Based on specific simulation steps for each of the three processes, it could be demonstrated that dispersal limitation had the strongest influence on gastropod community structures in Lake Ohrid. However, it was not the exclusive assembly process but acted together with the other two processes - environmental filtering, and species interaction. In fact, the relative importance of the three community assembly processes varied both with lake depth and eco-zones, though the processes were better predicted by the latter. The study thus corroborated the high importance of dispersal limitation for both maintaining species richness in Lake Ohrid (through its impact on community structure) and generating endemic biodiversity (via its influence on diversification processes). However, according to the metacommunity speciation model, the inferred importance of environmental filtering and biotic interaction also suggests a small but significant influence of ecological speciation. These findings contribute to the main goal of the SCOPSCO initiative - inferring the drivers of biotic evolution - and might provide an integrative perspective on biological and limnological dynamics in ancient Lake Ohrid.

Seasonal dynamics of ant community structure in the Moroccan Argan Forest.

PubMed

El Keroumi, Abderrahim; Naamani, Khalid; Soummane, Hassna; Dahbi, Abdallah

2012-01-01

In this study we describe the structure and composition of ant communities in the endemic Moroccan Argan forest, using pitfall traps sampling technique throughout the four seasons between May 2006 and February 2007. The study focused on two distinct climatic habitats within the Essaouira Argan forest, a semi-continental site at Lahssinate, and a coastal site at Boutazarte. Thirteen different ant species were identified, belonging to seven genera. Monomorium subopacum Smith and Tapinoma simrothi Krausse-Heldrungen (Hymenoptera: Formicidae) were the most abundant and behaviorally dominant ant species in the arganeraie. In addition, more specimens were captured in the semi-continental site than in the coastal area. However, no significant difference was observed in species richness, evenness, or diversity between both sites. Composition and community structure showed clear seasonal dynamics. The number of species, their abundance, their diversity, and their evenness per Argan tree were significantly dissimilar among seasons. The richness (except between summer and autumn), and the abundance and the evenness of ant species among communities, showed a significant difference between the dry period (summer and spring) and the rainy period (winter and autumn). Higher abundance and richness values occurred in the dry period of the year. Ant species dominance and seasonal climatic variations in the arganeraie might be among the main factors affecting the composition, structure, and foraging activity of ant communities. This study, together with recent findings on ant predation behavior below Argan trees, highlights the promising use of dominant ant species as potential agents of Mediterranean fruit fly bio-control in the Argan forest and surrounding ecosystems.

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.

Denitrification in a large river: consideration of geomorphic controls on microbial activity and community structure.

PubMed

Tatariw, Corianne; Chapman, Elise L; Sponseller, Ryan A; Mortazavi, Behzad; Edmonds, Jennifer W

2013-10-01

Ecological theory argues that the controls over ecosystem processes are structured hierarchically, with broader-scale drivers acting as constraints over the interactions and dynamics at nested levels of organization. In river ecosystems, these interactions may arise from broadscale variation in channel form that directly shapes benthic habitat structure and indirectly constrains resource supply and biological activity within individual reaches. To evaluate these interactions, we identified sediment characteristics, water chemistry, and denitrifier community structure as factors influencing benthic denitrification rates in a sixth-order river that flows through two physiographic provinces and the transitional zone between them, each with distinct geomorphological properties. We found that denitrification rates tracked spatial changes in sediment characteristics and varied seasonally with expected trends in stream primary production. Highest rates were observed during the spring and summer seasons in the physiographic province dominated by fine-grained sediments, illustrating how large-scale changes in river structure can constrain the location of denitrification hotspots. In addition, nirS and nirK community structure each responded differently to variation in channel form, possibly due to changes in dissolved oxygen and organic matter supply. This shift in denitrifier community structure coincident with higher rates of N removal via denitrification suggests that microbial community structure may influence biogeochemical processes.

Ecosystem Research Experience with Two Indigenous Communities of Colombia: The Ecohealth Calendar as a Participatory and Innovative Methodological Tool.

PubMed

SantoDomingo, Andrés Felipe; Castro-Díaz, Laura; González-Uribe, Catalina

2016-12-01

Eco-bio-social factors may increase or decrease a community's susceptibility to vector-borne disease transmission. Traditional studies have contributed information about the association between eco-bio-social factors and health outcomes, but few have provided this information in an integrative way characterizing annual dynamics among indigenous communities. Transdisciplinary research was conducted with the Bari of Karikachaboquira and the Wayúu of Marbacella and El Horno, using qualitative and participatory methods, including seasonal graphics, semi-structured interviews, geo-referencing routes, and participatory observation. The information was triangulated and discussed with local actors in order to validate and complement the results. An ecohealth calendar was obtained for each community, linking the socioecological dynamics to specific diseases, especially malaria. Local dynamics can change, depending on environmental conditions, and these determine the presence or absence of diseases. For both communities, the rainy season is the period with the greatest proliferation of mosquitoes (including Anopheles spp.), during which malaria cases occur. The ecohealth calendar integrates eco-bio-social information from local communities, through participatory and potentially empowering processes, into a comprehensive layout. This can break down the conceptual, demographic, and cultural barriers in the context of community-based interventions and research to action based on an ecosystem framework.

In the mood: the dynamics of collective sentiments on Twitter

PubMed Central

Charlton, Nathaniel; Singleton, Colin; Greetham, Danica Vukadinović

2016-01-01

We study the relationship between the sentiment levels of Twitter users and the evolving network structure that the users created by @-mentioning each other. We use a large dataset of tweets to which we apply three sentiment scoring algorithms, including the open source SentiStrength program. Specifically we make three contributions. Firstly, we find that people who have potentially the largest communication reach (according to a dynamic centrality measure) use sentiment differently than the average user: for example, they use positive sentiment more often and negative sentiment less often. Secondly, we find that when we follow structurally stable Twitter communities over a period of months, their sentiment levels are also stable, and sudden changes in community sentiment from one day to the next can in most cases be traced to external events affecting the community. Thirdly, based on our findings, we create and calibrate a simple agent-based model that is capable of reproducing measures of emotive response comparable with those obtained from our empirical dataset. PMID:27429774

Relationship between the Decomposition Process of Coarse Woody Debris and Fungal Community Structure as Detected by High-Throughput Sequencing in a Deciduous Broad-Leaved Forest in Japan

PubMed Central

Yamashita, Satoshi; Masuya, Hayato; Abe, Shin; Masaki, Takashi; Okabe, Kimiko

2015-01-01

We examined the relationship between the community structure of wood-decaying fungi, detected by high-throughput sequencing, and the decomposition rate using 13 years of data from a forest dynamics plot. For molecular analysis and wood density measurements, drill dust samples were collected from logs and stumps of Fagus and Quercus in the plot. Regression using a negative exponential model between wood density and time since death revealed that the decomposition rate of Fagus was greater than that of Quercus. The residual between the expected value obtained from the regression curve and the observed wood density was used as a decomposition rate index. Principal component analysis showed that the fungal community compositions of both Fagus and Quercus changed with time since death. Principal component analysis axis scores were used as an index of fungal community composition. A structural equation model for each wood genus was used to assess the effect of fungal community structure traits on the decomposition rate and how the fungal community structure was determined by the traits of coarse woody debris. Results of the structural equation model suggested that the decomposition rate of Fagus was affected by two fungal community composition components: one that was affected by time since death and another that was not affected by the traits of coarse woody debris. In contrast, the decomposition rate of Quercus was not affected by coarse woody debris traits or fungal community structure. These findings suggest that, in the case of Fagus coarse woody debris, the fungal community structure is related to the decomposition process of its host substrate. Because fungal community structure is affected partly by the decay stage and wood density of its substrate, these factors influence each other. Further research on interactive effects is needed to improve our understanding of the relationship between fungal community structure and the woody debris decomposition process. PMID:26110605

Team Learning: Through the Relational Dynamics of Co-operation and Rivalry in Team Communities

ERIC Educational Resources Information Center

Lotz, Maja

2010-01-01

This paper explores the constructive links between cooperation, rivalry, and learning within the structure of team communities. Drawing upon social learning theory and qualitative data from case studies conducted in Danish team-based firms, the main purpose is to argue that both cooperation and rivalry are important triggers for mobilizing…

Soil microbial community successional patterns during forest ecosystem restoration.

PubMed

Banning, Natasha C; Gleeson, Deirdre B; Grigg, Andrew H; Grant, Carl D; Andersen, Gary L; Brodie, Eoin L; Murphy, D V

2011-09-01

Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables.

Soil Microbial Community Successional Patterns during Forest Ecosystem Restoration ▿†

PubMed Central

Banning, Natasha C.; Gleeson, Deirdre B.; Grigg, Andrew H.; Grant, Carl D.; Andersen, Gary L.; Brodie, Eoin L.; Murphy, D. V.

2011-01-01

Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables. PMID:21724890

Finding overlapping communities in multilayer networks

PubMed Central

Liu, Weiyi; Suzumura, Toyotaro; Ji, Hongyu; Hu, Guangmin

2018-01-01

Finding communities in multilayer networks is a vital step in understanding the structure and dynamics of these layers, where each layer represents a particular type of relationship between nodes in the natural world. However, most community discovery methods for multilayer networks may ignore the interplay between layers or the unique topological structure in a layer. Moreover, most of them can only detect non-overlapping communities. In this paper, we propose a new community discovery method for multilayer networks, which leverages the interplay between layers and the unique topology in a layer to reveal overlapping communities. Through a comprehensive analysis of edge behaviors within and across layers, we first calculate the similarities for edges from the same layer and the cross layers. Then, by leveraging these similarities, we can construct a dendrogram for the multilayer networks that takes both the unique topological structure and the important interplay into consideration. Finally, by introducing a new community density metric for multilayer networks, we can cut the dendrogram to get the overlapping communities for these layers. By applying our method on both synthetic and real-world datasets, we demonstrate that our method has an accurate performance in discovering overlapping communities in multilayer networks. PMID:29694387

Finding overlapping communities in multilayer networks.

PubMed

Liu, Weiyi; Suzumura, Toyotaro; Ji, Hongyu; Hu, Guangmin

2018-01-01

Finding communities in multilayer networks is a vital step in understanding the structure and dynamics of these layers, where each layer represents a particular type of relationship between nodes in the natural world. However, most community discovery methods for multilayer networks may ignore the interplay between layers or the unique topological structure in a layer. Moreover, most of them can only detect non-overlapping communities. In this paper, we propose a new community discovery method for multilayer networks, which leverages the interplay between layers and the unique topology in a layer to reveal overlapping communities. Through a comprehensive analysis of edge behaviors within and across layers, we first calculate the similarities for edges from the same layer and the cross layers. Then, by leveraging these similarities, we can construct a dendrogram for the multilayer networks that takes both the unique topological structure and the important interplay into consideration. Finally, by introducing a new community density metric for multilayer networks, we can cut the dendrogram to get the overlapping communities for these layers. By applying our method on both synthetic and real-world datasets, we demonstrate that our method has an accurate performance in discovering overlapping communities in multilayer networks.

Taxonomic and functional trait diversity of wild bees in different urban settings.

PubMed

Normandin, Étienne; Vereecken, Nicolas J; Buddle, Christopher M; Fournier, Valérie

2017-01-01

Urbanization is one of the major anthropogenic processes contributing to local habitat loss and extirpation of numerous species, including wild bees, the most widespread pollinators. Little is known about the mechanisms through which urbanization impacts wild bee communities, or the types of urban green spaces that best promote their conservation in cities. The main objective of this study was to describe and compare wild bee community diversity, structure, and dynamics in two Canadian cities, Montreal and Quebec City. A second objective was to compare functional trait diversity among three habitat types (cemeteries, community gardens and urban parks) within each city. Bees were collected using pan traps and netting on the same 46 sites, multiple times, over the active season in 2012 and 2013. A total of 32,237 specimens were identified, representing 200 species and 6 families, including two new continental records, Hylaeus communis Nylander (1852) and Anthidium florentinum (Fabricius, 1775). Despite high community evenness, we found significant abundance of diverse species, including exotic ones. Spatio-temporal analysis showed higher stability in the most urbanized city (Montreal) but low nestedness of species assemblages among the three urban habitats in both cities. Our study demonstrates that cities are home to diverse communities of wild bees, but in turn affect bee community structure and dynamics. We also found that community gardens harbour high levels of functional trait diversity. Urban agriculture therefore contributes substantially to the provision of functionally diverse bee communities and possibly to urban pollination services.

Taxonomic and functional trait diversity of wild bees in different urban settings

PubMed Central

Buddle, Christopher M.; Fournier, Valérie

2017-01-01

Urbanization is one of the major anthropogenic processes contributing to local habitat loss and extirpation of numerous species, including wild bees, the most widespread pollinators. Little is known about the mechanisms through which urbanization impacts wild bee communities, or the types of urban green spaces that best promote their conservation in cities. The main objective of this study was to describe and compare wild bee community diversity, structure, and dynamics in two Canadian cities, Montreal and Quebec City. A second objective was to compare functional trait diversity among three habitat types (cemeteries, community gardens and urban parks) within each city. Bees were collected using pan traps and netting on the same 46 sites, multiple times, over the active season in 2012 and 2013. A total of 32,237 specimens were identified, representing 200 species and 6 families, including two new continental records, Hylaeus communis Nylander (1852) and Anthidium florentinum (Fabricius, 1775). Despite high community evenness, we found significant abundance of diverse species, including exotic ones. Spatio-temporal analysis showed higher stability in the most urbanized city (Montreal) but low nestedness of species assemblages among the three urban habitats in both cities. Our study demonstrates that cities are home to diverse communities of wild bees, but in turn affect bee community structure and dynamics. We also found that community gardens harbour high levels of functional trait diversity. Urban agriculture therefore contributes substantially to the provision of functionally diverse bee communities and possibly to urban pollination services. PMID:28286711

High refuge availability on coral reefs increases the vulnerability of reef-associated predators to overexploitation.

PubMed

Rogers, Alice; Blanchard, Julia L; Newman, Steven P; Dryden, Charlie S; Mumby, Peter J

2018-02-01

Refuge availability and fishing alter predator-prey interactions on coral reefs, but our understanding of how they interact to drive food web dynamics, community structure and vulnerability of different trophic groups is unclear. Here, we apply a size-based ecosystem model of coral reefs, parameterized with empirical measures of structural complexity, to predict fish biomass, productivity and community structure in reef ecosystems under a broad range of refuge availability and fishing regimes. In unfished ecosystems, the expected positive correlation between reef structural complexity and biomass emerges, but a non-linear effect of predation refuges is observed for the productivity of predatory fish. Reefs with intermediate complexity have the highest predator productivity, but when refuge availability is high and prey are less available, predator growth rates decrease, with significant implications for fisheries. Specifically, as fishing intensity increases, predators in habitats with high refuge availability exhibit vulnerability to over-exploitation, resulting in communities dominated by herbivores. Our study reveals mechanisms for threshold dynamics in predators living in complex habitats and elucidates how predators can be food-limited when most of their prey are able to hide. We also highlight the importance of nutrient recycling via the detrital pathway, to support high predator biomasses on coral reefs. © 2018 by the Ecological Society of America.

Grazers structure the bacterial and algal diversity of aquatic metacommunities.

PubMed

Birtel, Julia; Matthews, Blake

2016-12-01

Consumers can have strong effects on the biotic and abiotic dynamics of spatially-structured ecosystems. In metacommunities, dispersing consumers can alter local assembly dynamics either directly through trophic interactions or indirectly by modifying local environmental conditions. In aquatic systems, very little is known about how key grazers, such as Daphnia, structure the microbial diversity of metacommunities and influence bacterial-mediated ecosystem functions. In an outdoor mesocosm experiment with replicate metacommunities (two 300 L mesocosms), we tested how the presence and absence of Daphnia and the initial density of the microbial community (manipulated via dilution) influenced the diversity and community structure of algae and bacteria, and several ecosystem properties (e.g., pH, dissolved substances) and functions (e.g., enzyme activity, respiration). We found that Daphnia strongly affected the local and regional diversity of both phytoplankton and bacteria, the taxonomic composition of bacterial communities, the biomass of algae, and ecosystem metabolism (i.e., respiration). Diluting the microbial inoculum (0.2-5 μm size fraction) to the metacommunities increased local phytoplankton diversity, decreased bacteria beta-diversity, and changed the relative abundance of bacterial classes. Changes in the rank abundance of different bacterial groups exhibited phylogenetic signal, implying that closely related bacteria species might share similar responses to the presence of Daphnia. © 2016 by the Ecological Society of America.

Social significance of community structure: Statistical view

NASA Astrophysics Data System (ADS)

Li, Hui-Jia; Daniels, Jasmine J.

2015-01-01

Community structure analysis is a powerful tool for social networks that can simplify their topological and functional analysis considerably. However, since community detection methods have random factors and real social networks obtained from complex systems always contain error edges, evaluating the significance of a partitioned community structure is an urgent and important question. In this paper, integrating the specific characteristics of real society, we present a framework to analyze the significance of a social community. The dynamics of social interactions are modeled by identifying social leaders and corresponding hierarchical structures. Instead of a direct comparison with the average outcome of a random model, we compute the similarity of a given node with the leader by the number of common neighbors. To determine the membership vector, an efficient community detection algorithm is proposed based on the position of the nodes and their corresponding leaders. Then, using a log-likelihood score, the tightness of the community can be derived. Based on the distribution of community tightness, we establish a connection between p -value theory and network analysis, and then we obtain a significance measure of statistical form . Finally, the framework is applied to both benchmark networks and real social networks. Experimental results show that our work can be used in many fields, such as determining the optimal number of communities, analyzing the social significance of a given community, comparing the performance among various algorithms, etc.

Dominant forest tree mycorrhizal type mediates understory plant invasions

Treesearch

Insu Jo; Kevin M. Potter; Grant M. Domke; Songlin Fei

2017-01-01

Forest mycorrhizal type mediates nutrient dynamics, which in turn can influence forest community structure and processes. Using forest inventory data, we explored how dominant forest tree mycorrhizal type affects understory plant invasions with consideration of forest structure and soil properties. We found that arbuscular mycorrhizal (AM) dominant forests, which are...

Regional processes in mangrove ecosystems: Spatial scaling relationships, biomass, and turnover rates following catastrophic disturbance

USGS Publications Warehouse

Ward, G.A.; Smith, T. J.; Whelan, K.R.T.; Doyle, T.W.

2006-01-01

Physiological processes and local-scale structural dynamics of mangroves are relatively well studied. Regional-scale processes, however, are not as well understood. Here we provide long-term data on trends in structure and forest turnover at a large scale, following hurricane damage in mangrove ecosystems of South Florida, U.S.A. Twelve mangrove vegetation plots were monitored at periodic intervals, between October 1992 and March 2005. Mangrove forests of this region are defined by a -1.5 scaling relationship between mean stem diameter and stem density, mirroring self-thinning theory for mono-specific stands. This relationship is reflected in tree size frequency scaling exponents which, through time, have exhibited trends toward a community average that is indicative of full spatial resource utilization. These trends, together with an asymptotic standing biomass accumulation, indicate that coastal mangrove ecosystems do adhere to size-structured organizing principles as described for upland tree communities. Regenerative dynamics are different between areas inside and outside of the primary wind-path of Hurricane Andrew which occurred in 1992. Forest dynamic turnover rates, however, are steady through time. This suggests that ecological, more-so than structural factors, control forest productivity. In agreement, the relative mean rate of biomass growth exhibits an inverse relationship with the seasonal range of porewater salinities. The ecosystem average in forest scaling relationships may provide a useful investigative tool of mangrove community biomass relationships, as well as offer a robust indicator of general ecosystem health for use in mangrove forest ecosystem management and restoration. ?? Springer 2006.

Molecular tools for investigating microbial community structure and function in oxygen-deficient marine waters.

PubMed

Hawley, Alyse K; Kheirandish, Sam; Mueller, Andreas; Leung, Hilary T C; Norbeck, Angela D; Brewer, Heather M; Pasa-Tolic, Ljiljana; Hallam, Steven J

2013-01-01

Water column oxygen (O2)-deficiency shapes food-web structure by progressively directing nutrients and energy away from higher trophic levels into microbial community metabolism resulting in fixed nitrogen loss and greenhouse gas production. Although respiratory O2 consumption during organic matter degradation is a natural outcome of a productive surface ocean, global-warming-induced stratification intensifies this process leading to oxygen minimum zone (OMZ) expansion. Here, we describe useful tools for detection and quantification of potential key microbial players and processes in OMZ community metabolism including quantitative polymerase chain reaction primers targeting Marine Group I Thaumarchaeota, SUP05, Arctic96BD-19, and SAR324 small-subunit ribosomal RNA genes and protein extraction methods from OMZ waters compatible with high-resolution mass spectrometry for profiling microbial community structure and functional dynamics. © 2013 Elsevier Inc. All rights reserved.

Measuring the Social Relations: Social Distance in Social Structure --- a Study of Prison Community

NASA Astrophysics Data System (ADS)

Pabjan, B.

2005-08-01

Social relations and their influence on various phenomena are one of the key issues not only in sociology. The crucial problem, however, is how to measure the social relations and their implications in society. We try to adapt a physical perspective to the ``typical'' sociological analysis and to measure the qualitative nature of human community adapting the category of social distance. This category is used to explore the properties of social relations in the structure and the communication system of prison community. The issues that are discussed: the specific properties of social relations as the constitutive factors for different type of group structure and type of communication. How the elementary social networks (short-range group structures) form the dynamics of prison community? What is the role of the numerical force of the group for prison community? Is there the interplay between the microstructures and macrostructures? The work is based on our research carried out in 17 prisons in Poland in 2003, 2004 and 2005. There were about 2000 prisoners in the sample.

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.

Regional synchrony in full-scale activated sludge bioreactors due to deterministic microbial community assembly

PubMed Central

Griffin, James S; Wells, George F

2017-01-01

Seasonal community structure and regionally synchronous population dynamics have been observed in natural microbial ecosystems, but have not been well documented in wastewater treatment bioreactors. Few studies of community dynamics in full-scale activated sludge systems facing similar meteorological conditions have been done to compare the importance of deterministic and neutral community assembly mechanisms. We subjected weekly activated sludge samples from six regional full-scale bioreactors at four wastewater treatment plants obtained over 1 year to Illumina sequencing of 16S ribosomal RNA genes, resulting in a library of over 17 million sequences. All samples derived from reactors treating primarily municipal wastewater. Despite variation in operational characteristics and location, communities displayed temporal synchrony at the individual operational taxonomic unit (OTU), broad phylogenetic affiliation and community-wide scale. Bioreactor communities were dominated by 134 abundant and highly regionally synchronized OTU populations that accounted for over 50% of the total reads. Non-core OTUs displayed abundance-dependent population synchrony. Alpha diversity varied by reactor, but showed a highly reproducible and synchronous seasonal fluctuation. Community similarity was dominated by seasonal changes, but individual reactors maintained minor stable differences after 1 year. Finally, the impacts of mass migration driven by direct biomass transfers between reactors was investigated, but had no significant effect on community similarity or diversity in the sink community. Our results show that population dynamics in activated sludge bioreactors are consistent with niche-driven assembly guided by seasonal temperature fluctuations. PMID:27996980

Microbial Community Succession During Lactate Amendment of Chromium Contaminated Groundwater Reveals a Predominance of Pelosinus spp.

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

Mosher, Jennifer J; Phelps, Tommy Joe; Drake, Meghan M

2012-01-01

Microbial community structure and metabolism in contaminated ecosystems are potentially controlled not only by the different populations within the community, but a myriad of dynamic physicochemical parameters as well. The goal of the current work was to determine the impact of organic acid enrichment, in this case lactate, on the succession of the native microbial community from a contaminated groundwater aquifer. Triplicate anaerobic, continuous-flow glass reactors were inoculated with Hanford 100-H groundwater and incubated for 95 days to obtain a stable, enriched community. The microbial community experienced a shift in the population dynamics over time to eventually form a communitymore » with far less diversity than the original. The final community was dominated by Pelosinus spp. and to a lesser degree, Acetobacterium spp. with small amounts of other bacteria and archaea including methanogens. The resultant diversity was far decreased from 63 genera within 12 phyla to 11 bacterial genera (from three phyla) and 2 archaeal genera (from one phylum). Isolation efforts were successful in attaining new species of Pelosinus and known members of Methanosarcina barkerii along with several sulfate- and Fe(III)- reducing consortia members. The continuous-flow reactors allowed for testing physiochemical factors with microbial community dynamics on a smaller, replicable, scale while also facilitating the isolation of several previously uncultured community members. These lab-scale simulations will presumably allow for a deeper understanding of the community metabolism with specific carbon amendments that can inform future in situ efforts.« less

The σ law of evolutionary dynamics in community-structured population.

PubMed

Tang, Changbing; Li, Xiang; Cao, Lang; Zhan, Jingyuan

2012-08-07

Evolutionary game dynamics in finite populations provide a new framework to understand the selection of traits with frequency-dependent fitness. Recently, a simple but fundamental law of evolutionary dynamics, which we call σ law, describes how to determine the selection between two competing strategies: in most evolutionary processes with two strategies, A and B, strategy A is favored over B in weak selection if and only if σR+S>T+σP. This relationship holds for a wide variety of structured populations with mutation rate and weak selection under certain assumptions. In this paper, we propose a model of games based on a community-structured population and revisit this law under the Moran process. By calculating the average payoffs of A and B individuals with the method of effective sojourn time, we find that σ features not only the structured population characteristics, but also the reaction rate between individuals. That is to say, an interaction between two individuals are not uniform, and we can take σ as a reaction rate between any two individuals with the same strategy. We verify this viewpoint by the modified replicator equation with non-uniform interaction rates in a simplified version of the prisoner's dilemma game (PDG). Copyright © 2012 Elsevier Ltd. All rights reserved.

Effect of covering composting piles with mature compost on ammonia emission and microbial community structure of composting process.

PubMed

Maeda, Koki; Morioka, Riki; Osada, Takashi

2009-01-01

To control ammonia (NH(3)) volatilization from the dairy cattle (Bos taurus) manure composting process, a compost pile was covered with mature compost and the gas emissions evaluated using the dynamic chamber system. The peak of NH(3) volatilization observed immediately after piling up of the compost was reduced from 196 to 62 mg/m(3) by covering the compost pile with mature compost. The accumulation of NH(4)-N to the covered mature compost was also observed. Covering and mixing the compost with mature compost had no effect on the microbial community structure. However, over time the microbial community structure changed because of a decrease in easily degradable organic compounds in the compost piles. The availability of volatile fatty acids (VFA) was considered to be important for microbial community structure in the compost. After the VFA had disappeared, the NO(3)-N concentration increased and the cellulose degrading bacteria such as Cytophaga increased in number.

THE EVOLUTION OF RESTRAINT IN BACTERIAL BIOFILMS UNDER NONTRANSITIVE COMPETITION

PubMed Central

Prado, Federico; Kerr, Benjamin

2009-01-01

Theoretical and empirical evidence indicates that competing species can coexist if dispersal, migration, and competitive interactions occur over relatively small spatial scales. In particular, spatial structure appears to be critical to certain communities with nontransitive competition. A typical nontransitive system involves three competing species that satisfy a relationship similar to the children’s game of rock–paper–scissors. Although the ecological dynamics of nontransitive systems in spatially structured communities have received some attention, fewer studies have incorporated evolutionary change. Here we investigate evolution within toxic bacterial biofilms using an agent-based simulation that represents a nontransitive community containing three populations of Escherichia coli. In structured, nontransitive communities, strains evolve that do not maximize their competitive ability: They do not reduce their probability of death to a minimum or increase their toxicity to a maximum. That is, types evolve that exercise restraint. We show that nontransitivity and spatial structure (in the form of localized interactions) are both necessary for the evolution of restraint in these biofilms. PMID:18039324

The evolution of restraint in bacterial biofilms under nontransitive competition.

PubMed

Prado, Federico; Kerr, Benjamin

2008-03-01

Theoretical and empirical evidence indicates that competing species can coexist if dispersal, migration, and competitive interactions occur over relatively small spatial scales. In particular, spatial structure appears to be critical to certain communities with nontransitive competition. A typical nontransitive system involves three competing species that satisfy a relationship similar to the children's game of rock-paper-scissors. Although the ecological dynamics of nontransitive systems in spatially structured communities have received some attention, fewer studies have incorporated evolutionary change. Here we investigate evolution within toxic bacterial biofilms using an agent-based simulation that represents a nontransitive community containing three populations of Escherichia coli. In structured, nontransitive communities, strains evolve that do not maximize their competitive ability: They do not reduce their probability of death to a minimum or increase their toxicity to a maximum. That is, types evolve that exercise restraint. We show that nontransitivity and spatial structure (in the form of localized interactions) are both necessary for the evolution of restraint in these biofilms.

a New Dynamic Community Model for Social Networks

NASA Astrophysics Data System (ADS)

Lu, Zhe-Ming; Wu, Zhen; Guo, Shi-Ze; Chen, Zhe; Song, Guang-Hua

2014-09-01

In this paper, based on the phenomenon that individuals join into and jump from the organizations in the society, we propose a dynamic community model to construct social networks. Two parameters are adopted in our model, one is the communication rate Pa that denotes the connection strength in the organization and the other is the turnover rate Pb, that stands for the frequency of jumping among the organizations. Based on simulations, we analyze not only the degree distribution, the clustering coefficient, the average distance and the network diameter but also the group distribution which is closely related to their community structure. Moreover, we discover that the networks generated by the proposed model possess the small-world property and can well reproduce the networks of social contacts.

Dynamics of bloggers’ communities: Bipartite networks from empirical data and agent-based modeling

NASA Astrophysics Data System (ADS)

Mitrović, Marija; Tadić, Bosiljka

2012-11-01

We present an analysis of the empirical data and the agent-based modeling of the emotional behavior of users on the Web portals where the user interaction is mediated by posted comments, like Blogs and Diggs. We consider the dataset of discussion-driven popular Diggs, in which all comments are screened by machine-learning emotion detection in the text, to determine positive and negative valence (attractiveness and aversiveness) of each comment. By mapping the data onto a suitable bipartite network, we perform an analysis of the network topology and the related time-series of the emotional comments. The agent-based model is then introduced to simulate the dynamics and to capture the emergence of the emotional behaviors and communities. The agents are linked to posts on a bipartite network, whose structure evolves through their actions on the posts. The emotional states (arousal and valence) of each agent fluctuate in time, subject to the current contents of the posts to which the agent is exposed. By an agent’s action on a post its current emotions are transferred to the post. The model rules and the key parameters are inferred from the considered empirical data to ensure their realistic values and mutual consistency. The model assumes that the emotional arousal over posts drives the agent’s action. The simulations are preformed for the case of constant flux of agents and the results are analyzed in full analogy with the empirical data. The main conclusions are that the emotion-driven dynamics leads to long-range temporal correlations and emergent networks with community structure, that are comparable with the ones in the empirical system of popular posts. In view of pure emotion-driven agents actions, this type of comparisons provide a quantitative measure for the role of emotions in the dynamics on real blogs. Furthermore, the model reveals the underlying mechanisms which relate the post popularity with the emotion dynamics and the prevalence of negative emotions (critique). We also demonstrate how the community structure is tuned by varying a relevant parameter in the model. All data used in these works are fully anonymized.

Structural stability as a consistent predictor of phenological events.

PubMed

Song, Chuliang; Saavedra, Serguei

2018-06-13

The timing of the first and last seasonal appearance of a species in a community typically follows a pattern that is governed by temporal factors. While it has been shown that changes in the environment are linked to phenological changes, the direction of this link appears elusive and context-dependent. Thus, finding consistent predictors of phenological events is of central importance for a better assessment of expected changes in the temporal dynamics of ecological communities. Here we introduce a measure of structural stability derived from species interaction networks as an estimator of the expected range of environmental conditions compatible with the existence of a community. We test this measure as a predictor of changes in species richness recorded on a daily basis in a high-arctic plant-pollinator community during two spring seasons. We find that our measure of structural stability is the only consistent predictor of changes in species richness among different ecological and environmental variables. Our findings suggest that measures based on the notion of structural stability can synthesize the expected variation of environmental conditions tolerated by a community, and explain more consistently the phenological changes observed in ecological communities. © 2018 The Author(s).

Detecting macroecological patterns in bacterial communities across independent studies of global soils.

PubMed

Ramirez, Kelly S; Knight, Christopher G; de Hollander, Mattias; Brearley, Francis Q; Constantinides, Bede; Cotton, Anne; Creer, Si; Crowther, Thomas W; Davison, John; Delgado-Baquerizo, Manuel; Dorrepaal, Ellen; Elliott, David R; Fox, Graeme; Griffiths, Robert I; Hale, Chris; Hartman, Kyle; Houlden, Ashley; Jones, David L; Krab, Eveline J; Maestre, Fernando T; McGuire, Krista L; Monteux, Sylvain; Orr, Caroline H; van der Putten, Wim H; Roberts, Ian S; Robinson, David A; Rocca, Jennifer D; Rowntree, Jennifer; Schlaeppi, Klaus; Shepherd, Matthew; Singh, Brajesh K; Straathof, Angela L; Bhatnagar, Jennifer M; Thion, Cécile; van der Heijden, Marcel G A; de Vries, Franciska T

2018-02-01

The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential 'indicator' taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.

Impact of individual interest shift on information dissemination in modular networks

NASA Astrophysics Data System (ADS)

Zhao, Narisa; Cui, Xuelian

2017-01-01

Social networks exhibit strong community structure. Many researches have been done to explore the impacts of community structure on information diffusion but few combined with human behaviors together. In this paper, we focus on how the individual interests' changing behavior impacts the dynamics of information propagation. Firstly, we propose an information dissemination model considering both the community structure and individual interest shift where social reinforcement and time decaying are taken into account. The accuracy of the model is evaluated by comparing the simulation and theoretical results. Further, the numerical results illustrate that both the community structure and the interests changing behavior have effects on the outbreak size of the information dissemination. Specially, lower modularity and higher community connection density will accelerate the speed of information propagation especially when the information maximal lifetime is shorter. In addition, the changes of individual interests in the message have a great impact on the final density of the received through increasing or decreasing the number of satisfied individuals directly. What is more, our findings suggest that when the modularity of the network is higher and the community clustering coefficient is lower individual interest shift behavior will have a heavier effect on the spread scope.

Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions

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

Men, Yujie; Yu, Ke; Bælum, Jacob

ABSTRACT The aim of this study is to obtain a systems-level understanding of the interactions betweenDehalococcoidesand corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities, and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in theVeillonellaceaebin-genome were detected in the metatranscriptome of the enrichment without exogenous cobalamin than in the one with the addition of cobalamin. Among these genes, sporulation-related genes exhibited the highest differential expression when cobalamin wasmore » not added, suggesting a possible release route of corrinoids from corrinoid producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoidde novobiosynthesis pathway was also assigned to theVeillonellaceaebin-genome. Targeted quantitative PCR (qPCR) analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin than in the enrichment with cobalamin. Furthermore, the corrinoid salvaging and modification pathway ofDehalococcoideswas upregulated in response to the cobalamin stress. This study provides important insights into the microbial interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions. IMPORTANCEThe key chloroethene-dechlorinating bacteriumDehalococcoides mccartyiis a cobalamin auxotroph, thus acquiring corrinoids from other community members. Therefore, it is important to investigate the microbe-microbe interactions betweenDehalococcoidesand the corrinoid-providing microorganisms in a community. This study provides systems-level information, i.e., taxonomic and functional compositions and dynamics of the supportive microorganisms in dechlorinating communities under different cobalamin conditions. The findings shed light on the important roles ofVeillonellaceaespecies in the communities compared to other coexisting community members in producing and providing corrinoids forDehalococcoidesspecies under cobalamin-limited conditions.« less

Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions

PubMed Central

Yu, Ke; Bælum, Jacob; Gao, Ying; Tremblay, Julien; Prestat, Emmanuel; Stenuit, Ben; Tringe, Susannah G.; Jansson, Janet; Zhang, Tong; Alvarez-Cohen, Lisa

2017-01-01

ABSTRACT The aim of this study is to obtain a systems-level understanding of the interactions between Dehalococcoides and corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities, and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in the Veillonellaceae bin-genome were detected in the metatranscriptome of the enrichment without exogenous cobalamin than in the one with the addition of cobalamin. Among these genes, sporulation-related genes exhibited the highest differential expression when cobalamin was not added, suggesting a possible release route of corrinoids from corrinoid producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoid de novo biosynthesis pathway was also assigned to the Veillonellaceae bin-genome. Targeted quantitative PCR (qPCR) analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin than in the enrichment with cobalamin. Furthermore, the corrinoid salvaging and modification pathway of Dehalococcoides was upregulated in response to the cobalamin stress. This study provides important insights into the microbial interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions. IMPORTANCE The key chloroethene-dechlorinating bacterium Dehalococcoides mccartyi is a cobalamin auxotroph, thus acquiring corrinoids from other community members. Therefore, it is important to investigate the microbe-microbe interactions between Dehalococcoides and the corrinoid-providing microorganisms in a community. This study provides systems-level information, i.e., taxonomic and functional compositions and dynamics of the supportive microorganisms in dechlorinating communities under different cobalamin conditions. The findings shed light on the important roles of Veillonellaceae species in the communities compared to other coexisting community members in producing and providing corrinoids for Dehalococcoides species under cobalamin-limited conditions. PMID:28188205

Linking benthic microbial community dynamics to diel redox variations in a near shore costal environment, Héeia Fishpond

NASA Astrophysics Data System (ADS)

Frank, K. L.; Rogers, K. L.; Wheat, C. G.; Alegado, R.

2016-12-01

Microbes play crucial roles in mediating biogeochemical cycling in coastal marine habitats. In shallow coastal ecosystems, excess primary productivity and respiration of pelagic phototrophic organisms generate striking diel variations in dissolved oxygen concentrations, leading to substantial vertical migration of redox transition zones in the sediment. However, the relationship between microbial community dynamics and the establishment of these geochemical gradients, especially over a diel time frame, remains poorly constrained. Here we examine the biogeochemical drivers of diel redox dynamics by integrating comprehensive geochemical, taxonomic, functional gene abundance, and thermodynamic datasets from Héeia Fishpond (HFP) sediment cores. HFP, an 88-acre tidally-influenced, shallow Hawaiian coastal estuarine system, is analogous to a large mesocosm embedded in a natural coastal environment, making it an ideal site for coastal biogeochemical studies. Taxonomic assessments of bacterial diversity via 16S rRNA genes revealed centimeter- scale variability with depth, with similar taxa present in all samples, but their relative abundances varied substantially among horizons. There were significant correlation between changes in geochemical composition and changes in community structure. Additionally, functional gene abundance was correlated with energy potential and aligned with activity. The taxanomic data and porewater geochemistry from HFP sediments suggest that redox variations observed in iron and sulfur speciation result from depth-related changes in microbial activity and community structure over a diel period. By linking community diversity to metabolic activity in the context of the geochemical environment, this research provides valuable insight into the connectivity of iron and sulfur metabolic modes.

Fish community-based measures of estuarine ecological quality and pressure-impact relationships

NASA Astrophysics Data System (ADS)

Fonseca, Vanessa F.; Vasconcelos, Rita P.; Gamito, Rita; Pasquaud, Stéphanie; Gonçalves, Catarina I.; Costa, José L.; Costa, Maria J.; Cabral, Henrique N.

2013-12-01

Community-based responses of fish fauna to anthropogenic pressures have been extensively used to assess the ecological quality of estuarine ecosystems. Several methodologies have been developed recently combining metrics reflecting community structure and function. A fish community facing significant environmental disturbances will be characterized by a simplified structure, with lower diversity and complexity. However, estuaries are naturally dynamic ecosystems exposed to numerous human pressures, making it difficult to distinguish between natural and anthropogenic-induced changes to the biological community. In the present work, the variability of several fish metrics was assessed in relation to different pressures in estuarine sites. The response of a multimetric index (Estuarine Fish Assessment Index) was also analysed. Overall, fish metrics and the multimetric index signalled anthropogenic stress, particularly environmental chemical pollution. The fish assemblage associated with this type of pressure was characterized by lower species diversity, lower number of functional guilds, lower abundance of marine migrants and of piscivorous individuals, and higher abundance of estuarine resident species. A decreased ecological quality status, based on the EFAI, was also determined for sites associated with this pressure group. Ultimately, the definition of each pressure groups favoured a stressor-specific analysis, evidencing pressure patterns and accounting for multiple factors in a highly dynamic environment.

Ecological consequences of Late Quaternary extinctions of megafauna

PubMed Central

Johnson, C.N.

2009-01-01

Abstract Large herbivorous vertebrates have strong interactions with vegetation, affecting the structure, composition and dynamics of plant communities in many ways. Living large herbivores are a small remnant of the assemblages of giants that existed in most terrestrial ecosystems 50 000 years ago. The extinction of so many large herbivores may well have triggered large changes in plant communities. In several parts of the world, palaeoecological studies suggest that extinct megafauna once maintained vegetation openness, and in wooded landscapes created mosaics of different structural types of vegetation with high habitat and species diversity. Following megafaunal extinction, these habitats reverted to more dense and uniform formations. Megafaunal extinction also led to changes in fire regimes and increased fire frequency due to accumulation of uncropped plant material, but there is a great deal of variation in post-extinction changes in fire. Plant communities that once interacted with extinct large herbivores still contain many species with obsolete defences against browsing and non-functional adaptations for seed dispersal. Such plants may be in decline, and, as a result, many plant communities may be in various stages of a process of relaxation from megafauna-conditioned to megafauna-naive states. Understanding the past role of giant herbivores provides fundamental insight into the history, dynamics and conservation of contemporary plant communities. PMID:19324773

High taxonomic variability despite stable functional structure across microbial communities.

PubMed

Louca, Stilianos; Jacques, Saulo M S; Pires, Aliny P F; Leal, Juliana S; Srivastava, Diane S; Parfrey, Laura Wegener; Farjalla, Vinicius F; Doebeli, Michael

2016-12-05

Understanding the processes that are driving variation of natural microbial communities across space or time is a major challenge for ecologists. Environmental conditions strongly shape the metabolic function of microbial communities; however, other processes such as biotic interactions, random demographic drift or dispersal limitation may also influence community dynamics. The relative importance of these processes and their effects on community function remain largely unknown. To address this uncertainty, here we examined bacterial and archaeal communities in replicate 'miniature' aquatic ecosystems contained within the foliage of wild bromeliads. We used marker gene sequencing to infer the taxonomic composition within nine metabolic functional groups, and shotgun environmental DNA sequencing to estimate the relative abundances of these groups. We found that all of the bromeliads exhibited remarkably similar functional community structures, but that the taxonomic composition within individual functional groups was highly variable. Furthermore, using statistical analyses, we found that non-neutral processes, including environmental filtering and potentially biotic interactions, at least partly shaped the composition within functional groups and were more important than spatial dispersal limitation and demographic drift. Hence both the functional structure and taxonomic composition within functional groups of natural microbial communities may be shaped by non-neutral and roughly separate processes.

Forest canopy structural controls over throughfall affect soil microbial community structure in an epiphyte-laden maritime oak stand

NASA Astrophysics Data System (ADS)

Van Stan, J. T., II; Rosier, C. L.; Schrom, J. O.; Wu, T.; Reichard, J. S.; Kan, J.

2014-12-01

Identifying spatiotemporal influences on soil microbial community (SMC) structure is critical to understanding of patterns in nutrient cycling and related ecological services. Since forest canopy structure alters the spatiotemporal patterning of precipitation water and solute supplies to soils (via the "throughfall" mechanism), is it possible changes in SMC structure variability could arise from modifications in canopy elements? Our study investigates this question by monitoring throughfall water and dissolved ion supply to soils beneath a continuum of canopy structure: from a large gap (0% cover) to heavy Tillandsia usneoides L. (Spanish moss) canopy (>90% cover). Throughfall water supply diminished with increasing canopy cover, yet increased washoff/leaching of Na+, Cl-, PO43-, and SO42- from the canopy to the soils (p < 0.01). Presence of T. usneoides diminished throughfall NO3-, but enhanced NH4+, concentrations supplied to subcanopy soils. The mineral soil horizon (0-10 cm) from canopy gaps, bare canopy, and T. usneoides-laden canopy significantly differed (p < 0.05) in soil chemistry parameters (pH, Ca2+, Mg2+, CEC). PCR-DGGE banding patterns beneath similar canopy covers (experiencing similar throughfall dynamics) also produced high similarities per ANalyses Of SIMilarity (ANO-SIM), and clustered together when analyzed by Nonmetric Multidimensional Scaling (NMDS). Correlation analysis of DGGE banding patterns, throughfall dynamics, and soil chemistry yielded significant correlations (p < 0.05) between fungal communities and soil chemical properties significantly differing between canopy cover types (pH: r2 = 0.50; H+ %-base saturation: r2 = 0.48; Ca2+ %-base saturation: r2 = 0.43). Bacterial community structure correlated with throughfall NO3-, NH4+, and Ca2+ concentrations (r2 = 0.37, p = 0.16). These results suggest that modifications of forest canopy structures are capable of affecting mineral-soil horizon SMC structure via the throughfall mechanism when canopies' biomass distribution is highly heterogeneous.

A multi-decade time series of kelp forest community structure at San Nicolas Island, California

USGS Publications Warehouse

Lafferty, Kevin D.; Kenner, Michael C.; Estes, James A.; Tinker, M. Tim; Bodkin, James L.; Cowen, Robert K.; Harrold, Christopher; Novak, Mark; Rassweiler, Andrew; Reed, Daniel C.

2013-01-01

San Nicolas Island is surrounded by broad areas of shallow subtidal habitat, characterized by dynamic kelp forest communities that undergo dramatic and abrupt shifts in community composition. Although these reefs are fished, the physical isolation of the island means that they receive less impact from human activities than most reefs in Southern California, making San Nicolas an ideal place to evaluate alternative theories about the dynamics of these communities. Here we present monitoring data from seven sampling stations surrounding the island, including data on fish, invertebrate, and algal abundance. These data are unusual among subtidal monitoring data sets in that they combine relatively frequent sampling (twice per year) with an exceptionally long time series (since 1980). Other outstanding qualities of the data set are the high taxonomic resolution captured and the monitoring of permanent quadrats and swaths where the history of the community structure at specific locations has been recorded through time. Finally, the data span a period that includes two of the strongest ENSO events on record, a major shift in the Pacific decadal oscillation, and the reintroduction of sea otters to the island in 1987 after at least 150 years of absence. These events provide opportunities to evaluate the effects of bottom-up forcing, top-down control, and physical disturbance on shallow rocky reef communities.

Socio-hydrological modelling of floods: investigating community resilience, adaptation capacity and risk

NASA Astrophysics Data System (ADS)

Ciullo, Alessio; Viglione, Alberto; Castellarin, Attilio

2016-04-01

Changes in flood risk occur because of changes in climate and hydrology, and in societal exposure and vulnerability. Research on change in flood risk has demonstrated that the mutual interactions and continuous feedbacks between floods and societies has to be taken into account in flood risk management. The present work builds on an existing conceptual model of an hypothetical city located in the proximity of a river, along whose floodplains the community evolves over time. The model reproduces the dynamic co-evolution of four variables: flooding, population density of the flooplain, amount of structural protection measures and memory of floods. These variables are then combined in a way to mimic the temporal change of community resilience, defined as the (inverse of the) amount of time for the community to recover from a shock, and adaptation capacity, defined as ratio between damages due to subsequent events. Also, temporal changing exposure, vulnerability and probability of flooding are also modelled, which results in a dynamically varying flood-risk. Examples are provided that show how factors such as collective memory and risk taking attitude influence the dynamics of community resilience, adaptation capacity and risk.

Multiplex social ecological network analysis reveals how social changes affect community robustness more than resource depletion.

PubMed

Baggio, Jacopo A; BurnSilver, Shauna B; Arenas, Alex; Magdanz, James S; Kofinas, Gary P; De Domenico, Manlio

2016-11-29

Network analysis provides a powerful tool to analyze complex influences of social and ecological structures on community and household dynamics. Most network studies of social-ecological systems use simple, undirected, unweighted networks. We analyze multiplex, directed, and weighted networks of subsistence food flows collected in three small indigenous communities in Arctic Alaska potentially facing substantial economic and ecological changes. Our analysis of plausible future scenarios suggests that changes to social relations and key households have greater effects on community robustness than changes to specific wild food resources.

Recognizing the ‘sparsely settled forest’: Multi-decade socioecological change dynamics and community exemplars

Treesearch

Derek B. Van Berkel; Bronwyn Rayfield; Sebastián Martinuzzi; Martin J. Lechowicz; Eric White; Kathleen P. Bell; Chris R. Colocousis; Kent F. Kovacs; Anita T. Morzillo; Darla K. Munroe; Benoit Parmentier; Volker C. Radeloff; Brian J. McGill

2018-01-01

Sparsely settled forests (SSF) are poorly studied, coupled natural and human systems involving rural communities in forest ecosystems that are neither largely uninhabited wildland nor forests on the edges of urban areas. We developed and applied a multidisciplinary approach to define, map, and examine changes in the spatial extent and structure of both the landscapes...

Interactive effects of large herbivores and plant diversity on insect abundance in a meadow steppe in China

Treesearch

Hui Zhu; Deli Wang; Qinfeng Guo; Jun Liu; Ling Wang

2015-01-01

The structure and dynamics of insect community in grasslands can be influenced by grazing management via altered characteristics of plant community. However, attempts to better understand the complex relationships among plants, insects, and large herbivores is still hampered largely by the interactive effects of plants, insects, and large grazers on each other. In this...

Understanding vaginal microbiome complexity from an ecological perspective

PubMed Central

Hickey, Roxana J.; Zhou, Xia; Pierson, Jacob D.; Ravel, Jacques; Forney, Larry J.

2012-01-01

The various microbiota normally associated with the human body have an important influence on human development, physiology, immunity, and nutrition. This is certainly true for the vagina wherein communities of mutualistic bacteria constitute the first line of defense for the host by excluding invasive, nonindigenous organisms that may cause disease. In recent years much has been learned about the bacterial species composition of these communities and how they differ between individuals of different ages and ethnicities. A deeper understanding of their origins and the interrelationships of constituent species is needed to understand how and why they change over time or in response to changes in the host environment. Moreover, there are few unifying theories to explain the ecological dynamics of vaginal ecosystems as they respond to disturbances caused by menses and human activities such as intercourse, douching, and other habits and practices. This fundamental knowledge is needed to diagnose and assess risk to disease. Here we summarize what is known about the species composition, structure, and function of bacterial communities in the human vagina and the applicability of ecological models of community structure and function to understanding the dynamics of this and other ecosystems that comprise the human microbiome. PMID:22683415

Effects of temperature variability on community structure in a natural microbial food web.

PubMed

Zander, Axel; Bersier, Louis-Félix; Gray, Sarah M

2017-01-01

Climate change research has demonstrated that changing temperatures will have an effect on community-level dynamics by altering species survival rates, shifting species distributions, and ultimately, creating mismatches in community interactions. However, most of this work has focused on increasing temperature, and still little is known about how the variation in temperature extremes will affect community dynamics. We used the model aquatic community held within the leaves of the carnivorous plant, Sarracenia purpurea, to test how food web dynamics will be affected by high temperature variation. We tested the community response of the first (bacterial density), second (protist diversity and composition), and third trophic level (predator mortality), and measured community respiration. We collected early and late successional stage inquiline communities from S. purpurea from two North American and two European sites with similar average July temperature. We then created a common garden experiment in which replicates of these communities underwent either high or normal daily temperature variation, with the average temperature equal among treatments. We found an impact of temperature variation on the first two, but not on the third trophic level. For bacteria in the high-variation treatment, density experienced an initial boost in growth but then decreased quickly through time. For protists in the high-variation treatment, alpha-diversity decreased faster than in the normal-variation treatment, beta-diversity increased only in the European sites, and protist community composition tended to diverge more in the late successional stage. The mortality of the predatory mosquito larvae was unaffected by temperature variation. Community respiration was lower in the high-variation treatment, indicating a lower ecosystem functioning. Our results highlight clear impacts of temperature variation. A more mechanistic understanding of the effects that temperature, and especially temperature variation, will have on community dynamics is still greatly needed. © 2016 John Wiley & Sons Ltd.

Dynamics of Research Team Formation in Complex Networks

NASA Astrophysics Data System (ADS)

Sun, Caihong; Wan, Yuzi; Chen, Yu

Most organizations encourage the formation of teams to accomplish complicated tasks, and vice verse, effective teams could bring lots benefits and profits for organizations. Network structure plays an important role in forming teams. In this paper, we specifically study the dynamics of team formation in large research communities in which knowledge of individuals plays an important role on team performance and individual utility. An agent-based model is proposed, in which heterogeneous agents from research communities are described and empirically tested. Each agent has a knowledge endowment and a preference for both income and leisure. Agents provide a variable input (‘effort’) and their knowledge endowments to production. They could learn from others in their team and those who are not in their team but have private connections in community to adjust their own knowledge endowment. They are allowed to join other teams or work alone when it is welfare maximizing to do so. Various simulation experiments are conducted to examine the impacts of network topology, knowledge diffusion among community network, and team output sharing mechanisms on the dynamics of team formation.

Imaging the Population Dynamics of Bacterial Communities in the Zebrafish Gut

NASA Astrophysics Data System (ADS)

Jemielita, Matthew; Taormina, Michael; Burns, Adam; Zac Stephens, W.; Hampton, Jennifer; Guillemin, Karen; Parthasarathy, Raghuveer

2013-03-01

The vertebrate gut is home to a diverse microbial ecosystem whose composition has a strong influence on the development and health of the host organism. While researchers are increasingly able to identify the constituent members of the microbiome, very little is known about the spatial and temporal dynamics of commensal microbial communities, including the mechanisms by which communities nucleate, grow, and interact. We address these issues using a model organism: the larval zebrafish (Danio rerio) prepared microbe-free and inoculated with controlled compositions of fluorophore-expressing bacteria. Live imaging with light sheet fluorescence microscopy enables visualization of individual bacterial cells as well as growing colonies over the entire volume of the gut over periods up to 24 hours. We analyze the structure and dynamics of imaged bacterial communities, uncovering correlations between population size, growth rates, and the timing of inoculations that suggest the existence of active changes in the host environment induced by early bacterial exposure. Our data provide the first visualizations of gut microbiota development over an extended period of time in a vertebrate.

Disconnect of microbial structure and function: enzyme activities and bacterial communities in nascent stream corridors.

PubMed

Frossard, Aline; Gerull, Linda; Mutz, Michael; Gessner, Mark O

2012-03-01

A fundamental issue in microbial and general ecology is the question to what extent environmental conditions dictate the structure of communities and the linkages with functional properties of ecosystems (that is, ecosystem function). We approached this question by taking advantage of environmental gradients established in soil and sediments of small stream corridors in a recently created, early successional catchment. Specifically, we determined spatial and temporal patterns of bacterial community structure and their linkages with potential microbial enzyme activities along the hydrological flow paths of the catchment. Soil and sediments were sampled in a total of 15 sites on four occasions spread throughout a year. Denaturing gradient gel electrophoresis (DGGE) was used to characterize bacterial communities, and substrate analogs linked to fluorescent molecules served to track 10 different enzymes as specific measures of ecosystem function. Potential enzyme activities varied little among sites, despite contrasting environmental conditions, especially in terms of water availability. Temporal changes, in contrast, were pronounced and remarkably variable among the enzymes tested. This suggests much greater importance of temporal dynamics than spatial heterogeneity in affecting specific ecosystem functions. Most strikingly, bacterial community structure revealed neither temporal nor spatial patterns. The resulting disconnect between bacterial community structure and potential enzyme activities indicates high functional redundancy within microbial communities even in the physically and biologically simplified stream corridors of early successional landscapes.

Solving Component Structural Dynamic Failures Due to Extremely High Frequency Structural Response on the Space Shuttle Program

NASA Technical Reports Server (NTRS)

Frady, Greg; Nesman, Thomas; Zoladz, Thomas; Szabo, Roland

2010-01-01

For many years, the capabilities to determine the root-cause failure of component failures have been limited to the analytical tools and the state of the art data acquisition systems. With this limited capability, many anomalies have been resolved by adding material to the design to increase robustness without the ability to determine if the design solution was satisfactory until after a series of expensive test programs were complete. The risk of failure and multiple design, test, and redesign cycles were high. During the Space Shuttle Program, many crack investigations in high energy density turbomachines, like the SSME turbopumps and high energy flows in the main propulsion system, have led to the discovery of numerous root-cause failures and anomalies due to the coexistences of acoustic forcing functions, structural natural modes, and a high energy excitation, such as an edge tone or shedding flow, leading the technical community to understand many of the primary contributors to extremely high frequency high cycle fatique fluid-structure interaction anomalies. These contributors have been identified using advanced analysis tools and verified using component and system tests during component ground tests, systems tests, and flight. The structural dynamics and fluid dynamics communities have developed a special sensitivity to the fluid-structure interaction problems and have been able to adjust and solve these problems in a time effective manner to meet budget and schedule deadlines of operational vehicle programs, such as the Space Shuttle Program over the years.

Finding Statistically Significant Communities in Networks

PubMed Central

Lancichinetti, Andrea; Radicchi, Filippo; Ramasco, José J.; Fortunato, Santo

2011-01-01

Community structure is one of the main structural features of networks, revealing both their internal organization and the similarity of their elementary units. Despite the large variety of methods proposed to detect communities in graphs, there is a big need for multi-purpose techniques, able to handle different types of datasets and the subtleties of community structure. In this paper we present OSLOM (Order Statistics Local Optimization Method), the first method capable to detect clusters in networks accounting for edge directions, edge weights, overlapping communities, hierarchies and community dynamics. It is based on the local optimization of a fitness function expressing the statistical significance of clusters with respect to random fluctuations, which is estimated with tools of Extreme and Order Statistics. OSLOM can be used alone or as a refinement procedure of partitions/covers delivered by other techniques. We have also implemented sequential algorithms combining OSLOM with other fast techniques, so that the community structure of very large networks can be uncovered. Our method has a comparable performance as the best existing algorithms on artificial benchmark graphs. Several applications on real networks are shown as well. OSLOM is implemented in a freely available software (http://www.oslom.org), and we believe it will be a valuable tool in the analysis of networks. PMID:21559480

Effects of pyrite and sphalerite on population compositions, dynamics and copper extraction efficiency in chalcopyrite bioleaching process.

PubMed

Xiao, Yunhua; Liu, Xueduan; Dong, Weiling; Liang, Yili; Niu, Jiaojiao; Gu, Yabing; Ma, Liyuan; Hao, Xiaodong; Zhang, Xian; Xu, Zhen; Yin, Huaqun

2017-07-01

This study used an artificial microbial community with four known moderately thermophilic acidophiles (three bacteria including Acidithiobacillus caldus S1, Sulfobacillus thermosulfidooxidans ST and Leptospirillum ferriphilum YSK, and one archaea, Ferroplasma thermophilum L1) to explore the variation of microbial community structure, composition, dynamics and function (e.g., copper extraction efficiency) in chalcopyrite bioleaching (C) systems with additions of pyrite (CP) or sphalerite (CS). The community compositions and dynamics in the solution and on the ore surface were investigated by real-time quantitative PCR (qPCR). The results showed that the addition of pyrite or sphalerite changed the microbial community composition and dynamics dramatically during the chalcopyrite bioleaching process. For example, A. caldus (above 60%) was the dominant species at the initial stage in three groups, and at the middle stage, still dominated C group (above 70%), but it was replaced by L. ferriphilum (above 60%) in CP and CS groups; at the final stage, L. ferriphilum dominated C group, while F. thermophilum dominated CP group on the ore surface. Furthermore, the additions of pyrite or sphalerite both made the increase of redox potential (ORP) and the concentrations of Fe 3+ and H + , which would affect the microbial community compositions and copper extraction efficiency. Additionally, pyrite could enhance copper extraction efficiency (e.g., improving around 13.2% on day 6) during chalcopyrite bioleaching; on the contrary, sphalerite restrained it.

Unexpected Diversity during Community Succession in the Apple Flower Microbiome

PubMed Central

Shade, Ashley; McManus, Patricia S.; Handelsman, Jo

2013-01-01

ABSTRACT Despite its importance to the host, the flower microbiome is poorly understood. We report a culture-independent, community-level assessment of apple flower microbial diversity and dynamics. We collected flowers from six apple trees at five time points, starting before flowers opened and ending at petal fall. We applied streptomycin to half of the trees when flowers opened. Assessment of microbial diversity using tag pyrosequencing of 16S rRNA genes revealed that the apple flower communities were rich and diverse and dominated by members of TM7 and Deinococcus-Thermus, phyla about which relatively little is known. From thousands of taxa, we identified six successional groups with coherent dynamics whose abundances peaked at different times before and after bud opening. We designated the groups Pioneer, Early, Mid, Late, Climax, and Generalist communities. The successional pattern was attributed to a set of prevalent taxa that were persistent and gradually changing in abundance. These taxa had significant associations with other community members, as demonstrated with a cooccurrence network based on local similarity analysis. We also detected a set of less-abundant, transient taxa that contributed to general tree-to-tree variability but not to the successional pattern. Communities on trees sprayed with streptomycin had slightly lower phylogenetic diversity than those on unsprayed trees but did not differ in structure or succession. Our results suggest that changes in apple flower microbial community structure are predictable over the life of the flower, providing a basis for ecological understanding and disease management. PMID:23443006

Reverse engineering a social agent-based hidden markov model--visage.

PubMed

Chen, Hung-Ching Justin; Goldberg, Mark; Magdon-Ismail, Malik; Wallace, William A

2008-12-01

We present a machine learning approach to discover the agent dynamics that drives the evolution of the social groups in a community. We set up the problem by introducing an agent-based hidden Markov model for the agent dynamics: an agent's actions are determined by micro-laws. Nonetheless, We learn the agent dynamics from the observed communications without knowing state transitions. Our approach is to identify the appropriate micro-laws corresponding to an identification of the appropriate parameters in the model. The model identification problem is then formulated as a mixed optimization problem. To solve the problem, we develop a multistage learning process for determining the group structure, the group evolution, and the micro-laws of a community based on the observed set of communications among actors, without knowing the semantic contents. Finally, to test the quality of our approximations and the feasibility of the approach, we present the results of extensive experiments on synthetic data as well as the results on real communities, such as Enron email and Movie newsgroups. Insight into agent dynamics helps us understand the driving forces behind social evolution.

NASA Handbook for Spacecraft Structural Dynamics Testing

NASA Technical Reports Server (NTRS)

Kern, Dennis L.; Scharton, Terry D.

2005-01-01

Recent advances in the area of structural dynamics and vibrations, in both methodology and capability, have the potential to make spacecraft system testing more effective from technical, cost, schedule, and hardware safety points of view. However, application of these advanced test methods varies widely among the NASA Centers and their contractors. Identification and refinement of the best of these test methodologies and implementation approaches has been an objective of efforts by the Jet Propulsion Laboratory on behalf of the NASA Office of the Chief Engineer. But to develop the most appropriate overall test program for a flight project from the selection of advanced methodologies, as well as conventional test methods, spacecraft project managers and their technical staffs will need overall guidance and technical rationale. Thus, the Chief Engineer's Office has recently tasked JPL to prepare a NASA Handbook for Spacecraft Structural Dynamics Testing. An outline of the proposed handbook, with a synopsis of each section, has been developed and is presented herein. Comments on the proposed handbook are solicited from the spacecraft structural dynamics testing community.

NASA Handbook for Spacecraft Structural Dynamics Testing

NASA Technical Reports Server (NTRS)

Kern, Dennis L.; Scharton, Terry D.

2004-01-01

Recent advances in the area of structural dynamics and vibrations, in both methodology and capability, have the potential to make spacecraft system testing more effective from technical, cost, schedule, and hardware safety points of view. However, application of these advanced test methods varies widely among the NASA Centers and their contractors. Identification and refinement of the best of these test methodologies and implementation approaches has been an objective of efforts by the Jet Propulsion Laboratory on behalf of the NASA Office of the Chief Engineer. But to develop the most appropriate overall test program for a flight project from the selection of advanced methodologies, as well as conventional test methods, spacecraft project managers and their technical staffs will need overall guidance and technical rationale. Thus, the Chief Engineer's Office has recently tasked JPL to prepare a NASA Handbook for Spacecraft Structural Dynamics Testing. An outline of the proposed handbook, with a synopsis of each section, has been developed and is presented herein. Comments on the proposed handbook is solicited from the spacecraft structural dynamics testing community.

Disentangling the role of floral sensory stimuli in pollination networks.

PubMed

Kantsa, Aphrodite; Raguso, Robert A; Dyer, Adrian G; Olesen, Jens M; Tscheulin, Thomas; Petanidou, Theodora

2018-03-12

Despite progress in understanding pollination network structure, the functional roles of floral sensory stimuli (visual, olfactory) have never been addressed comprehensively in a community context, even though such traits are known to mediate plant-pollinator interactions. Here, we use a comprehensive dataset of floral traits and a novel dynamic data-pooling methodology to explore the impacts of floral sensory diversity on the structure of a pollination network in a Mediterranean scrubland. Our approach tracks transitions in the network behaviour of each plant species throughout its flowering period and, despite dynamism in visitor composition, reveals significant links to floral scent, and/or colour as perceived by pollinators. Having accounted for floral phenology, abundance and phylogeny, the persistent association between floral sensory traits and visitor guilds supports a deeper role for sensory bias and diffuse coevolution in structuring plant-pollinator networks. This knowledge of floral sensory diversity, by identifying the most influential phenotypes, could help prioritize efforts for plant-pollinator community restoration.

Palms, peccaries and perturbations: widespread effects of small-scale disturbance in tropical forests

PubMed Central

2012-01-01

Background Disturbance is an important process structuring ecosystems worldwide and has long been thought to be a significant driver of diversity and dynamics. In forests, most studies of disturbance have focused on large-scale disturbance such as hurricanes or tree-falls. However, smaller sub-canopy disturbances could also have significant impacts on community structure. One such sub-canopy disturbance in tropical forests is abscising leaves of large arborescent palm (Arececeae) trees. These leaves can weigh up to 15 kg and cause physical damage and mortality to juvenile plants. Previous studies examining this question suffered from the use of static data at small spatial scales. Here we use data from a large permanent forest plot combined with dynamic data on the survival and growth of > 66,000 individuals over a seven-year period to address whether falling palm fronds do impact neighboring seedling and sapling communities, or whether there is an interaction between the palms and peccaries rooting for fallen palm fruit in the same area as falling leaves. We tested the wider generalisation of these hypotheses by comparing seedling and sapling survival under fruiting and non-fruiting trees in another family, the Myristicaceae. Results We found a spatially-restricted but significant effect of large arborescent fruiting palms on the spatial structure, population dynamics and species diversity of neighbouring sapling and seedling communities. However, these effects were not found around slightly smaller non-fruiting palm trees, suggesting it is seed predators such as peccaries rather than falling leaves that impact on the communities around palm trees. Conversely, this hypothesis was not supported in data from other edible species, such as those in the family Myristicaceae. Conclusions Given the abundance of arborescent palm trees in Amazonian forests, it is reasonable to conclude that their presence does have a significant, if spatially-restricted, impact on juvenile plants, most likely on the survival and growth of seedlings and saplings damaged by foraging peccaries. Given the abundance of fruit produced by each palm, the widespread effects of these small-scale disturbances appear, over long time-scales, to cause directional changes in community structure at larger scales. PMID:22429883

Palms, peccaries and perturbations: widespread effects of small-scale disturbance in tropical forests.

PubMed

Queenborough, Simon A; Metz, Margaret R; Wiegand, Thorsten; Valencia, Renato

2012-03-19

Disturbance is an important process structuring ecosystems worldwide and has long been thought to be a significant driver of diversity and dynamics. In forests, most studies of disturbance have focused on large-scale disturbance such as hurricanes or tree-falls. However, smaller sub-canopy disturbances could also have significant impacts on community structure. One such sub-canopy disturbance in tropical forests is abscising leaves of large arborescent palm (Arececeae) trees. These leaves can weigh up to 15 kg and cause physical damage and mortality to juvenile plants. Previous studies examining this question suffered from the use of static data at small spatial scales. Here we use data from a large permanent forest plot combined with dynamic data on the survival and growth of > 66,000 individuals over a seven-year period to address whether falling palm fronds do impact neighboring seedling and sapling communities, or whether there is an interaction between the palms and peccaries rooting for fallen palm fruit in the same area as falling leaves. We tested the wider generalisation of these hypotheses by comparing seedling and sapling survival under fruiting and non-fruiting trees in another family, the Myristicaceae. We found a spatially-restricted but significant effect of large arborescent fruiting palms on the spatial structure, population dynamics and species diversity of neighbouring sapling and seedling communities. However, these effects were not found around slightly smaller non-fruiting palm trees, suggesting it is seed predators such as peccaries rather than falling leaves that impact on the communities around palm trees. Conversely, this hypothesis was not supported in data from other edible species, such as those in the family Myristicaceae. Given the abundance of arborescent palm trees in Amazonian forests, it is reasonable to conclude that their presence does have a significant, if spatially-restricted, impact on juvenile plants, most likely on the survival and growth of seedlings and saplings damaged by foraging peccaries. Given the abundance of fruit produced by each palm, the widespread effects of these small-scale disturbances appear, over long time-scales, to cause directional changes in community structure at larger scales.

Dominant forest tree mycorrhizal type mediates understory plant invasions

Treesearch

Insu Jo; Kevin M. Potter; Grant M. Domke; Songlin Fei

2018-01-01

Forest mycorrhizal type mediates nutrient dynamics, which in turn can influence forest community structure and processes. Using forest inventory data, we explored how dominant forest tree myc- orrhizal type affects understory plant invasions with consideration of forest structure and soil properties. We found that arbuscular mycorrhizal (AM) dominant forests, which are...

Dynamic Analyses Including Joints Of Truss Structures

NASA Technical Reports Server (NTRS)

Belvin, W. Keith

1991-01-01

Method for mathematically modeling joints to assess influences of joints on dynamic response of truss structures developed in study. Only structures with low-frequency oscillations considered; only Coulomb friction and viscous damping included in analysis. Focus of effort to obtain finite-element mathematical models of joints exhibiting load-vs.-deflection behavior similar to measured load-vs.-deflection behavior of real joints. Experiments performed to determine stiffness and damping nonlinearities typical of joint hardware. Algorithm for computing coefficients of analytical joint models based on test data developed to enable study of linear and nonlinear effects of joints on global structural response. Besides intended application to large space structures, applications in nonaerospace community include ground-based antennas and earthquake-resistant steel-framed buildings.

Biological soil crusts across disturbance–recovery scenarios: effect of grazing regime on community dynamics.

PubMed

Concostrina-Zubiri, L; Huber-Sannwald, E; Martínez, I; Flores Flores, J L; Reyes-Agüero, J A; Escude, A; Belnap, J

Grazing represents one of the most common disturbances in drylands worldwide, affecting both ecosystem structure and functioning. Despite the efforts to understand the nature and magnitude of grazing effects on ecosystem components and processes, contrasting results continue to arise. This is particularly remarkable for the biological soil crust (BSC) communities (i.e., cyanobacteria, lichens, and bryophytes), which play an important role in soil dynamics. Here we evaluated simultaneously the effect of grazing impact on BSC communities (resistance) and recovery after livestock exclusion (resilience) in a semiarid grassland of Central Mexico. In particular, we examined BSC species distribution, species richness, taxonomical group cover (i.e., cyanobacteria, lichen, bryophyte), and composition along a disturbance gradient with different grazing regimes (low, medium, high impact) and along a recovery gradient with differently aged livestock exclosures (short-, medium-, long-term exclusion). Differences in grazing impact and time of recovery from grazing both resulted in slight changes in species richness; however, there were pronounced shifts in species composition and group cover. We found we could distinguish four highly diverse and dynamic BSC species groups: (1) species with high resistance and resilience to grazing, (2) species with high resistance but low resilience, (3) species with low resistance but high resilience, and (4) species with low resistance and resilience. While disturbance resulted in a novel diversity configuration, which may profoundly affect ecosystem functioning, we observed that 10 years of disturbance removal did not lead to the ecosystem structure found after 27 years of recovery. These findings are an important contribution to our understanding of BCS dynamics from a species and community perspective placed in a land use change context.

Biological soil crusts across disturbance-recovery scenarios: effect of grazing regime on community dynamics

USGS Publications Warehouse

Concostrina-Zubiri, L.; Huber-Sannwald, E.; Martínez, I.; Flores Flores, J. L.; Reyes-Agüero, J. A.; Escudero, A.; Belnap, Jayne

2014-01-01

Grazing represents one of the most common disturbances in drylands worldwide, affecting both ecosystem structure and functioning. Despite the efforts to understand the nature and magnitude of grazing effects on ecosystem components and processes, contrasting results continue to arise. This is particularly remarkable for the biological soil crust (BSC) communities (i.e., cyanobacteria, lichens, and bryophytes), which play an important role in soil dynamics. Here we evaluated simultaneously the effect of grazing impact on BSC communities (resistance) and recovery after livestock exclusion (resilience) in a semiarid grassland of Central Mexico. In particular, we examined BSC species distribution, species richness, taxonomical group cover (i.e., cyanobacteria, lichen, bryophyte), and composition along a disturbance gradient with different grazing regimes (low, medium, high impact) and along a recovery gradient with differently aged livestock exclosures (short-, medium-, long-term exclusion). Differences in grazing impact and time of recovery from grazing both resulted in slight changes in species richness; however, there were pronounced shifts in species composition and group cover. We found we could distinguish four highly diverse and dynamic BSC species groups: (1) species with high resistance and resilience to grazing, (2) species with high resistance but low resilience, (3) species with low resistance but high resilience, and (4) species with low resistance and resilience. While disturbance resulted in a novel diversity configuration, which may profoundly affect ecosystem functioning, we observed that 10 years of disturbance removal did not lead to the ecosystem structure found after 27 years of recovery. These findings are an important contribution to our understanding of BCS dynamics from a species and community perspective placed in a land use change context.

Dynamics of Bacterial and Fungal Communities during the Outbreak and Decline of an Algal Bloom in a Drinking Water Reservoir.

PubMed

Zhang, Haihan; Jia, Jingyu; Chen, Shengnan; Huang, Tinglin; Wang, Yue; Zhao, Zhenfang; Feng, Ji; Hao, Huiyan; Li, Sulin; Ma, Xinxin

2018-02-18

The microbial communities associated with algal blooms play a pivotal role in organic carbon, nitrogen and phosphorus cycling in freshwater ecosystems. However, there have been few studies focused on unveiling the dynamics of bacterial and fungal communities during the outbreak and decline of algal blooms in drinking water reservoirs. To address this issue, the compositions of bacterial and fungal communities were assessed in the Zhoucun drinking water reservoir using 16S rRNA and internal transcribed spacer (ITS) gene Illumina MiSeq sequencing techniques. The results showed the algal bloom was dominated by Synechococcus, Microcystis, and Prochlorothrix. The bloom was characterized by a steady decrease of total phosphorus (TP) from the outbreak to the decline period (p < 0.05) while Fe concentration increased sharply during the decline period (p < 0.05). The highest algal biomass and cell concentrations observed during the bloom were 51.7 mg/L and 1.9×108 cell/L, respectively. The cell concentration was positively correlated with CODMn (r = 0.89, p = 0.02). Illumina Miseq sequencing showed that algal bloom altered the water bacterial and fungal community structure. During the bloom, the dominant bacterial genus were Acinetobacter sp., Limnobacter sp., Synechococcus sp., and Roseomonas sp. The relative size of the fungal community also changed with algal bloom and its composition mainly contained Ascomycota, Basidiomycota and Chytridiomycota. Heat map profiling indicated that algal bloom had a more consistent effect upon fungal communities at genus level. Redundancy analysis (RDA) also demonstrated that the structure of water bacterial communities was significantly correlated to conductivity and ammonia nitrogen. Meanwhile, water temperature, Fe and ammonia nitrogen drive the dynamics of water fungal communities. The results from this work suggested that water bacterial and fungal communities changed significantly during the outbreak and decline of algal bloom in Zhoucun drinking water reservoir. Our study highlights the potential role of microbial diversity as a driving force for the algal bloom and biogeochemical cycling of reservoir ecology.

Dynamics of Bacterial and Fungal Communities during the Outbreak and Decline of an Algal Bloom in a Drinking Water Reservoir

PubMed Central

Zhang, Haihan; Jia, Jingyu; Chen, Shengnan; Huang, Tinglin; Wang, Yue; Zhao, Zhenfang; Feng, Ji; Hao, Huiyan; Li, Sulin; Ma, Xinxin

2018-01-01

The microbial communities associated with algal blooms play a pivotal role in organic carbon, nitrogen and phosphorus cycling in freshwater ecosystems. However, there have been few studies focused on unveiling the dynamics of bacterial and fungal communities during the outbreak and decline of algal blooms in drinking water reservoirs. To address this issue, the compositions of bacterial and fungal communities were assessed in the Zhoucun drinking water reservoir using 16S rRNA and internal transcribed spacer (ITS) gene Illumina MiSeq sequencing techniques. The results showed the algal bloom was dominated by Synechococcus, Microcystis, and Prochlorothrix. The bloom was characterized by a steady decrease of total phosphorus (TP) from the outbreak to the decline period (p < 0.05) while Fe concentration increased sharply during the decline period (p < 0.05). The highest algal biomass and cell concentrations observed during the bloom were 51.7 mg/L and 1.9×108 cell/L, respectively. The cell concentration was positively correlated with CODMn (r = 0.89, p = 0.02). Illumina Miseq sequencing showed that algal bloom altered the water bacterial and fungal community structure. During the bloom, the dominant bacterial genus were Acinetobacter sp., Limnobacter sp., Synechococcus sp., and Roseomonas sp. The relative size of the fungal community also changed with algal bloom and its composition mainly contained Ascomycota, Basidiomycota and Chytridiomycota. Heat map profiling indicated that algal bloom had a more consistent effect upon fungal communities at genus level. Redundancy analysis (RDA) also demonstrated that the structure of water bacterial communities was significantly correlated to conductivity and ammonia nitrogen. Meanwhile, water temperature, Fe and ammonia nitrogen drive the dynamics of water fungal communities. The results from this work suggested that water bacterial and fungal communities changed significantly during the outbreak and decline of algal bloom in Zhoucun drinking water reservoir. Our study highlights the potential role of microbial diversity as a driving force for the algal bloom and biogeochemical cycling of reservoir ecology. PMID:29463021

Microstencils to generate defined, multi-species patterns of bacteria

DOE PAGES

Timm, Collin M.; Hansen, Ryan R.; Doktycz, Mitchel J.; ...

2015-11-12

Microbial communities are complex heterogeneous systems that are influenced by physical and chemical interactions with their environment, host, and community members. Techniques that facilitate the quantitative evaluation of how microscale organization influences the morphogenesis of multispecies communities could provide valuable insights into the dynamic behavior and organization of natural communities, the design of synthetic environments for multispecies culture, and the engineering of artificial consortia. In this work, we demonstrate a method for patterning microbes into simple arrangements that allow the quantitative measurement of growth dynamics as a function of their proximity to one another. The method combines parylene-based liftoff techniquesmore » with microfluidic delivery to simultaneously pattern multiple bacterial species with high viability using low-cost, customizable methods. Furthermore, quantitative measurements of bacterial growth for two competing isolates demonstrate that spatial coordination can play a critical role in multispecies growth and structure.« less

Microstencils to generate defined, multi-species patterns of bacteria

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

Timm, Collin M.; Hansen, Ryan R.; Doktycz, Mitchel J.

Microbial communities are complex heterogeneous systems that are influenced by physical and chemical interactions with their environment, host, and community members. Techniques that facilitate the quantitative evaluation of how microscale organization influences the morphogenesis of multispecies communities could provide valuable insights into the dynamic behavior and organization of natural communities, the design of synthetic environments for multispecies culture, and the engineering of artificial consortia. In this work, we demonstrate a method for patterning microbes into simple arrangements that allow the quantitative measurement of growth dynamics as a function of their proximity to one another. The method combines parylene-based liftoff techniquesmore » with microfluidic delivery to simultaneously pattern multiple bacterial species with high viability using low-cost, customizable methods. Furthermore, quantitative measurements of bacterial growth for two competing isolates demonstrate that spatial coordination can play a critical role in multispecies growth and structure.« less

Succession of the functional microbial communities and the metabolic functions in maize straw composting process.

PubMed

Wei, Huawei; Wang, Liuhong; Hassan, Muhammad; Xie, Bing

2018-05-01

Illumina MiSeq sequencing and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) were applied to study the dynamic changes and effects of microbial community structures as well as the metabolic function of bacterial community in maize straw composting process. Results showed that humic acid contents in loosely combined humus (HA1) and stably combined humus (HA2) increased after composting and Staphylococcus, Cellulosimicrobium and Ochrobactrum possibly participated in the transformation of the process. The bacterial communities differed in different stages of the composting. Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria were reported the dominant phyla throughout the process and the relative abundance of the dominant phyla varied significantly (p < 0.05) over time. Moreover, the total phosphorus (TP) had the greatest influence on the microbial community structure among C/N ratio, available phosphorus (AP) and humic substances. Metabolism, cellular processes and environmental information processing might be the primary functions of microbial community during the composting. Copyright © 2018 Elsevier Ltd. All rights reserved.

Spatial and temporal changes in Actinobacterial dominance in experimental artificial groundwater recharge.

PubMed

Kolehmainen, Reija E; Tiirola, Marja; Puhakka, Jaakko A

2008-11-01

Artificial groundwater recharge (AGR) is used in the drinking water industry to supplement groundwater resources and to minimise the use of chemicals in water treatment. This study analysed the spatial and temporal changes of microbial communities in AGR using two test systems: a nutrient-amended fluidized-bed reactor (FBR) and a sand column. Structural changes in the feed lake water (Lake Roine), FBR, and sand column bacterial communities were determined by denaturing gradient gel electrophoresis (DGGE) and the length heterogeneity analysis of amplified 16S rRNA genes (LH-PCR). Two clone libraries were created to link the LH-PCR results to the dominant bacterial groups. The lake water bacterial community was relatively stable, with three bands dominating in all LH-PCR products. The most dominant fragment accounted for up to 72% and was derived from Actinobacteria. Based on the clone libraries and LH-PCR data, Actinobacteria also dominated in the unattached bacterial community of the FBR, whereas several Proteobacterial groups were more abundant on the FBR carrier particles. In the stabilised AGR system a major change in the community structure of the lake water bacteria took place during passage within the first 0.6m in the sand column as the community composition shifted from Actinobacteria-dominated populations to a diverse, mainly Proteobacterial communities. Concurrently, most of the dissolved organic carbon (DOC) was removed at this stage. In summary, the study showed that the make-up of microbial communities in experimental AGR systems responded to changes in their environment. LH-PCR showed potential as a method to determine microbial community dynamics in long-term studies at real-scale AGR sites. This is the first step to provide data on microbial community dynamics in AGR for drinking water production.

Infaunal macrobenthic community dynamics in a manipulated hyperhaline ecosystem: a long-term study

PubMed Central

2013-01-01

Background Understanding the responses of ecological communities to human-induced perturbations is crucial for establishing conservation goals. Ecological communities are dynamic entities undergoing fluctuations due to their intrinsic characteristics as well as anthropogenic pressures varying over time. In this respect, long-term studies, based on large spatial and temporal datasets, may provide useful information in understanding patterns and processes influencing the communities’ structure. Theoretical evidence suggests that a role of biodiversity is acting as a compensatory buffer against environmental variability by decreasing the temporal variance in ecosystem functioning and by raising the level of community response to perturbations through the selection of better performing species. Therefore, the spatial and temporal changes in the specialization of the community components may be used as an effective tool to monitor the effects of natural and anthropogenic alterations of the environment in dynamic systems. We examined the temporal dynamics of macroinvertebrate community structure in the hyperhaline habitat of Tarquinia Saltworks (central Italy). We aimed at: (i) investigating the relationships between the level of community specialization and the alterations of the environment across fourteen years; (ii) comparing the ability of aggregate community parameters such as the average abundance vs. species specialization in describing patterns of community composition. Results We arranged the data in three sub-sets according to three periods, each characterized by different environmental conditions. The mean abundance of sampled macroinvertebrates showed a significant change (p < 0.01) only in the community inhabiting the saltwork basin closely connected to the sea, characterized by the highest environmental variation (i.e. the coefficient of variation, CV, of the aggregate environmental variability over the study period, CVrange = 0.010 - 0.2). Here we found marine species like Modiolus adriaticus (Lamarck, 1819), Neanthes irrorata (Malmgren, 1867), and Amphiglena mediterranea (Leydig, 1851), which inhabited the saltworks during the halt period but disappeared during the subsequent eutrophication phase. Conversely, species specialization showed a significant decrease for each sampled community in the presence of habitat degradation and a recovery after ecological restoration. The widest fluctuations of specialization were recorded for the community inhabiting the saltwork basin with the highest long-term environmental variability. Conclusions Recent advances have shown how the increased temporal and spatial variability of species’ abundance within the communities may be a signal of habitat disturbance, even in the absence of an apparent decline. Such approach could also be used as a sensitive monitoring tool, able to detect whether or not communities are subjected to increasing biotic homogenization. Also, the increased functional similarity triggered by habitat degradation may impact on species at higher trophic levels, such as the waterbirds wintering in the area or using it as a stopover during migration. PMID:24192133

Interlinkages between bacterial populations dynamics and the operational parameters in a moving bed membrane bioreactor treating urban sewage.

PubMed

Reboleiro-Rivas, P; Martín-Pascual, J; Morillo, J A; Juárez-Jiménez, B; Poyatos, J M; Rodelas, B; González-López, J

2016-01-01

Bacteria are key players in biological wastewater treatments (WWTs), thus a firm knowledge of the bacterial population dynamics is crucial to understand environmental/operational factors affecting the efficiency and stability of the biological depuration process. Unfortunately, little is known about the microbial ecology of the advanced biological WWTs combining suspended biomass (SB) and attached biofilms (AB). This study explored in depth the bacterial community structure and population dynamics in each biomass fraction from a pilot-scale moving bed membrane bioreactor (MBMBR) treating municipal sewage, by means of temperature-gradient gel electrophoresis (TGGE) and 454-pyrosequencing. Eight experimental phases were conducted, combining different carrier filling ratios, hydraulic retention times and concentrations of mixed liquor total suspended solids. The bacterial community, dominated by Proteobacteria (20.9-53.8%) and Actinobacteria (20.6-57.6%), was very similar in both biomass fractions and able to maintain its functional stability under all the operating conditions, ensuring a successful and steady depuration process. Multivariate statistical analysis demonstrated that solids concentration, carrier filling ratio, temperature and organic matter concentration in the influent were the significant factors explaining population dynamics. Bacterial diversity increased as carrier filling ratio increased (from 20% to 35%, v/v), and solids concentration was the main factor triggering the shifts of the community structure. These findings provide new insights on the influence of operational parameters on the biology of the innovative MBMBRs. Copyright © 2015 Elsevier Ltd. All rights reserved.

Temperature-driven regime shifts in the dynamics of size-structured populations.

PubMed

Ohlberger, Jan; Edeline, Eric; Vøllestad, Leif Asbjørn; Stenseth, Nils C; Claessen, David

2011-02-01

Global warming impacts virtually all biota and ecosystems. Many of these impacts are mediated through direct effects of temperature on individual vital rates. Yet how this translates from the individual to the population level is still poorly understood, hampering the assessment of global warming impacts on population structure and dynamics. Here, we study the effects of temperature on intraspecific competition and cannibalism and the population dynamical consequences in a size-structured fish population. We use a physiologically structured consumer-resource model in which we explicitly model the temperature dependencies of the consumer vital rates and the resource population growth rate. Our model predicts that increased temperature decreases resource density despite higher resource growth rates, reflecting stronger intraspecific competition among consumers. At a critical temperature, the consumer population dynamics destabilize and shift from a stable equilibrium to competition-driven generation cycles that are dominated by recruits. As a consequence, maximum age decreases and the proportion of younger and smaller-sized fish increases. These model predictions support the hypothesis of decreasing mean body sizes due to increased temperatures. We conclude that in size-structured fish populations, global warming may increase competition, favor smaller size classes, and induce regime shifts that destabilize population and community dynamics.

Predictive models of forest dynamics.

PubMed

Purves, Drew; Pacala, Stephen

2008-06-13

Dynamic global vegetation models (DGVMs) have shown that forest dynamics could dramatically alter the response of the global climate system to increased atmospheric carbon dioxide over the next century. But there is little agreement between different DGVMs, making forest dynamics one of the greatest sources of uncertainty in predicting future climate. DGVM predictions could be strengthened by integrating the ecological realities of biodiversity and height-structured competition for light, facilitated by recent advances in the mathematics of forest modeling, ecological understanding of diverse forest communities, and the availability of forest inventory data.

Similar resilience attributes in lakes with different management practices

USGS Publications Warehouse

Baho, Didier L.; Drakare, Stina; Johnson, Richard K.; Allen, Craig R.; Angeler, David G.

2014-01-01

Liming has been used extensively in Scandinavia and elsewhere since the 1970s to counteract the negative effects of acidification. Communities in limed lakes usually return to acidified conditions once liming is discontinued, suggesting that liming is unlikely to shift acidified lakes to a state equivalent to pre-acidification conditions that requires no further management intervention. While this suggests a low resilience of limed lakes, attributes that confer resilience have not been assessed, limiting our understanding of the efficiency of costly management programs. In this study, we assessed community metrics (diversity, richness, evenness, biovolume), multivariate community structure and the relative resilience of phytoplankton in limed, acidified and circum-neutral lakes from 1997 to 2009, using multivariate time series modeling. We identified dominant temporal frequencies in the data, allowing us to track community change at distinct temporal scales. We assessed two attributes of relative resilience (cross-scale and within-scale structure) of the phytoplankton communities, based on the fluctuation frequency patterns identified. We also assessed species with stochastic temporal dynamics. Liming increased phytoplankton diversity and richness; however, multivariate community structure differed in limed relative to acidified and circum-neutral lakes. Cross-scale and within-scale attributes of resilience were similar across all lakes studied but the contribution of those species exhibiting stochastic dynamics was higher in the acidified and limed compared to circum-neutral lakes. From a resilience perspective, our results suggest that limed lakes comprise a particular condition of an acidified lake state. This explains why liming does not move acidified lakes out of a “degraded” basin of attraction. In addition, our study demonstrates the potential of time series modeling to assess the efficiency of restoration and management outcomes through quantification of the attributes contributing to resilience in ecosystems.

Dynamic Infinite Mixed-Membership Stochastic Blockmodel.

PubMed

Fan, Xuhui; Cao, Longbing; Xu, Richard Yi Da

2015-09-01

Directional and pairwise measurements are often used to model interactions in a social network setting. The mixed-membership stochastic blockmodel (MMSB) was a seminal work in this area, and its ability has been extended. However, models such as MMSB face particular challenges in modeling dynamic networks, for example, with the unknown number of communities. Accordingly, this paper proposes a dynamic infinite mixed-membership stochastic blockmodel, a generalized framework that extends the existing work to potentially infinite communities inside a network in dynamic settings (i.e., networks are observed over time). Additional model parameters are introduced to reflect the degree of persistence among one's memberships at consecutive time stamps. Under this framework, two specific models, namely mixture time variant and mixture time invariant models, are proposed to depict two different time correlation structures. Two effective posterior sampling strategies and their results are presented, respectively, using synthetic and real-world data.

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.

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

Community Structure in Social Networks: Applications for Epidemiological Modelling

PubMed Central

Kitchovitch, Stephan; Liò, Pietro

2011-01-01

During an infectious disease outbreak people will often change their behaviour to reduce their risk of infection. Furthermore, in a given population, the level of perceived risk of infection will vary greatly amongst individuals. The difference in perception could be due to a variety of factors including varying levels of information regarding the pathogen, quality of local healthcare, availability of preventative measures, etc. In this work we argue that we can split a social network, representing a population, into interacting communities with varying levels of awareness of the disease. We construct a theoretical population and study which such communities suffer most of the burden of the disease and how their awareness affects the spread of infection. We aim to gain a better understanding of the effects that community-structured networks and variations in awareness, or risk perception, have on the disease dynamics and to promote more community-resolved modelling in epidemiology. PMID:21789238

Assessment of the Structural Conditions of the San Clemente a Vomano Abbey

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

Benedettini, Francesco; Alaggio, Rocco; Fusco, Felice

2008-07-08

The simultaneous use of a Finite Element (FE) accurate modeling, dynamical tests, model updating and nonlinear analysis are used to describe the integrated approach used by the authors to assess the structural conditions and the seismic vulnerability of an historical masonry structure: the Abbey Church of San Clemente al Vomano, situated in the Notaresco territory (TE, Italy) commissioned by Ermengarda, daughter of the Emperor Ludovico II, and built at the end of IX century together with a monastery to host a monastic community. Dynamical tests 'in operational conditions' and modal identification have been used to perform the FE model validation.more » Both a simple and direct method as the kinematic analysis applied on meaningful sub-structures and a nonlinear 3D dynamic analysis conducted by using the FE model have been used to forecast the seismic performance of the Church.« less

Netgram: Visualizing Communities in Evolving Networks

PubMed Central

Mall, Raghvendra; Langone, Rocco; Suykens, Johan A. K.

2015-01-01

Real-world complex networks are dynamic in nature and change over time. The change is usually observed in the interactions within the network over time. Complex networks exhibit community like structures. A key feature of the dynamics of complex networks is the evolution of communities over time. Several methods have been proposed to detect and track the evolution of these groups over time. However, there is no generic tool which visualizes all the aspects of group evolution in dynamic networks including birth, death, splitting, merging, expansion, shrinkage and continuation of groups. In this paper, we propose Netgram: a tool for visualizing evolution of communities in time-evolving graphs. Netgram maintains evolution of communities over 2 consecutive time-stamps in tables which are used to create a query database using the sql outer-join operation. It uses a line-based visualization technique which adheres to certain design principles and aesthetic guidelines. Netgram uses a greedy solution to order the initial community information provided by the evolutionary clustering technique such that we have fewer line cross-overs in the visualization. This makes it easier to track the progress of individual communities in time evolving graphs. Netgram is a generic toolkit which can be used with any evolutionary community detection algorithm as illustrated in our experiments. We use Netgram for visualization of topic evolution in the NIPS conference over a period of 11 years and observe the emergence and merging of several disciplines in the field of information processing systems. PMID:26356538

Challenges in microbial ecology: building predictive understanding of community function and dynamics

PubMed Central

Widder, Stefanie; Allen, Rosalind J; Pfeiffer, Thomas; Curtis, Thomas P; Wiuf, Carsten; Sloan, William T; Cordero, Otto X; Brown, Sam P; Momeni, Babak; Shou, Wenying; Kettle, Helen; Flint, Harry J; Haas, Andreas F; Laroche, Béatrice; Kreft, Jan-Ulrich; Rainey, Paul B; Freilich, Shiri; Schuster, Stefan; Milferstedt, Kim; van der Meer, Jan R; Groβkopf, Tobias; Huisman, Jef; Free, Andrew; Picioreanu, Cristian; Quince, Christopher; Klapper, Isaac; Labarthe, Simon; Smets, Barth F; Wang, Harris; Soyer, Orkun S

2016-01-01

The importance of microbial communities (MCs) cannot be overstated. MCs underpin the biogeochemical cycles of the earth's soil, oceans and the atmosphere, and perform ecosystem functions that impact plants, animals and humans. Yet our ability to predict and manage the function of these highly complex, dynamically changing communities is limited. Building predictive models that link MC composition to function is a key emerging challenge in microbial ecology. Here, we argue that addressing this challenge requires close coordination of experimental data collection and method development with mathematical model building. We discuss specific examples where model–experiment integration has already resulted in important insights into MC function and structure. We also highlight key research questions that still demand better integration of experiments and models. We argue that such integration is needed to achieve significant progress in our understanding of MC dynamics and function, and we make specific practical suggestions as to how this could be achieved. PMID:27022995

Kombucha tea fermentation: Microbial and biochemical dynamics.

PubMed

Chakravorty, Somnath; Bhattacharya, Semantee; Chatzinotas, Antonis; Chakraborty, Writachit; Bhattacharya, Debanjana; Gachhui, Ratan

2016-03-02

Kombucha tea, a non-alcoholic beverage, is acquiring significant interest due to its claimed beneficial properties. The microbial community of Kombucha tea consists of bacteria and yeast which thrive in two mutually non-exclusive compartments: the soup or the beverage and the biofilm floating on it. The microbial community and the biochemical properties of the beverage have so far mostly been described in separate studies. This, however, may prevent understanding the causal links between the microbial communities and the beneficial properties of Kombucha tea. Moreover, an extensive study into the microbial and biochemical dynamics has also been missing. In this study, we thus explored the structure and dynamics of the microbial community along with the biochemical properties of Kombucha tea at different time points up to 21 days of fermentation. We hypothesized that several biochemical properties will change during the course of fermentation along with the shifts in the yeast and bacterial communities. The yeast community of the biofilm did not show much variation over time and was dominated by Candida sp. (73.5-83%). The soup however, showed a significant shift in dominance from Candida sp. to Lachancea sp. on the 7th day of fermentation. This is the first report showing Candida as the most dominating yeast genus during Kombucha fermentation. Komagateibacter was identified as the single largest bacterial genus present in both the biofilm and the soup (~50%). The bacterial diversity was higher in the soup than in the biofilm with a peak on the seventh day of fermentation. The biochemical properties changed with the progression of the fermentation, i.e., beneficial properties of the beverage such as the radical scavenging ability increased significantly with a maximum increase at day 7. We further observed a significantly higher D-saccharic acid-1,4-lactone content and caffeine degradation property compared to previously described Kombucha tea fermentations. Our data thus indicate that the microbial community structure and dynamics play an important role in the biochemistry of the fermentation of the beverage. We envisage that combined molecular and biochemical analyses like in our study will provide valuable insights for better understanding the role of the microbial community for the beneficial properties of the beverage. Copyright © 2016 Elsevier B.V. All rights reserved.

The Roles of Sea-Ice, Light and Sedimentation in Structuring Shallow Antarctic Benthic Communities

PubMed Central

Clark, Graeme F.; Stark, Jonathan S.; Palmer, Anne S.; Riddle, Martin J.; Johnston, Emma L.

2017-01-01

On polar coasts, seasonal sea-ice duration strongly influences shallow marine environments by affecting environmental conditions, such as light, sedimentation, and physical disturbance. Sea-ice dynamics are changing in response to climate, but there is limited understanding of how this might affect shallow marine environments and benthos. Here we present a unique set of physical and biological data from a single region of Antarctic coast, and use it to gain insights into factors shaping polar benthic communities. At sites encompassing a gradient of sea-ice duration, we measured temporal and spatial variation in light and sedimentation and hard-substrate communities at different depths and substrate orientations. Biological trends were highly correlated with sea-ice duration, and appear to be driven by opposing gradients in light and sedimentation. As sea-ice duration decreased, there was increased light and reduced sedimentation, and concurrent shifts in community structure from invertebrate to algal dominance. Trends were strongest on shallower, horizontal surfaces, which are most exposed to light and sedimentation. Depth and substrate orientation appear to mediate exposure of benthos to these factors, thereby tempering effects of sea-ice and increasing biological heterogeneity. However, while light and sedimentation both varied spatially with sea-ice, their dynamics differed temporally. Light was sensitive to the site-specific date of sea-ice breakout, whereas sedimentation fluctuated at a regional scale coincident with the summer phytoplankton bloom. Sea-ice duration is clearly the overarching force structuring these shallow Antarctic benthic communities, but direct effects are imposed via light and sedimentation, and mediated by habitat characteristics. PMID:28076438

The Roles of Sea-Ice, Light and Sedimentation in Structuring Shallow Antarctic Benthic Communities.

PubMed

Clark, Graeme F; Stark, Jonathan S; Palmer, Anne S; Riddle, Martin J; Johnston, Emma L

2017-01-01

On polar coasts, seasonal sea-ice duration strongly influences shallow marine environments by affecting environmental conditions, such as light, sedimentation, and physical disturbance. Sea-ice dynamics are changing in response to climate, but there is limited understanding of how this might affect shallow marine environments and benthos. Here we present a unique set of physical and biological data from a single region of Antarctic coast, and use it to gain insights into factors shaping polar benthic communities. At sites encompassing a gradient of sea-ice duration, we measured temporal and spatial variation in light and sedimentation and hard-substrate communities at different depths and substrate orientations. Biological trends were highly correlated with sea-ice duration, and appear to be driven by opposing gradients in light and sedimentation. As sea-ice duration decreased, there was increased light and reduced sedimentation, and concurrent shifts in community structure from invertebrate to algal dominance. Trends were strongest on shallower, horizontal surfaces, which are most exposed to light and sedimentation. Depth and substrate orientation appear to mediate exposure of benthos to these factors, thereby tempering effects of sea-ice and increasing biological heterogeneity. However, while light and sedimentation both varied spatially with sea-ice, their dynamics differed temporally. Light was sensitive to the site-specific date of sea-ice breakout, whereas sedimentation fluctuated at a regional scale coincident with the summer phytoplankton bloom. Sea-ice duration is clearly the overarching force structuring these shallow Antarctic benthic communities, but direct effects are imposed via light and sedimentation, and mediated by habitat characteristics.

Phylogenetic and Metagenomic Analyses of Substrate-Dependent Bacterial Temporal Dynamics in Microbial Fuel Cells

PubMed Central

Zhang, Husen; Chen, Xi; Braithwaite, Daniel; He, Zhen

2014-01-01

Understanding the microbial community structure and genetic potential of anode biofilms is key to improve extracellular electron transfers in microbial fuel cells. We investigated effect of substrate and temporal dynamics of anodic biofilm communities using phylogenetic and metagenomic approaches in parallel with electrochemical characterizations. The startup non-steady state anodic bacterial structures were compared for a simple substrate, acetate, and for a complex substrate, landfill leachate, using a single-chamber air-cathode microbial fuel cell. Principal coordinate analysis showed that distinct community structures were formed with each substrate type. The bacterial diversity measured as Shannon index decreased with time in acetate cycles, and was restored with the introduction of leachate. The change of diversity was accompanied by an opposite trend in the relative abundance of Geobacter-affiliated phylotypes, which were acclimated to over 40% of total Bacteria at the end of acetate-fed conditions then declined in the leachate cycles. The transition from acetate to leachate caused a decrease in output power density from 243±13 mW/m2 to 140±11 mW/m2, accompanied by a decrease in Coulombic electron recovery from 18±3% to 9±3%. The leachate cycles selected protein-degrading phylotypes within phylum Synergistetes. Metagenomic shotgun sequencing showed that leachate-fed communities had higher cell motility genes including bacterial chemotaxis and flagellar assembly, and increased gene abundance related to metal resistance, antibiotic resistance, and quorum sensing. These differentially represented genes suggested an altered anodic biofilm community in response to additional substrates and stress from the complex landfill leachate. PMID:25202990

Phylogenetic and metagenomic analyses of substrate-dependent bacterial temporal dynamics in microbial fuel cells.

PubMed

Zhang, Husen; Chen, Xi; Braithwaite, Daniel; He, Zhen

2014-01-01

Understanding the microbial community structure and genetic potential of anode biofilms is key to improve extracellular electron transfers in microbial fuel cells. We investigated effect of substrate and temporal dynamics of anodic biofilm communities using phylogenetic and metagenomic approaches in parallel with electrochemical characterizations. The startup non-steady state anodic bacterial structures were compared for a simple substrate, acetate, and for a complex substrate, landfill leachate, using a single-chamber air-cathode microbial fuel cell. Principal coordinate analysis showed that distinct community structures were formed with each substrate type. The bacterial diversity measured as Shannon index decreased with time in acetate cycles, and was restored with the introduction of leachate. The change of diversity was accompanied by an opposite trend in the relative abundance of Geobacter-affiliated phylotypes, which were acclimated to over 40% of total Bacteria at the end of acetate-fed conditions then declined in the leachate cycles. The transition from acetate to leachate caused a decrease in output power density from 243±13 mW/m2 to 140±11 mW/m2, accompanied by a decrease in Coulombic electron recovery from 18±3% to 9±3%. The leachate cycles selected protein-degrading phylotypes within phylum Synergistetes. Metagenomic shotgun sequencing showed that leachate-fed communities had higher cell motility genes including bacterial chemotaxis and flagellar assembly, and increased gene abundance related to metal resistance, antibiotic resistance, and quorum sensing. These differentially represented genes suggested an altered anodic biofilm community in response to additional substrates and stress from the complex landfill leachate.

Do ecohydrology and community dynamics feed back to banded-ecosystem structure and productivity?

NASA Astrophysics Data System (ADS)

Callegaro, Chiara; Ursino, Nadia

2016-04-01

Mixed communities including grass, shrubs and trees are often reported to populate self-organized vegetation patterns. Patterns of survey data suggest that species diversity and complementarity strengthen the dynamics of banded environments. Resource scarcity and local facilitation trigger self organization, whereas coexistence of multiple species in vegetated self-organizing patches, implying competition for water and nutrients and favorable reproduction sites, is made possible by differing adaptation strategies. Mixed community spatial self-organization has so far received relatively little attention, compared with local net facilitation of isolated species. We assumed that soil moisture availability is a proxy for the environmental niche of plant species according to Ursino and Callegaro (2016). Our modelling effort was focused on niche differentiation of coexisting species within a tiger bush type ecosystem. By minimal numerical modelling and stability analysis we try to answer a few open scientific questions: Is there an adaptation strategy that increases biodiversity and ecosystem functioning? Does specific adaptation to environmental niches influence the structure of self-organizing vegetation pattern? What specific niche distribution along the environmental gradient gives the highest global productivity?

The impact of vegan production on the kimchi microbiome.

PubMed

Zabat, Michelle A; Sano, William H; Cabral, Damien J; Wurster, Jenna I; Belenky, Peter

2018-09-01

Despite previous inquiry into the fermentative bacterial community of kimchi, there has been little insight into the impacts of starting ingredients on the establishment and dynamics of the microbial community. Recently some industrial producers have begun to utilize vegan production methods that omit fermented seafood ingredients. The community-level impacts of this change are unknown. In this study, we investigated the differences in the taxonomic composition of the microbial communities of non-vegan kimchi and vegan kimchi prepared through quick fermentation at room temperature. In addition to tracking the community dynamics over the fermentation process, we looked at the impact of the constituent ingredients and the production facility environment on the microbial community of fermenting kimchi. Our results indicate that the bacterial community of the prepared vegan product closely mirrors the progression and final structure of the non-vegan final product. We also found that room temperature-fermented kimchi differs minimally from more traditional cold-fermented kimchi. Finally, we found that the bacterial community of the starting ingredients show a low relative abundance of the lactic acid bacteria in fermented kimchi, whereas the production facility is dominated by these bacteria. Copyright © 2018 Elsevier Ltd. All rights reserved.

Dynamics of a microbial community associated with manure hot spots as revealed by phospholipid fatty acid analyses.

PubMed Central

Frostegård, A; Petersen, S O; Bååth, E; Nielsen, T H

1997-01-01

Microbial community dynamics associated with manure hot spots were studied by using a model system consisting of a gel-stabilized mixture of soil and manure, placed between layers of soil, during a 3-week incubation period. The microbial biomass, measured as the total amount of phospholipid fatty acids (PLFA), had doubled within a 2-mm distance from the soil-manure interface after 3 days. Principal-component analyses demonstrated that this increase was accompanied by reproducible changes in the composition of PLFA, indicating changes in the microbial community structure. The effect of the manure was strongest in the 2-mm-thick soil layer closest to the interface, in which the PLFA composition was statistically significantly different (P < 0.05) from that of the unaffected soil layers throughout the incubation period. An effect was also observed in the soil layer 2 to 4 mm from the interface. The changes in microbial biomass and community structure were mainly attributed to the diffusion of dissolved organic carbon from the manure. During the initial period of microbial growth, PLFA, which were already more abundant in the manure than in the soil, increased in the manure core and in the 2-mm soil layer closest to the interface. After day 3, the PLFA composition of these layers gradually became more similar to that of the soil. The dynamics of individual PLFA suggested that both taxonomic and physiological changes occurred during growth. Examples of the latter were decreases in the ratios of 16:1 omega 7t to 16:1 omega 7c and of cyclopropyl fatty acids to their respective precursors, indicating a more active bacterial community. An inverse relationship between bacterial PLFA and the eucaryotic 20:4 PLFA (arachidonic acid) suggested that grazing was important. PMID:9172342

Consumer trait variation influences tritrophic interactions in salt marsh communities.

PubMed

Hughes, Anne Randall; Hanley, Torrance C; Orozco, Nohelia P; Zerebecki, Robyn A

2015-07-01

The importance of intraspecific variation has emerged as a key question in community ecology, helping to bridge the gap between ecology and evolution. Although much of this work has focused on plant species, recent syntheses have highlighted the prevalence and potential importance of morphological, behavioral, and life history variation within animals for ecological and evolutionary processes. Many small-bodied consumers live on the plant that they consume, often resulting in host plant-associated trait variation within and across consumer species. Given the central position of consumer species within tritrophic food webs, such consumer trait variation may play a particularly important role in mediating trophic dynamics, including trophic cascades. In this study, we used a series of field surveys and laboratory experiments to document intraspecific trait variation in a key consumer species, the marsh periwinkle Littoraria irrorata, based on its host plant species (Spartina alterniflora or Juncus roemerianus) in a mixed species assemblage. We then conducted a 12-week mesocosm experiment to examine the effects of Littoraria trait variation on plant community structure and dynamics in a tritrophic salt marsh food web. Littoraria from different host plant species varied across a suite of morphological and behavioral traits. These consumer trait differences interacted with plant community composition and predator presence to affect overall plant stem height, as well as differentially alter the density and biomass of the two key plant species in this system. Whether due to genetic differences or phenotypic plasticity, trait differences between consumer types had significant ecological consequences for the tritrophic marsh food web over seasonal time scales. By altering the cascading effects of the top predator on plant community structure and dynamics, consumer differences may generate a feedback over longer time scales, which in turn influences the degree of trait divergence in subsequent consumer populations.

The roles of competition and habitat in the dynamics of populations and species distributions Ecology

Treesearch

Charles B. Yackulic; Janice Reid; James D. Nichols; James E. Hines; Raymond Davis; Eric Forsman

2014-01-01

The role of competition in structuring biotic communities at fine spatial scales is well known from detailed process-based studies. Our understanding of competition’s importance at broader scales is less resolved and mainly based on static species distribution maps. Here, we bridge this gap by examining the joint occupancy dynamics of an invading species (Barred Owl,...

Emergence of communities and diversity in social networks

PubMed Central

Han, Xiao; Cao, Shinan; Shen, Zhesi; Zhang, Boyu; Wang, Wen-Xu; Cressman, Ross

2017-01-01

Communities are common in complex networks and play a significant role in the functioning of social, biological, economic, and technological systems. Despite widespread interest in detecting community structures in complex networks and exploring the effect of communities on collective dynamics, a deep understanding of the emergence and prevalence of communities in social networks is still lacking. Addressing this fundamental problem is of paramount importance in understanding, predicting, and controlling a variety of collective behaviors in society. An elusive question is how communities with common internal properties arise in social networks with great individual diversity. Here, we answer this question using the ultimatum game, which has been a paradigm for characterizing altruism and fairness. We experimentally show that stable local communities with different internal agreements emerge spontaneously and induce social diversity into networks, which is in sharp contrast to populations with random interactions. Diverse communities and social norms come from the interaction between responders with inherent heterogeneous demands and rational proposers via local connections, where the former eventually become the community leaders. This result indicates that networks are significant in the emergence and stabilization of communities and social diversity. Our experimental results also provide valuable information about strategies for developing network models and theories of evolutionary games and social dynamics. PMID:28235785

Emergence of communities and diversity in social networks.

PubMed

Han, Xiao; Cao, Shinan; Shen, Zhesi; Zhang, Boyu; Wang, Wen-Xu; Cressman, Ross; Stanley, H Eugene

2017-03-14

Communities are common in complex networks and play a significant role in the functioning of social, biological, economic, and technological systems. Despite widespread interest in detecting community structures in complex networks and exploring the effect of communities on collective dynamics, a deep understanding of the emergence and prevalence of communities in social networks is still lacking. Addressing this fundamental problem is of paramount importance in understanding, predicting, and controlling a variety of collective behaviors in society. An elusive question is how communities with common internal properties arise in social networks with great individual diversity. Here, we answer this question using the ultimatum game, which has been a paradigm for characterizing altruism and fairness. We experimentally show that stable local communities with different internal agreements emerge spontaneously and induce social diversity into networks, which is in sharp contrast to populations with random interactions. Diverse communities and social norms come from the interaction between responders with inherent heterogeneous demands and rational proposers via local connections, where the former eventually become the community leaders. This result indicates that networks are significant in the emergence and stabilization of communities and social diversity. Our experimental results also provide valuable information about strategies for developing network models and theories of evolutionary games and social dynamics.

Ectomycorrhizal fungi and interspecific competition: species interactions, community structure, coexistence mechanisms, and future research directions.

PubMed

Kennedy, Peter

2010-09-01

The field of ectomycorrhizal fungal (EMF) ecology has largely developed outside the ecological mainstream, owing in large part to the challenges in studying the structure and dynamics of EMF communities. With advances in molecular identification and other research techniques, however, there has been growing interest among mycologists and ecologists in understanding how different ecological factors affect EMF community structure and diversity. While factors such as soil chemistry and host specificity have long been considered important, an increasing number of laboratory and field studies have documented that interspecific competition also has a major impact on EMF species interactions and may significantly influence EMF community structure. In this review, I examine the progress that has been made in understanding the nature of EMF competition. Currently, there are four conclusions that can be drawn: negative competitive effects are rarely reciprocal; competitive outcomes are environmentally context-dependent; field distributions often reflect competitive interactions; and timing of colonization influences competitive success. In addition, I highlight recent studies documenting links between competitive coexistence and EMF community structure, including checkerboard distributions, lottery models, storage effects, and colonization-competition tradeoffs. Finally, I discuss several aspects of EMF competition needing further investigation and some newer methods with which to address them.

Community structure and succession regulation of fungal consortia in the lignocellulose-degrading process on natural biomass.

PubMed

Tian, Baoyu; Wang, Chunxiang; Lv, Ruirui; Zhou, Junxiong; Li, Xin; Zheng, Yi; Jin, Xiangyu; Wang, Mengli; Ye, Yongxia; Huang, Xinyi; Liu, Ping

2014-01-01

The study aims to investigate fungal community structures and dynamic changes in forest soil lignocellulose-degrading process. rRNA gene clone libraries for the samples collected in different stages of lignocellulose degradation process were constructed and analyzed. A total of 26 representative RFLP types were obtained from original soil clone library, including Mucoromycotina (29.5%), unclassified Zygomycetes (33.5%), Ascomycota (32.4%), and Basidiomycota (4.6%). When soil accumulated with natural lignocellulose, 16 RFLP types were identified from 8-day clone library, including Basidiomycota (62.5%), Ascomycota (36.1%), and Fungi incertae sedis (1.4%). After enrichment for 15 days, identified 11 RFLP types were placed in 3 fungal groups: Basidiomycota (86.9%), Ascomycota (11.5%), and Fungi incertae sedis (1.6%). The results showed richer, more diversity and abundance fungal groups in original forest soil. With the degradation of lignocellulose, fungal groups Mucoromycotina and Ascomycota decreased gradually, and wood-rotting fungi Basidiomycota increased and replaced the opportunist fungi to become predominant group. Most of the fungal clones identified in sample were related to the reported lignocellulose-decomposing strains. Understanding of the microbial community structure and dynamic change during natural lignocellulose-degrading process will provide us with an idea and a basis to construct available commercial lignocellulosic enzymes or microbial complex.

Long-term performance and bacterial community dynamics in biocovers for mitigating methane and malodorous gases.

PubMed

Lee, Eun-Hee; Moon, Kyung-Eun; Cho, Kyung-Suk

2017-01-20

The long-term performance of lab-scale biocovers for the simulation of engineered landfill cover soils was evaluated. Methane (CH 4 ), trimethylamine (TMA), and dimethyl sulfide (DMS) were introduced into the biocovers as landfill gases for 134 days and the removal performance was evaluated. The biocover systems were capable of simultaneously removing methane, TMA, and DMS. Methane was mostly eliminated in the top layer of the systems, while TMA and DMS were removed in the bottom layer. Overall, the methane removal capacity and efficiency were 224.8±55.6g-CH 4 m -2 d -1 and 66.6±12.8%, respectively, whereas 100% removal efficiencies of both TMA and DMS were achieved. Using quantitative PCR and pyrosequencing assay, the bacterial and methanotrophic communities in the top and bottom layers were analyzed along with the removal performance of landfill gases in the biocovers. The top and bottom soil layers possessed distinct communities from the original inoculum, but their structure dynamics were different from each other. While the structures of the bacterial and methanotrophic communities showed little change in the top layer, both communities in the bottom layer were considerably shifted by adding TMA and DMA. These findings provide information that can extend the understanding of full-scale biocover performance in landfills. Copyright © 2016 Elsevier B.V. All rights reserved.

Coastal Bacterioplankton Community Dynamics in Response to a Natural Disturbance

PubMed Central

Rappé, Michael S.

2013-01-01

In order to characterize how disturbances to microbial communities are propagated over temporal and spatial scales in aquatic environments, the dynamics of bacterial assemblages throughout a subtropical coastal embayment were investigated via SSU rRNA gene analyses over an 8-month period, which encompassed a large storm event. During non-perturbed conditions, sampling sites clustered into three groups based on their microbial community composition: an offshore oceanic group, a freshwater group, and a distinct and persistent coastal group. Significant differences in measured environmental parameters or in the bacterial community due to the storm event were found only within the coastal cluster of sampling sites, and only at 5 of 12 locations; three of these sites showed a significant response in both environmental and bacterial community characteristics. These responses were most pronounced at sites close to the shoreline. During the storm event, otherwise common bacterioplankton community members such as marine Synechococcus sp. and members of the SAR11 clade of Alphaproteobacteria decreased in relative abundance in the affected coastal zone, whereas several lineages of Gammaproteobacteria, Betaproteobacteria, and members of the Roseobacter clade of Alphaproteobacteria increased. The complex spatial patterns in both environmental conditions and microbial community structure related to freshwater runoff and wind convection during the perturbation event leads us to conclude that spatial heterogeneity was an important factor influencing both the dynamics and the resistance of the bacterioplankton communities to disturbances throughout this complex subtropical coastal system. This heterogeneity may play a role in facilitating a rapid rebound of regions harboring distinctly coastal bacterioplankton communities to their pre-disturbed taxonomic composition. PMID:23409156

Endophytic bacterial community of grapevine leaves influenced by sampling date and phytoplasma infection process

PubMed Central

2014-01-01

Background Endophytic bacteria benefit host plant directly or indirectly, e.g. by biocontrol of the pathogens. Up to now, their interactions with the host and with other microorganisms are poorly understood. Consequently, a crucial step for improving the knowledge of those relationships is to determine if pathogens or plant growing season influence endophytic bacterial diversity and dynamic. Results Four healthy, four phytoplasma diseased and four recovered (symptomatic plants that spontaneously regain a healthy condition) grapevine plants were sampled monthly from June to October 2010 in a vineyard in north-western Italy. Metagenomic DNA was extracted from sterilized leaves and the endophytic bacterial community dynamic and diversity were analyzed by taxon specific real-time PCR, Length-Heterogeneity PCR and genus-specific PCR. These analyses revealed that both sampling date and phytoplasma infection influenced the endophytic bacterial composition. Interestingly, in June, when the plants are symptomless and the pathogen is undetectable (i) the endophytic bacterial community associated with diseased grapevines was different from those in the other sampling dates, when the phytoplasmas are detectable inside samples; (ii) the microbial community associated with recovered plants differs from that living inside healthy and diseased plants. Interestingly, LH-PCR database identified bacteria previously reported as biocontrol agents in the examined grapevines. Of these, Burkholderia, Methylobacterium and Pantoea dynamic was influenced by the phytoplasma infection process and seasonality. Conclusion Results indicated that endophytic bacterial community composition in grapevine is correlated to both phytoplasma infection and sampling date. For the first time, data underlined that, in diseased plants, the pathogen infection process can decrease the impact of seasonality on community dynamic. Moreover, based on experimental evidences, it was reasonable to hypothesize that after recovery the restructured microbial community could maintain the main structure between seasons. PMID:25048741

Endophytic bacterial community of grapevine leaves influenced by sampling date and phytoplasma infection process.

PubMed

Bulgari, Daniela; Casati, Paola; Quaglino, Fabio; Bianco, Piero A

2014-07-21

Endophytic bacteria benefit host plant directly or indirectly, e.g. by biocontrol of the pathogens. Up to now, their interactions with the host and with other microorganisms are poorly understood. Consequently, a crucial step for improving the knowledge of those relationships is to determine if pathogens or plant growing season influence endophytic bacterial diversity and dynamic. Four healthy, four phytoplasma diseased and four recovered (symptomatic plants that spontaneously regain a healthy condition) grapevine plants were sampled monthly from June to October 2010 in a vineyard in north-western Italy. Metagenomic DNA was extracted from sterilized leaves and the endophytic bacterial community dynamic and diversity were analyzed by taxon specific real-time PCR, Length-Heterogeneity PCR and genus-specific PCR. These analyses revealed that both sampling date and phytoplasma infection influenced the endophytic bacterial composition. Interestingly, in June, when the plants are symptomless and the pathogen is undetectable (i) the endophytic bacterial community associated with diseased grapevines was different from those in the other sampling dates, when the phytoplasmas are detectable inside samples; (ii) the microbial community associated with recovered plants differs from that living inside healthy and diseased plants. Interestingly, LH-PCR database identified bacteria previously reported as biocontrol agents in the examined grapevines. Of these, Burkholderia, Methylobacterium and Pantoea dynamic was influenced by the phytoplasma infection process and seasonality. Results indicated that endophytic bacterial community composition in grapevine is correlated to both phytoplasma infection and sampling date. For the first time, data underlined that, in diseased plants, the pathogen infection process can decrease the impact of seasonality on community dynamic. Moreover, based on experimental evidences, it was reasonable to hypothesize that after recovery the restructured microbial community could maintain the main structure between seasons.

Responses of microbial community to pH stress in bioleaching of low grade copper sulfide.

PubMed

Wang, Yuguang; Li, Kai; Chen, Xinhua; Zhou, Hongbo

2018-02-01

The microbial diversity and dynamics in the leachates and on the ore surfaces of different depth of the column were analyzed during bioleaching of low grade copper sulfide at different pH, after inoculation with the same inoculum containing mesophiles and moderate thermophiles. The results indicate that low pH was beneficial to enhance copper extraction. The highest copper extraction (86%) was obtained when pH was controlled at 1.0-1.5. The microbial structures on the ore surfaces were independent of community structures in the leachate, even at the top portion of column. Microbial richness and evenness increased with decreasing pH during bioleaching. pH had significant effects on microbial community structure in the leachate and on the mineral surface of different depth of the column. Leptospirillum ferriphilum accounted for the highest proportions of the community at most times when pH was operated during bioleaching, especially at the end of run. Copyright © 2017 Elsevier Ltd. All rights reserved.

Local community detection as pattern restoration by attractor dynamics of recurrent neural networks.

PubMed

Okamoto, Hiroshi

2016-08-01

Densely connected parts in networks are referred to as "communities". Community structure is a hallmark of a variety of real-world networks. Individual communities in networks form functional modules of complex systems described by networks. Therefore, finding communities in networks is essential to approaching and understanding complex systems described by networks. In fact, network science has made a great deal of effort to develop effective and efficient methods for detecting communities in networks. Here we put forward a type of community detection, which has been little examined so far but will be practically useful. Suppose that we are given a set of source nodes that includes some (but not all) of "true" members of a particular community; suppose also that the set includes some nodes that are not the members of this community (i.e., "false" members of the community). We propose to detect the community from this "imperfect" and "inaccurate" set of source nodes using attractor dynamics of recurrent neural networks. Community detection by the proposed method can be viewed as restoration of the original pattern from a deteriorated pattern, which is analogous to cue-triggered recall of short-term memory in the brain. We demonstrate the effectiveness of the proposed method using synthetic networks and real social networks for which correct communities are known. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Interspecific competition influences the organization of a diverse sessile insect community

NASA Astrophysics Data System (ADS)

Cornelissen, Tatiana; de Carvalho Guimarães, Carla Daniele; Rodrigues Viana, João Paulo; Silva, Bárbara

2013-10-01

Interspecific competition has played a major role in determining the effects of species interactions in terrestrial communities and the perception of its role on shaping population dynamics and community structure has changed throughout the years. In this study, we evaluated the existence of interspecific competition in the herbivore community of the dioecious plant Baccharis pseudomyriocephala (Asteraceae), which holds a diverse community of gall-forming insects. Sixty plants were studied and gall richness and abundance among plants were evaluated. To address whether a plant already occupied by a gall species is preferred or avoided by another gall species, null models were used for all 60 plants combined and for male and female plants separately. Our results have shown that the 11 species of gall-formers found on B. pseudomyriocephala co-occur less than expected by chance alone, indicating that interspecific competition might be an important force structuring the insect community in this tropical host plant, regardless of plant gender.

Fish community reassembly after a coral mass mortality: higher trophic groups are subject to increased rates of extinction.

PubMed

Alonso, David; Pinyol-Gallemí, Aleix; Alcoverro, Teresa; Arthur, Rohan

2015-05-01

Since Gleason and Clements, our understanding of community dynamics has been influenced by theories emphasising either dispersal or niche assembly as central to community structuring. Determining the relative importance of these processes in structuring real-world communities remains a challenge. We tracked reef fish community reassembly after a catastrophic coral mortality in a relatively unfished archipelago. We revisited the stochastic model underlying MacArthur and Wilson's Island Biogeography Theory, with a simple extension to account for trophic identity. Colonisation and extinction rates calculated from decadal presence-absence data based on (1) species neutrality, (2) trophic identity and (3) site-specificity were used to model post-disturbance reassembly, and compared with empirical observations. Results indicate that species neutrality holds within trophic guilds, and trophic identity significantly increases overall model performance. Strikingly, extinction rates increased clearly with trophic position, indicating that fish communities may be inherently susceptible to trophic downgrading even without targeted fishing of top predators. © 2015 John Wiley & Sons Ltd/CNRS.

Network structure, topology, and dynamics in generalized models of synchronization

NASA Astrophysics Data System (ADS)

Lerman, Kristina; Ghosh, Rumi

2012-08-01

Network structure is a product of both its topology and interactions between its nodes. We explore this claim using the paradigm of distributed synchronization in a network of coupled oscillators. As the network evolves to a global steady state, nodes synchronize in stages, revealing the network's underlying community structure. Traditional models of synchronization assume that interactions between nodes are mediated by a conservative process similar to diffusion. However, social and biological processes are often nonconservative. We propose a model of synchronization in a network of oscillators coupled via nonconservative processes. We study the dynamics of synchronization of a synthetic and real-world networks and show that the traditional and nonconservative models of synchronization reveal different structures within the same network.

Stress during pregnancy alters temporal and spatial dynamics of the maternal and offspring microbiome in a sex-specific manner

PubMed Central

Jašarević, Eldin; Howard, Christopher D.; Misic, Ana M.; Beiting, Daniel P.; Bale, Tracy L.

2017-01-01

The microbiome is a regulator of host immunity, metabolism, neurodevelopment, and behavior. During early life, bacterial communities within maternal gut and vaginal compartments can have an impact on directing these processes. Maternal stress experience during pregnancy may impact offspring development by altering the temporal and spatial dynamics of the maternal microbiome during pregnancy. To examine the hypothesis that maternal stress disrupts gut and vaginal microbial dynamics during critical prenatal and postnatal windows, we used high-resolution 16S rRNA marker gene sequencing to examine outcomes in our mouse model of early prenatal stress. Consistent with predictions, maternal fecal communities shift across pregnancy, a process that is disrupted by stress. Vaginal bacterial community structure and composition exhibit lasting disruption following stress exposure. Comparison of maternal and offspring microbiota revealed that similarities in bacterial community composition was predicted by a complex interaction between maternal body niche and offspring age and sex. Importantly, early prenatal stress influenced offspring bacterial community assembly in a temporal and sex-specific manner. Taken together, our results demonstrate that early prenatal stress may influence offspring development through converging modifications to gut microbial composition during pregnancy and transmission of dysbiotic vaginal microbiome at birth. PMID:28266645

When small changes matter: the role of cross-scale interactions between habitat and ecological connectivity in recovery.

PubMed

Thrush, Simon F; Hewitt, Judi E; Lohrer, Andrew M; Chiaroni, Luca D

2013-01-01

Interaction between the diversity of local communities and the degree of connectivity between them has the potential to influence local recovery rates and thus profoundly affect community dynamics in the face of the cumulative impacts that occur across regions. Although such complex interactions have been modeled, field experiments in natural ecosystems to investigate the importance of interactions between local and regional processes are rare, especially so in coastal marine seafloor habitats subjected to many types of disturbance. We conducted a defaunation experiment at eight subtidal sites, incorporating manipulation of habitat structure, to test the relative importance of local habitat features and colonist supply in influencing macrobenthic community recovery rate. Our sites varied in community composition, habitat characteristics, and hydrodynamic conditions, and we conducted the experiment in two phases, exposing defaunated plots to colonists during periods of either high or low larval colonist supply. In both phases of the experiment, five months after disturbance, we were able to develop models that explained a large proportion of variation in community recovery rate between sites. Our results emphasize that the connectivity to the regional species pool influences recovery rate, and although local habitat effects were important, the strength of these effects was affected by broader-scale site characteristics and connectivity. Empirical evidence that cross-scale interactions are important in disturbance-recovery dynamics emphasizes the complex dynamics underlying seafloor community responses to cumulative disturbance.

Microbiota Dynamics Associated with Environmental Conditions and Potential Roles of Cellulolytic Communities in Traditional Chinese Cereal Starter Solid-State Fermentation

PubMed Central

Li, Pan; Liang, Hebin; Lin, Wei-Tie; Feng, Feng

2015-01-01

Traditional Chinese solid-state fermented cereal starters contain highly complex microbial communities and enzymes. Very little is known, however, about the microbial dynamics related to environmental conditions, and cellulolytic communities have never been proposed to exist during cereal starter fermentation. In this study, we performed Illumina MiSeq sequencing combined with PCR-denaturing gradient gel electrophoresis to investigate microbiota, coupled with clone library construction to trace cellulolytic communities in both fermentation stages. A succession of microbial assemblages was observed during the fermentation of starters. Lactobacillales and Saccharomycetales dominated the initial stages, with a continuous decline in relative abundance. However, thermotolerant and drought-resistant Bacillales, Eurotiales, and Mucorales were considerably accelerated during the heating stages, and these organisms dominated until the end of fermentation. Enterobacteriales were consistently ubiquitous throughout the process. For the cellulolytic communities, only the genera Sanguibacter, Beutenbergia, Agrobacterium, and Erwinia dominated the initial fermentation stages. In contrast, stages at high incubation temperature induced the appearance and dominance of Bacillus, Aspergillus, and Mucor. The enzymatic dynamics of amylase and glucoamylase also showed a similar trend, with the activities clearly increased in the first 7 days and subsequently decreased until the end of fermentation. Furthermore, β-glucosidase activity continuously and significantly increased during the fermentation process. Evidently, cellulolytic potential can adapt to environmental conditions by changes in the community structure during the fermentation of starters. PMID:26002897

Microbial Community Structure and Dynamics of Dark Fire-Cured Tobacco Fermentation▿ †

PubMed Central

Di Giacomo, Michele; Paolino, Marianna; Silvestro, Daniele; Vigliotta, Giovanni; Imperi, Francesco; Visca, Paolo; Alifano, Pietro; Parente, Dino

2007-01-01

The Italian Toscano cigar production includes a fermentation step that starts when dark fire-cured tobacco leaves are moistened and mixed with ca. 20% prefermented tobacco to form a 500-kg bulk. The dynamics of the process, lasting ca. 18 days, has never been investigated in detail, and limited information is available on microbiota involved. Here we show that Toscano fermentation is invariably associated with the following: (i) an increase in temperature, pH, and total microbial population; (ii) a decrease in reducing sugars, citric and malic acids, and nitrate content; and (iii) an increase in oxalic acid, nitrite, and tobacco-specific nitrosamine content. The microbial community structure and dynamics were investigated by culture-based and culture-independent approaches, including denaturing gradient gel electrophoresis and single-strand conformational polymorphism. Results demonstrate that fermentation is assisted by a complex microbial community, changing in structure and composition during the process. During the early phase, the moderately acidic and mesophilic environment supports the rapid growth of a yeast population predominated by Debaryomyces hansenii. At this stage, Staphylococcaceae (Jeotgalicoccus and Staphylococcus) and Lactobacillales (Aerococcus, Lactobacillus, and Weissella) are the most commonly detected bacteria. When temperature and pH increase, endospore-forming low-G+C content gram-positive bacilli (Bacillus spp.) become evident. This leads to a further pH increase and promotes growth of moderately halotolerant and alkaliphilic Actinomycetales (Corynebacterium and Yania) during the late phase. To postulate a functional role for individual microbial species assisting the fermentation process, a preliminary physiological and biochemical characterization of representative isolates was performed. PMID:17142368

The response of epiphytic microbes to habitat and growth status of Potamogeton malaianus Miq. in Lake Taihu.

PubMed

Cai, Xianlei; Gao, Guang; Tang, Xiangming; Dong, Baili; Dai, Jiangyu; Chen, Dan; Song, Yuzhi

2013-10-01

To investigate the effects of different habitats and plant growth status on abundance, biomass and community structure of epiphytic microbes, Potamogeton malaianus Miq. at two different habitats (Gonghu Bay and East Taihu) in Lake Taihu were collected in June, August and November (corresponding to the period of development of submerged macrophytes). The relative abundance of major epiphytic algae groups was determined with high performance liquid chromatography (HPLC), and the structures and dynamics of epiphytic bacteria were assessed by terminal restriction fragment length polymorphism (T-RFLP) analysis. Results showed that the biomass of epiphytic microbes was not significant difference between the two sites, and the analysis of similarity found no significant intra-lake heterogeneity in community structure, but the temporal heterogeneity of epiphytic microbes was significant, which linked to the growth state of submerged macrophytes and water temperature. The difference in community structure between June and August was larger than that between August and November at each site, indicating that the growth status of submerged macrophytes has a greater impact on the community structure of epiphytic microbes than the seasonal variation of environmental conditions. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spatially cascading effect of perturbations in experimental meta-ecosystems.

PubMed

Harvey, Eric; Gounand, Isabelle; Ganesanandamoorthy, Pravin; Altermatt, Florian

2016-09-14

Ecosystems are linked to neighbouring ecosystems not only by dispersal, but also by the movement of subsidy. Such subsidy couplings between ecosystems have important landscape-scale implications because perturbations in one ecosystem may affect community structure and functioning in neighbouring ecosystems via increased/decreased subsidies. Here, we combine a general theoretical approach based on harvesting theory and a two-patch protist meta-ecosystem experiment to test the effect of regional perturbations on local community dynamics. We first characterized the relationship between the perturbation regime and local population demography on detritus production using a mathematical model. We then experimentally simulated a perturbation gradient affecting connected ecosystems simultaneously, thus altering cross-ecosystem subsidy exchanges. We demonstrate that the perturbation regime can interact with local population dynamics to trigger unexpected temporal variations in subsidy pulses from one ecosystem to another. High perturbation intensity initially led to the highest level of subsidy flows; however, the level of perturbation interacted with population dynamics to generate a crash in subsidy exchange over time. Both theoretical and experimental results show that a perturbation regime interacting with local community dynamics can induce a collapse in population levels for recipient ecosystems. These results call for integrative management of human-altered landscapes that takes into account regional dynamics of both species and resource flows. © 2016 The Author(s).

Microbial Diversity in Engineered Haloalkaline Environments Shaped by Shared Geochemical Drivers Observed in Natural Analogues

PubMed Central

Warren, Lesley A.; Kendra, Kathryn E.

2015-01-01

Microbial communities in engineered terrestrial haloalkaline environments have been poorly characterized relative to their natural counterparts and are geologically recent in formation, offering opportunities to explore microbial diversity and assembly in dynamic, geochemically comparable contexts. In this study, the microbial community structure and geochemical characteristics of three geographically dispersed bauxite residue environments along a remediation gradient were assessed and subsequently compared with other engineered and natural haloalkaline systems. In bauxite residues, bacterial communities were similar at the phylum level (dominated by Proteobacteria and Firmicutes) to those found in soda lakes, oil sands tailings, and nuclear wastes; however, they differed at lower taxonomic levels, with only 23% of operational taxonomic units (OTUs) shared with other haloalkaline environments. Although being less diverse than natural analogues, bauxite residue harbored substantial novel bacterial taxa, with 90% of OTUs nonmatchable to cultured representative sequences. Fungal communities were dominated by Ascomycota and Basidiomycota, consistent with previous studies of hypersaline environments, and also harbored substantial novel (73% of OTUs) taxa. In bauxite residues, community structure was clearly linked to geochemical and physical environmental parameters, with 84% of variation in bacterial and 73% of variation in fungal community structures explained by environmental parameters. The major driver of bacterial community structure (salinity) was consistent across natural and engineered environments; however, drivers differed for fungal community structure between natural (pH) and engineered (total alkalinity) environments. This study demonstrates that both engineered and natural terrestrial haloalkaline environments host substantial repositories of microbial diversity, which are strongly shaped by geochemical drivers. PMID:25979895

Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning.

PubMed

Dini-Andreote, Francisco; de Cássia Pereira e Silva, Michele; Triadó-Margarit, Xavier; Casamayor, Emilio O; van Elsas, Jan Dirk; Salles, Joana Falcão

2014-10-01

The mechanisms underlying community assembly and promoting temporal succession are often overlooked in microbial ecology. Here, we studied an undisturbed salt marsh chronosequence, spanning over a century of ecosystem development, to understand bacterial succession in soil. We used 16S rRNA gene-based quantitative PCR to determine bacterial abundance and multitag 454 pyrosequencing for community composition and diversity analyses. Despite 10-fold lower 16S rRNA gene abundances, the initial stages of soil development held higher phylogenetic diversities than the soil at late succession. Temporal variations in phylogenetic β-diversity were greater at initial stages of soil development, possibly as a result of the great dynamism imposed by the daily influence of the tide, promoting high immigration rates. Allogenic succession of bacterial communities was mostly driven by shifts in the soil physical structure, as well as variations in pH and salinity, which collectively explained 84.5% of the variation concerning community assemblage. The community assembly data for each successional stage were integrated into a network co-occurrence analysis, revealing higher complexity at initial stages, coinciding with great dynamism in turnover and environmental variability. Contrary to a spatial niche-based perspective of bacterial community assembly, we suggest temporal niche partitioning as the dominant mechanism of assembly (promoting more phylotype co-occurrence) in the initial stages of succession, where continuous environmental change results in the existence of multiple niches over short periods of time.

Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning

PubMed Central

Dini-Andreote, Francisco; de Cássia Pereira e Silva, Michele; Triadó-Margarit, Xavier; Casamayor, Emilio O; van Elsas, Jan Dirk; Salles, Joana Falcão

2014-01-01

The mechanisms underlying community assembly and promoting temporal succession are often overlooked in microbial ecology. Here, we studied an undisturbed salt marsh chronosequence, spanning over a century of ecosystem development, to understand bacterial succession in soil. We used 16S rRNA gene-based quantitative PCR to determine bacterial abundance and multitag 454 pyrosequencing for community composition and diversity analyses. Despite 10-fold lower 16S rRNA gene abundances, the initial stages of soil development held higher phylogenetic diversities than the soil at late succession. Temporal variations in phylogenetic β-diversity were greater at initial stages of soil development, possibly as a result of the great dynamism imposed by the daily influence of the tide, promoting high immigration rates. Allogenic succession of bacterial communities was mostly driven by shifts in the soil physical structure, as well as variations in pH and salinity, which collectively explained 84.5% of the variation concerning community assemblage. The community assembly data for each successional stage were integrated into a network co-occurrence analysis, revealing higher complexity at initial stages, coinciding with great dynamism in turnover and environmental variability. Contrary to a spatial niche-based perspective of bacterial community assembly, we suggest temporal niche partitioning as the dominant mechanism of assembly (promoting more phylotype co-occurrence) in the initial stages of succession, where continuous environmental change results in the existence of multiple niches over short periods of time. PMID:24739625

Dynamic robustness of knowledge collaboration network of open source product development community

NASA Astrophysics Data System (ADS)

Zhou, Hong-Li; Zhang, Xiao-Dong

2018-01-01

As an emergent innovative design style, open source product development communities are characterized by a self-organizing, mass collaborative, networked structure. The robustness of the community is critical to its performance. Using the complex network modeling method, the knowledge collaboration network of the community is formulated, and the robustness of the network is systematically and dynamically studied. The characteristics of the network along the development period determine that its robustness should be studied from three time stages: the start-up, development and mature stages of the network. Five kinds of user-loss pattern are designed, to assess the network's robustness under different situations in each of these three time stages. Two indexes - the largest connected component and the network efficiency - are used to evaluate the robustness of the community. The proposed approach is applied in an existing open source car design community. The results indicate that the knowledge collaboration networks show different levels of robustness in different stages and different user loss patterns. Such analysis can be applied to provide protection strategies for the key users involved in knowledge dissemination and knowledge contribution at different stages of the network, thereby promoting the sustainable and stable development of the open source community.

Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input

PubMed Central

Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste; Makhalanyane, Thulani P.; Jansson, Janet K.; Hopkins, David W.; Aspray, Thomas J.; Seely, Mary; Trindade, Marla I.; Cowan, Don A.

2016-01-01

The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall. PMID:27680878

Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input.

PubMed

Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste; Makhalanyane, Thulani P; Jansson, Janet K; Hopkins, David W; Aspray, Thomas J; Seely, Mary; Trindade, Marla I; Cowan, Don A

2016-09-29

The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO 2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.

Nematode grazing promotes bacterial community dynamics in soil at the aggregate level

PubMed Central

Jiang, Yuji; Liu, Manqiang; Zhang, Jiabao; Chen, Yan; Chen, Xiaoyun; Chen, Lijun; Li, Huixin; Zhang, Xue-Xian; Sun, Bo

2017-01-01

Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment settings. Here, we investigated the complex microbial–microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities. A functional group of alkaline phosphomonoesterase (ALP) producing bacteria was included to test the hypothesis that nematode grazing may significantly affect specific bacteria-mediated ecological functions, that is, organic phosphate cycling in soil. Results of correlation analysis, structural equation modeling and interaction networks combined with laboratory microcosm experiments consistently indicated that bacterivorous nematodes enhanced bacterial diversity, and the abundance of bacterivores was positively correlated with bacterial biomass, including ALP-producing bacterial abundance. Significantly, such effects were more pronounced in large macroaggregates than in microaggregates. There was a positive correlation between the most dominant bacterivores Protorhabditis and the ALP-producing keystone 'species' Mesorhizobium. Taken together, these findings implicate important roles of nematodes in stimulating bacterial dynamics in a spatially dependent manner. PMID:28742069

Modeling household and community transmission of Ebola virus disease: Epidemic growth, spatial dynamics and insights for epidemic control

PubMed Central

Kiskowski, Maria; Chowell, Gerardo

2016-01-01

The mechanisms behind the sub-exponential growth dynamics of the West Africa Ebola virus disease epidemic could be related to improved control of the epidemic and the result of reduced disease transmission in spatially constrained contact structures. An individual-based, stochastic network model is used to model immediate and delayed epidemic control in the context of social contact networks and investigate the extent to which the relative role of these factors may be determined during an outbreak. We find that in general, epidemics quickly establish a dynamic equilibrium of infections in the form of a wave of fixed size and speed traveling through the contact network. Both greater epidemic control and limited community mixing decrease the size of an infectious wave. However, for a fixed wave size, epidemic control (in contrast with limited community mixing) results in lower community saturation and a wave that moves more quickly through the contact network. We also found that the level of epidemic control has a disproportionately greater reductive effect on larger waves, so that a small wave requires nearly as much epidemic control as a larger wave to end an epidemic. PMID:26399855

Nematode grazing promotes bacterial community dynamics in soil at the aggregate level.

PubMed

Jiang, Yuji; Liu, Manqiang; Zhang, Jiabao; Chen, Yan; Chen, Xiaoyun; Chen, Lijun; Li, Huixin; Zhang, Xue-Xian; Sun, Bo

2017-12-01

Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment settings. Here, we investigated the complex microbial-microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities. A functional group of alkaline phosphomonoesterase (ALP) producing bacteria was included to test the hypothesis that nematode grazing may significantly affect specific bacteria-mediated ecological functions, that is, organic phosphate cycling in soil. Results of correlation analysis, structural equation modeling and interaction networks combined with laboratory microcosm experiments consistently indicated that bacterivorous nematodes enhanced bacterial diversity, and the abundance of bacterivores was positively correlated with bacterial biomass, including ALP-producing bacterial abundance. Significantly, such effects were more pronounced in large macroaggregates than in microaggregates. There was a positive correlation between the most dominant bacterivores Protorhabditis and the ALP-producing keystone 'species' Mesorhizobium. Taken together, these findings implicate important roles of nematodes in stimulating bacterial dynamics in a spatially dependent manner.

Modeling household and community transmission of Ebola virus disease: Epidemic growth, spatial dynamics and insights for epidemic control.

PubMed

Kiskowski, Maria; Chowell, Gerardo

2016-01-01

The mechanisms behind the sub-exponential growth dynamics of the West Africa Ebola virus disease epidemic could be related to improved control of the epidemic and the result of reduced disease transmission in spatially constrained contact structures. An individual-based, stochastic network model is used to model immediate and delayed epidemic control in the context of social contact networks and investigate the extent to which the relative role of these factors may be determined during an outbreak. We find that in general, epidemics quickly establish a dynamic equilibrium of infections in the form of a wave of fixed size and speed traveling through the contact network. Both greater epidemic control and limited community mixing decrease the size of an infectious wave. However, for a fixed wave size, epidemic control (in contrast with limited community mixing) results in lower community saturation and a wave that moves more quickly through the contact network. We also found that the level of epidemic control has a disproportionately greater reductive effect on larger waves, so that a small wave requires nearly as much epidemic control as a larger wave to end an epidemic.

A Deep Stochastic Model for Detecting Community in Complex Networks

NASA Astrophysics Data System (ADS)

Fu, Jingcheng; Wu, Jianliang

2017-01-01

Discovering community structures is an important step to understanding the structure and dynamics of real-world networks in social science, biology and technology. In this paper, we develop a deep stochastic model based on non-negative matrix factorization to identify communities, in which there are two sets of parameters. One is the community membership matrix, of which the elements in a row correspond to the probabilities of the given node belongs to each of the given number of communities in our model, another is the community-community connection matrix, of which the element in the i-th row and j-th column represents the probability of there being an edge between a randomly chosen node from the i-th community and a randomly chosen node from the j-th community. The parameters can be evaluated by an efficient updating rule, and its convergence can be guaranteed. The community-community connection matrix in our model is more precise than the community-community connection matrix in traditional non-negative matrix factorization methods. Furthermore, the method called symmetric nonnegative matrix factorization, is a special case of our model. Finally, based on the experiments on both synthetic and real-world networks data, it can be demonstrated that our algorithm is highly effective in detecting communities.

An invasive herbivore structures plant competitive dynamics.

PubMed

Wong, Lydia; Grainger, Tess Nahanni; Start, Denon; Gilbert, Benjamin

2017-11-01

Species interactions are central to our understanding of ecological communities, but may change rapidly with the introduction of invasive species. Invasive species can alter species interactions and community dynamics directly by having larger detrimental effects on some species than others, or indirectly by changing the ways in which native species compete among themselves. We tested the direct and indirect effects of an invasive aphid herbivore on a native aphid species and two host milkweed species. The invasive aphid caused a 10-fold decrease in native aphid populations, and a 30% increase in plant mortality (direct effects). The invasive aphid also increased the strength of interspecific competition between the two native plant hosts (indirect effects). By investigating the role that indirect effects play in shaping species interactions in native communities, our study highlights an understudied component of species invasions. © 2017 The Author(s).

Community structure of zooplankton in the main entrance of Bahía Magdalena, México during 1996.

PubMed

Gómez-Gutiérrez, J; Palomares-García, R; Hernández-Trujillo, S; Carballido-Carranza, A

2001-06-01

The zooplankton community structure, including copepods, euphausiids, chaetognaths, and decapod larvae, was monitored during six circadian cycles using Bongo net (500 microns mesh net) samples from Bahía Magdalena, on the southwest coast of Baja California, México. Samples were obtained during three oceanographic surveys (March, July, and December 1996) to describe the changes in the zooplankton community structure throughout the main mouth of Bahía Magdalena. The zooplankton community structure showed strong changes with a close relation to environmental conditions. During March, a well-mixed water column with low temperature and salinity indicated an influence of the California Current water and local upwelling processes. During July, temperature increased and a wide salinity range was recorded. The stratification of the water column was intense during summer, enhancing the thermocline. The highest temperatures and salinity were recorded in December, related to the presence of the Costa Rica Coastal Current (CRCC). The thermocline deepened as water temperature increased. A typical temperate community structure with low specific richness dominated by Calanus pacificus, Nyctiphanes simplex, and Acartia clausi and high zooplankton biomass (average 9.3 and 5.5 ml 1000 m-3 respectively) during March and July shifted to a more complex tropical community structure with a low zooplankton biomass in December (average 0.37 ml 1000 m-3). The mouth of Bahía Magdalena has a vigorous exchange of water caused by tidal currents. The zooplankton community structure was not significantly different between the central part of Bahía Magdalena and the continental shelf outside the bay for all months. The results suggest a more dynamic inside-outside interaction of zooplankton assemblages than first thought.

Metacommunity ecology meets biogeography: effects of geographical region, spatial dynamics and environmental filtering on community structure in aquatic organisms.

PubMed

Heino, Jani; Soininen, Janne; Alahuhta, Janne; Lappalainen, Jyrki; Virtanen, Risto

2017-01-01

Metacommunity patterns and underlying processes in aquatic organisms have typically been studied within a drainage basin. We examined variation in the composition of six freshwater organismal groups across various drainage basins in Finland. We first modelled spatial structures within each drainage basin using Moran eigenvector maps. Second, we partitioned variation in community structure among three groups of predictors using constrained ordination: (1) local environmental variables, (2) spatial variables, and (3) dummy variable drainage basin identity. Third, we examined turnover and nestedness components of multiple-site beta diversity, and tested the best fit patterns of our datasets using the "elements of metacommunity structure" analysis. Our results showed that basin identity and local environmental variables were significant predictors of community structure, whereas within-basin spatial effects were typically negligible. In half of the organismal groups (diatoms, bryophytes, zooplankton), basin identity was a slightly better predictor of community structure than local environmental variables, whereas the opposite was true for the remaining three organismal groups (insects, macrophytes, fish). Both pure basin and local environmental fractions were, however, significant after accounting for the effects of the other predictor variable sets. All organismal groups exhibited high levels of beta diversity, which was mostly attributable to the turnover component. Our results showed consistent Clementsian-type metacommunity structures, suggesting that subgroups of species responded similarly to environmental factors or drainage basin limits. We conclude that aquatic communities across large scales are mostly determined by environmental and basin effects, which leads to high beta diversity and prevalence of Clementsian community types.

Flow-pattern identification and nonlinear dynamics of gas-liquid two-phase flow in complex networks.

PubMed

Gao, Zhongke; Jin, Ningde

2009-06-01

The identification of flow pattern is a basic and important issue in multiphase systems. Because of the complexity of phase interaction in gas-liquid two-phase flow, it is difficult to discern its flow pattern objectively. In this paper, we make a systematic study on the vertical upward gas-liquid two-phase flow using complex network. Three unique network construction methods are proposed to build three types of networks, i.e., flow pattern complex network (FPCN), fluid dynamic complex network (FDCN), and fluid structure complex network (FSCN). Through detecting the community structure of FPCN by the community-detection algorithm based on K -mean clustering, useful and interesting results are found which can be used for identifying five vertical upward gas-liquid two-phase flow patterns. To investigate the dynamic characteristics of gas-liquid two-phase flow, we construct 50 FDCNs under different flow conditions, and find that the power-law exponent and the network information entropy, which are sensitive to the flow pattern transition, can both characterize the nonlinear dynamics of gas-liquid two-phase flow. Furthermore, we construct FSCN and demonstrate how network statistic can be used to reveal the fluid structure of gas-liquid two-phase flow. In this paper, from a different perspective, we not only introduce complex network theory to the study of gas-liquid two-phase flow but also indicate that complex network may be a powerful tool for exploring nonlinear time series in practice.

Can the functional stability of forest ecosystems be evaluated from the spatial analysis of stands? A case study from the Bialowieza Primeval Forest (Poland)

Treesearch

Andrzej Bobiec

2000-01-01

Variability of external and internal factors entails specific spatial patterns and functional dynamics of communities. The study of the oak-lime-hornbeam (Quercus robur-Tilia cordata-Carpimus) forest in the Bialowieza Primeval Forest supports the concept of silvatic unit, determining the minimal structural area. To find out if the dynamics of a stand...

Dynamic Autoinoculation and the Microbial Ecology of a deep Water Hydrocarbon Irruption

DTIC Science & Technology

2012-12-11

gas hydrate) likely altered plume com- position near the source, leavrngintruswrscknimatedbythemost soluble compounds, such as gases (2-4, 9, 10, 12...well. These results may reconcile disparate observations of the physical dynamics and microbial community structure of the deep plume . Model...feeds bacterial metabolism and cellular growth. We focused entirely on the deep plume horizon spanning 1,000-1,300 m water depth, applying

Multiple regimes of robust patterns between network structure and biodiversity

NASA Astrophysics Data System (ADS)

Jover, Luis F.; Flores, Cesar O.; Cortez, Michael H.; Weitz, Joshua S.

2015-12-01

Ecological networks such as plant-pollinator and host-parasite networks have structured interactions that define who interacts with whom. The structure of interactions also shapes ecological and evolutionary dynamics. Yet, there is significant ongoing debate as to whether certain structures, e.g., nestedness, contribute positively, negatively or not at all to biodiversity. We contend that examining variation in life history traits is key to disentangling the potential relationship between network structure and biodiversity. Here, we do so by analyzing a dynamic model of virus-bacteria interactions across a spectrum of network structures. Consistent with prior studies, we find plausible parameter domains exhibiting strong, positive relationships between nestedness and biodiversity. Yet, the same model can exhibit negative relationships between nestedness and biodiversity when examined in a distinct, plausible region of parameter space. We discuss steps towards identifying when network structure could, on its own, drive the resilience, sustainability, and even conservation of ecological communities.

Multiple regimes of robust patterns between network structure and biodiversity

PubMed Central

Jover, Luis F.; Flores, Cesar O.; Cortez, Michael H.; Weitz, Joshua S.

2015-01-01

Ecological networks such as plant-pollinator and host-parasite networks have structured interactions that define who interacts with whom. The structure of interactions also shapes ecological and evolutionary dynamics. Yet, there is significant ongoing debate as to whether certain structures, e.g., nestedness, contribute positively, negatively or not at all to biodiversity. We contend that examining variation in life history traits is key to disentangling the potential relationship between network structure and biodiversity. Here, we do so by analyzing a dynamic model of virus-bacteria interactions across a spectrum of network structures. Consistent with prior studies, we find plausible parameter domains exhibiting strong, positive relationships between nestedness and biodiversity. Yet, the same model can exhibit negative relationships between nestedness and biodiversity when examined in a distinct, plausible region of parameter space. We discuss steps towards identifying when network structure could, on its own, drive the resilience, sustainability, and even conservation of ecological communities. PMID:26632996

Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication

PubMed Central

Stetz, Gabrielle; Verkhivker, Gennady M.

2017-01-01

Allosteric interactions in the Hsp70 proteins are linked with their regulatory mechanisms and cellular functions. Despite significant progress in structural and functional characterization of the Hsp70 proteins fundamental questions concerning modularity of the allosteric interaction networks and hierarchy of signaling pathways in the Hsp70 chaperones remained largely unexplored and poorly understood. In this work, we proposed an integrated computational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis and network modeling of the residue interactions. A novel aspect of this work is the incorporation of dynamic residue correlations and coevolutionary residue dependencies in the construction of allosteric interaction networks and signaling pathways. We found that functional sites involved in allosteric regulation of Hsp70 may be characterized by structural stability, proximity to global hinge centers and local structural environment that is enriched by highly coevolving flexible residues. These specific characteristics may be necessary for regulation of allosteric structural transitions and could distinguish regulatory sites from nonfunctional conserved residues. The observed confluence of dynamics correlations and coevolutionary residue couplings with global networking features may determine modular organization of allosteric interactions and dictate localization of key mediating sites. Community analysis of the residue interaction networks revealed that concerted rearrangements of local interacting modules at the inter-domain interface may be responsible for global structural changes and a population shift in the DnaK chaperone. The inter-domain communities in the Hsp70 structures harbor the majority of regulatory residues involved in allosteric signaling, suggesting that these sites could be integral to the network organization and coordination of structural changes. Using a network-based formalism of allostery, we introduced a community-hopping model of allosteric communication. Atomistic reconstruction of signaling pathways in the DnaK structures captured a direction-specific mechanism and molecular details of signal transmission that are fully consistent with the mutagenesis experiments. The results of our study reconciled structural and functional experiments from a network-centric perspective by showing that global properties of the residue interaction networks and coevolutionary signatures may be linked with specificity and diversity of allosteric regulation mechanisms. PMID:28095400

Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication.

PubMed

Stetz, Gabrielle; Verkhivker, Gennady M

2017-01-01

Allosteric interactions in the Hsp70 proteins are linked with their regulatory mechanisms and cellular functions. Despite significant progress in structural and functional characterization of the Hsp70 proteins fundamental questions concerning modularity of the allosteric interaction networks and hierarchy of signaling pathways in the Hsp70 chaperones remained largely unexplored and poorly understood. In this work, we proposed an integrated computational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis and network modeling of the residue interactions. A novel aspect of this work is the incorporation of dynamic residue correlations and coevolutionary residue dependencies in the construction of allosteric interaction networks and signaling pathways. We found that functional sites involved in allosteric regulation of Hsp70 may be characterized by structural stability, proximity to global hinge centers and local structural environment that is enriched by highly coevolving flexible residues. These specific characteristics may be necessary for regulation of allosteric structural transitions and could distinguish regulatory sites from nonfunctional conserved residues. The observed confluence of dynamics correlations and coevolutionary residue couplings with global networking features may determine modular organization of allosteric interactions and dictate localization of key mediating sites. Community analysis of the residue interaction networks revealed that concerted rearrangements of local interacting modules at the inter-domain interface may be responsible for global structural changes and a population shift in the DnaK chaperone. The inter-domain communities in the Hsp70 structures harbor the majority of regulatory residues involved in allosteric signaling, suggesting that these sites could be integral to the network organization and coordination of structural changes. Using a network-based formalism of allostery, we introduced a community-hopping model of allosteric communication. Atomistic reconstruction of signaling pathways in the DnaK structures captured a direction-specific mechanism and molecular details of signal transmission that are fully consistent with the mutagenesis experiments. The results of our study reconciled structural and functional experiments from a network-centric perspective by showing that global properties of the residue interaction networks and coevolutionary signatures may be linked with specificity and diversity of allosteric regulation mechanisms.

Data publication with the structural biology data grid supports live analysis

DOE PAGES

Meyer, Peter A.; Socias, Stephanie; Key, Jason; ...

2016-03-07

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of themore » original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. In conclusion, it is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.« less

Data publication with the structural biology data grid supports live analysis

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

Meyer, Peter A.; Socias, Stephanie; Key, Jason

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of themore » original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. In conclusion, it is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.« less

Data publication with the structural biology data grid supports live analysis.

PubMed

Meyer, Peter A; Socias, Stephanie; Key, Jason; Ransey, Elizabeth; Tjon, Emily C; Buschiazzo, Alejandro; Lei, Ming; Botka, Chris; Withrow, James; Neau, David; Rajashankar, Kanagalaghatta; Anderson, Karen S; Baxter, Richard H; Blacklow, Stephen C; Boggon, Titus J; Bonvin, Alexandre M J J; Borek, Dominika; Brett, Tom J; Caflisch, Amedeo; Chang, Chung-I; Chazin, Walter J; Corbett, Kevin D; Cosgrove, Michael S; Crosson, Sean; Dhe-Paganon, Sirano; Di Cera, Enrico; Drennan, Catherine L; Eck, Michael J; Eichman, Brandt F; Fan, Qing R; Ferré-D'Amaré, Adrian R; Fromme, J Christopher; Garcia, K Christopher; Gaudet, Rachelle; Gong, Peng; Harrison, Stephen C; Heldwein, Ekaterina E; Jia, Zongchao; Keenan, Robert J; Kruse, Andrew C; Kvansakul, Marc; McLellan, Jason S; Modis, Yorgo; Nam, Yunsun; Otwinowski, Zbyszek; Pai, Emil F; Pereira, Pedro José Barbosa; Petosa, Carlo; Raman, C S; Rapoport, Tom A; Roll-Mecak, Antonina; Rosen, Michael K; Rudenko, Gabby; Schlessinger, Joseph; Schwartz, Thomas U; Shamoo, Yousif; Sondermann, Holger; Tao, Yizhi J; Tolia, Niraj H; Tsodikov, Oleg V; Westover, Kenneth D; Wu, Hao; Foster, Ian; Fraser, James S; Maia, Filipe R N C; Gonen, Tamir; Kirchhausen, Tom; Diederichs, Kay; Crosas, Mercè; Sliz, Piotr

2016-03-07

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.

Data publication with the structural biology data grid supports live analysis

PubMed Central

Meyer, Peter A.; Socias, Stephanie; Key, Jason; Ransey, Elizabeth; Tjon, Emily C.; Buschiazzo, Alejandro; Lei, Ming; Botka, Chris; Withrow, James; Neau, David; Rajashankar, Kanagalaghatta; Anderson, Karen S.; Baxter, Richard H.; Blacklow, Stephen C.; Boggon, Titus J.; Bonvin, Alexandre M. J. J.; Borek, Dominika; Brett, Tom J.; Caflisch, Amedeo; Chang, Chung-I; Chazin, Walter J.; Corbett, Kevin D.; Cosgrove, Michael S.; Crosson, Sean; Dhe-Paganon, Sirano; Di Cera, Enrico; Drennan, Catherine L.; Eck, Michael J.; Eichman, Brandt F.; Fan, Qing R.; Ferré-D'Amaré, Adrian R.; Christopher Fromme, J.; Garcia, K. Christopher; Gaudet, Rachelle; Gong, Peng; Harrison, Stephen C.; Heldwein, Ekaterina E.; Jia, Zongchao; Keenan, Robert J.; Kruse, Andrew C.; Kvansakul, Marc; McLellan, Jason S.; Modis, Yorgo; Nam, Yunsun; Otwinowski, Zbyszek; Pai, Emil F.; Pereira, Pedro José Barbosa; Petosa, Carlo; Raman, C. S.; Rapoport, Tom A.; Roll-Mecak, Antonina; Rosen, Michael K.; Rudenko, Gabby; Schlessinger, Joseph; Schwartz, Thomas U.; Shamoo, Yousif; Sondermann, Holger; Tao, Yizhi J.; Tolia, Niraj H.; Tsodikov, Oleg V.; Westover, Kenneth D.; Wu, Hao; Foster, Ian; Fraser, James S.; Maia, Filipe R. N C.; Gonen, Tamir; Kirchhausen, Tom; Diederichs, Kay; Crosas, Mercè; Sliz, Piotr

2016-01-01

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis. PMID:26947396

From calls to communities: a model for time-varying social networks

NASA Astrophysics Data System (ADS)

Laurent, Guillaume; Saramäki, Jari; Karsai, Márton

2015-11-01

Social interactions vary in time and appear to be driven by intrinsic mechanisms that shape the emergent structure of social networks. Large-scale empirical observations of social interaction structure have become possible only recently, and modelling their dynamics is an actual challenge. Here we propose a temporal network model which builds on the framework of activity-driven time-varying networks with memory. The model integrates key mechanisms that drive the formation of social ties - social reinforcement, focal closure and cyclic closure, which have been shown to give rise to community structure and small-world connectedness in social networks. We compare the proposed model with a real-world time-varying network of mobile phone communication, and show that they share several characteristics from heterogeneous degrees and weights to rich community structure. Further, the strong and weak ties that emerge from the model follow similar weight-topology correlations as real-world social networks, including the role of weak ties.

Phytoplankton community structure and dynamics in the North Atlantic subtropical gyre

NASA Astrophysics Data System (ADS)

Cáceres, Carlos; Rivera, Antonella; González, Sonia; Anadón, Ricardo

2017-02-01

Phytoplankton fuel epipelagic ecosystems and affect global biogeochemical cycles. Nevertheless, there is still a lack of quantitative information about the factors that determine both phytoplankton community structure and dynamics, particularly in subtropical gyres. Here, we estimated size fractionated phytoplankton growth (μ) and microzooplankton grazing rates (m) along a transect in the subtropical North Atlantic, from the island of Hispaniola to the Iberian Peninsula, by conducting dilution experiments and fitting mixed models. We also examined the relationship between nutrient availability and the differences in both phytoplankton community structure and size fractionated phytoplankton growth rates at two spatial scales (i.e. subtropical gyre and within-province spatial scale). Our results revealed high values for both phytoplankton growth and microzooplankton grazing rates. Phytoplankton growth (0.00-1.19 d-1) displayed higher variability among stations, biogeochemical provinces and size fractions than the microzooplankton grazing rate (0.32-0.74 d-1). Differences in phytoplankton community structure were associated with dissolved inorganic nitrogen (0.72-5.85 μM; R2 = 0.19) and squared Brunt-Väisälä frequency (R2 = 0.21) at the whole gyre scale. Conversely, the differences in phytoplankton growth rate showed a weak relationship with those properties (R2 ⩽ 0.05) at that scale, but a stronger relationship at the within province scale (R2 ⩾ 0.07). These results support the idea that phytoplankton grow at high rates in oligotrophic subtropical gyres, this is likely due to the selection of phytoplankton groups with functional traits suited to exploit low nutrient availability. Thus, shedding new, multi-scale knowledge on the commonly misunderstood "ocean deserts".

The roles of ecological first principles and evolutionary contingency in unraveling ecosystem response and reconstruction during the Permian-Triassic transition.

NASA Astrophysics Data System (ADS)

Roopnarine, P. D.; Weik, A.; Dineen, A.; Angielczyk, K.

2016-12-01

The Permian-Triassic mass extinction (PTME) is the most severe mass extinction recorded in Earth's history. Effects on the biosphere were complicated and often contradictory, e.g. selective species extinctions and exceptional species survival; prolonged miniaturization of some Early Triassic clades but rapid increases of size in others; and both simplified and complex trophic structures in various E. Triassic ecosystems. Here we present the results of a new generalized model of paleocommunity global stability (number of species capable of persistent coexistence in the absence of external perturbation), suggesting that community dynamics in response to species extinction, and the addition of new species in the aftermath of the PTME, is best understood as a complex outcome of predictable community dynamics and contingent, unpredictable evolutionary pathways. We applied the model to the best known PTME transitional terrestrial ecosystem, the Karoo Basin of South Africa. The model verifies previous claims that global stability scales negatively with increasing species richness and the strength of interspecific interactions. We also show that global stability scales negatively with intrinsic population growth rates. Taxon-rich Permian communities could therefore have persisted only under a restricted range of those parameters. Communities during three phases of the PTME, however, exhibited greater global stability than would be predicted from the pre-PTME communities. Those communities could therefore have maintained relative stabilities under a broader range of parameters, implying that species could have adapted by modifying life history and ecological traits with lesser negative consequences to community stability. The earliest post-PTME community with increased species richness, however, was less stable than would be predicted from pre-PTME communities. In both the extinction and aftermath communities, nonlinear deviations from the general scaling of stability result from structural features unique to those communities, perhaps limiting our ability to forecast biospheric responses to extreme perturbations.

Batch-batch stable microbial community in the traditional fermentation process of huyumei broad bean pastes.

PubMed

Zhu, Linjiang; Fan, Zihao; Kuai, Hui; Li, Qi

2017-09-01

During natural fermentation processes, a characteristic microbial community structure (MCS) is naturally formed, and it is interesting to know about its batch-batch stability. This issue was explored in a traditional semi-solid-state fermentation process of huyumei, a Chinese broad bean paste product. The results showed that this MCS mainly contained four aerobic Bacillus species (8 log CFU per g), including B. subtilis, B. amyloliquefaciens, B. methylotrophicus, and B. tequilensis, and the facultative anaerobe B. cereus with a low concentration (4 log CFU per g), besides a very small amount of the yeast Zygosaccharomyces rouxii (2 log CFU per g). The dynamic change of the MCS in the brine fermentation process showed that the abundance of dominant species varied within a small range, and in the beginning of process the growth of lactic acid bacteria was inhibited and Staphylococcus spp. lost its viability. Also, the MCS and its dynamic change were proved to be highly reproducible among seven batches of fermentation. Therefore, the MCS naturally and stably forms between different batches of the traditional semi-solid-state fermentation of huyumei. Revealing microbial community structure and its batch-batch stability is helpful for understanding the mechanisms of community formation and flavour production in a traditional fermentation. This issue in a traditional semi-solid-state fermentation of huyumei broad bean paste was firstly explored. This fermentation process was revealed to be dominated by a high concentration of four aerobic species of Bacillus, a low concentration of B. cereus and a small amount of Zygosaccharomyces rouxii. Lactic acid bacteria and Staphylococcus spp. lost its viability at the beginning of fermentation. Such the community structure was proved to be highly reproducible among seven batches. © 2017 The Society for Applied Microbiology.

Rethinking the logistic approach for population dynamics of mutualistic interactions.

PubMed

García-Algarra, Javier; Galeano, Javier; Pastor, Juan Manuel; Iriondo, José María; Ramasco, José J

2014-12-21

Mutualistic communities have an internal structure that makes them resilient to external perturbations. Late research has focused on their stability and the topology of the relations between the different organisms to explain the reasons of the system robustness. Much less attention has been invested in analyzing the systems dynamics. The main population models in use are modifications of the r-K formulation of logistic equation with additional terms to account for the benefits produced by the interspecific interactions. These models have shortcomings as the so-called r-K formulation diverges under some conditions. In this work, we introduce a model for population dynamics under mutualism that preserves the original logistic formulation. It is mathematically simpler than the widely used type II models, although it shows similar complexity in terms of fixed points and stability of the dynamics. We perform an analytical stability analysis and numerical simulations to study the model behavior in general interaction scenarios including tests of the resilience of its dynamics under external perturbations. Despite its simplicity, our results indicate that the model dynamics shows an important richness that can be used to gain further insights in the dynamics of mutualistic communities. Copyright © 2014 Elsevier Ltd. All rights reserved.

Secondary successional trajectories of structural and catabolic bacterial communities in oil-polluted soil planted with hybrid poplar.

PubMed

Mukherjee, Shinjini; Sipilä, Timo; Pulkkinen, Pertti; Yrjälä, Kim

2015-02-01

Poplars have widely been used for rhizoremediation of a broad range of organic contaminants for the past two decades. Still, there is a knowledge gap regarding the rhizosphere-associated bacterial communities of poplars and their dynamics during the remediation process. It is envisaged that a detailed understanding of rhizosphere-associated microbial populations will greatly contribute to a better design and implementation of rhizoremediation. To investigate the long-term succession of structural and catabolic bacterial communities in oil-polluted soil planted with hybrid poplar, we carried out a 2-year field study. Hybrid aspen (Populus tremula × Populus tremuloides) seedlings were planted in polluted soil excavated from an accidental oil-spill site. Vegetated and un-vegetated soil samples were collected for microbial community analyses at seven different time points during the course of 2 years and sampling time points were chosen to cover the seasonal variation in the boreal climate zone. Bacterial community structure was accessed by means of 16S rRNA gene amplicon pyrosequencing, whereas catabolic diversity was monitored by pyrosequencing of alkane hydroxylase and extradiol dioxygenase genes. We observed a clear succession of bacterial communities on both structural and functional levels from early to late-phase communities. Sphingomonas type extradiol dioxygenases and alkane hydroxylase homologs of Rhodococcus clearly dominated the early-phase communities. The high-dominance/low-diversity functional gene communities underwent a transition to low-dominance/high-diversity communities in the late phase. These results pointed towards increased catabolic capacities and a change from specialist to generalist strategy of bacterial communities during the course of secondary succession. © 2014 John Wiley & Sons Ltd.

Environment and Spatial Influences on Aquatic Insect Communities in Cerrado Streams: the Relative Importance of Conductivity, Altitude, and Conservation Areas.

PubMed

Godoy, B S; Queiroz, L L; Lodi, S; Oliveira, L G

2017-04-01

The aquatic insect community is an important element for stream functionality and diversity, but the effects of altitude and conservation areas on the aquatic insect community have been poorly explored in neotropical ecozone. The lack of studies about the relative importance of space and environment on community structure is another obstacle within aquatic insect ecology, which precludes the inclusion of these studies in more current frameworks, like the metacommunity dynamics. We evaluated the relationship between the aquatic insect community structure at 19 streams in the Brazilian Cerrado and spatial and environmental variables, namely geographical distance among sites, stream altitude, chemical variables, and environmental protection areas. We partitioned the variance explained by spatial and environmental components using a partial redundancy analysis. The environment exhibited a strong spatial structure for abundance and number of genera, increasing these community parameters with elevated water conductivity. Only community composition had a large unexplained portion of variance, with a small portion constrained by environmental (altitude and conductivity) and spatial factors. A relevant point in the result was the streams with high conductivity were located outside of the conservation areas. These results suggest that the relationship between number of genera and abundance with environmental conditions is always associated with spatial configuration of streams. Our study shows that altitude is an important determinant of community structure, as it exerts indirect influences, and electrical conductivity directly determines community composition, and that some national parks may be inefficient in maintaining the diversity of aquatic insects in the Cerrado region.

Network Structure and Community Evolution on Twitter: Human Behavior Change in Response to the 2011 Japanese Earthquake and Tsunami

PubMed Central

Lu, Xin; Brelsford, Christa

2014-01-01

To investigate the dynamics of social networks and the formation and evolution of online communities in response to extreme events, we collected three datasets from Twitter shortly before and after the 2011 earthquake and tsunami in Japan. We find that while almost all users increased their online activity after the earthquake, Japanese speakers, who are assumed to be more directly affected by the event, expanded the network of people they interact with to a much higher degree than English speakers or the global average. By investigating the evolution of communities, we find that the behavior of joining or quitting a community is far from random: users tend to stay in their current status and are less likely to join new communities from solitary or shift to other communities from their current community. While non-Japanese speakers did not change their conversation topics significantly after the earthquake, nearly all Japanese users changed their conversations to earthquake-related content. This study builds a systematic framework for investigating human behaviors under extreme events with online social network data and our findings on the dynamics of networks and communities may provide useful insight for understanding how patterns of social interaction are influenced by extreme events. PMID:25346468

Network Structure and Community Evolution on Twitter: Human Behavior Change in Response to the 2011 Japanese Earthquake and Tsunami

NASA Astrophysics Data System (ADS)

Lu, Xin; Brelsford, Christa

2014-10-01

To investigate the dynamics of social networks and the formation and evolution of online communities in response to extreme events, we collected three datasets from Twitter shortly before and after the 2011 earthquake and tsunami in Japan. We find that while almost all users increased their online activity after the earthquake, Japanese speakers, who are assumed to be more directly affected by the event, expanded the network of people they interact with to a much higher degree than English speakers or the global average. By investigating the evolution of communities, we find that the behavior of joining or quitting a community is far from random: users tend to stay in their current status and are less likely to join new communities from solitary or shift to other communities from their current community. While non-Japanese speakers did not change their conversation topics significantly after the earthquake, nearly all Japanese users changed their conversations to earthquake-related content. This study builds a systematic framework for investigating human behaviors under extreme events with online social network data and our findings on the dynamics of networks and communities may provide useful insight for understanding how patterns of social interaction are influenced by extreme events.

Microbial community structure and dynamics during anaerobic digestion of various agricultural waste materials.

PubMed

Ziganshin, Ayrat M; Liebetrau, Jan; Pröter, Jürgen; Kleinsteuber, Sabine

2013-06-01

The influence of the feedstock type on the microbial communities involved in anaerobic digestion was investigated in laboratory-scale biogas reactors fed with different agricultural waste materials. Community composition and dynamics over 2 months of reactors' operation were investigated by amplicon sequencing and profiling terminal restriction fragment length polymorphisms of 16S rRNA genes. Major bacterial taxa belonged to the Clostridia and Bacteroidetes, whereas the archaeal community was dominated by methanogenic archaea of the orders Methanomicrobiales and Methanosarcinales. Correlation analysis revealed that the community composition was mainly influenced by the feedstock type with the exception of a temperature shift from 38 to 55 °C which caused the most pronounced community shifts. Bacterial communities involved in the anaerobic digestion of conventional substrates such as maize silage combined with cattle manure were relatively stable and similar to each other. In contrast, special waste materials such as chicken manure or Jatropha press cake were digested by very distinct and less diverse communities, indicating partial ammonia inhibition or the influence of other inhibiting factors. Anaerobic digestion of chicken manure relied on syntrophic acetate oxidation as the dominant acetate-consuming process due to the inhibition of aceticlastic methanogenesis. Jatropha as substrate led to the enrichment of fiber-degrading specialists belonging to the genera Actinomyces and Fibrobacter.

Rare but active taxa contribute to community dynamics of benthic biofilms in glacier-fed streams.

PubMed

Wilhelm, Linda; Besemer, Katharina; Fasching, Christina; Urich, Tim; Singer, Gabriel A; Quince, Christopher; Battin, Tom J

2014-08-01

Glaciers harbour diverse microorganisms, which upon ice melt can be released downstream. In glacier-fed streams microorganisms can attach to stones or sediments to form benthic biofilms. We used 454-pyrosequencing to explore the bulk (16S rDNA) and putatively active (16S rRNA) microbial communities of stone and sediment biofilms across 26 glacier-fed streams. We found differences in community composition between bulk and active communities among streams and a stronger congruence between biofilm types. Relative abundances of rRNA and rDNA were positively correlated across different taxa and taxonomic levels, but at lower taxonomic levels, the higher abundance in either the active or the bulk communities became more apparent. Here, environmental variables played a minor role in structuring active communities. However, we found a large number of rare taxa with higher relative abundances in rRNA compared with rDNA. This suggests that rare taxa contribute disproportionately to microbial community dynamics in glacier-fed streams. Our findings propose that high community turnover, where taxa repeatedly enter and leave the 'seed bank', contributes to the maintenance of microbial biodiversity in harsh ecosystems with continuous environmental perturbations, such as glacier-fed streams. © 2014 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Large Scale Data Analysis and Knowledge Extraction in Communication Data

DTIC Science & Technology

2017-03-31

this purpose, we developed a novel method the " Correlation Density Ran!C’ which finds probability density distribution of related frequent event on all...which is called " Correlation Density Rank", is developed to derive the community tree from the network. As in the real world, where a network is...Community Structure in Dynamic Social Networks using the Correlation Density Rank," 2014 ASE BigData/SocialCom/Cybersecurity Conference, Stanford

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.

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.

Impacts of clustering on interacting epidemics.

PubMed

Wang, Bing; Cao, Lang; Suzuki, Hideyuki; Aihara, Kazuyuki

2012-07-07

Since community structures in real networks play a major role for the epidemic spread, we therefore explore two interacting diseases spreading in networks with community structures. As a network model with community structures, we propose a random clique network model composed of different orders of cliques. We further assume that each disease spreads only through one type of cliques; this assumption corresponds to the issue that two diseases spread inside communities and outside them. Considering the relationship between the susceptible-infected-recovered (SIR) model and the bond percolation theory, we apply this theory to clique random networks under the assumption that the occupation probability is clique-type dependent, which is consistent with the observation that infection rates inside a community and outside it are different, and obtain a number of statistical properties for this model. Two interacting diseases that compete the same hosts are also investigated, which leads to a natural generalization of analyzing an arbitrary number of infectious diseases. For two-disease dynamics, the clustering effect is hypersensitive to the cohesiveness and concentration of cliques; this illustrates the impacts of clustering and the composition of subgraphs in networks on epidemic behavior. The analysis of coexistence/bistability regions provides significant insight into the relationship between the network structure and the potential epidemic prevalence. Copyright © 2012 Elsevier Ltd. All rights reserved.

Disturbance Frequency Determines Morphology and Community Development in Multi-Species Biofilm at the Landscape Scale

PubMed Central

Milferstedt, Kim; Santa-Catalina, Gaëlle; Godon, Jean-Jacques; Escudié, Renaud; Bernet, Nicolas

2013-01-01

Many natural and engineered biofilm systems periodically face disturbances. Here we present how the recovery time of a biofilm between disturbances (expressed as disturbance frequency) shapes the development of morphology and community structure in a multi-species biofilm at the landscape scale. It was hypothesized that a high disturbance frequency favors the development of a stable adapted biofilm system while a low disturbance frequency promotes a dynamic biofilm response. Biofilms were grown in laboratory-scale reactors over a period of 55-70 days and exposed to the biocide monochloramine at two frequencies: daily or weekly pulse injections. One untreated reactor served as control. Biofilm morphology and community structure were followed on comparably large biofilm areas at the landscape scale using automated image analysis (spatial gray level dependence matrices) and community fingerprinting (single-strand conformation polymorphisms). We demonstrated that a weekly disturbed biofilm developed a resilient morphology and community structure. Immediately after the disturbance, the biofilm simplified but recovered its initial complex morphology and community structure between two biocide pulses. In the daily treated reactor, one organism largely dominated a morphologically simple and stable biofilm. Disturbances primarily affected the abundance distribution of already present bacterial taxa but did not promote growth of previously undetected organisms. Our work indicates that disturbances can be used as lever to engineer biofilms by maintaining a biofilm between two developmental states. PMID:24303024

Visibility graph analysis on quarterly macroeconomic series of China based on complex network theory

NASA Astrophysics Data System (ADS)

Wang, Na; Li, Dong; Wang, Qiwen

2012-12-01

The visibility graph approach and complex network theory provide a new insight into time series analysis. The inheritance of the visibility graph from the original time series was further explored in the paper. We found that degree distributions of visibility graphs extracted from Pseudo Brownian Motion series obtained by the Frequency Domain algorithm exhibit exponential behaviors, in which the exponential exponent is a binomial function of the Hurst index inherited in the time series. Our simulations presented that the quantitative relations between the Hurst indexes and the exponents of degree distribution function are different for different series and the visibility graph inherits some important features of the original time series. Further, we convert some quarterly macroeconomic series including the growth rates of value-added of three industry series and the growth rates of Gross Domestic Product series of China to graphs by the visibility algorithm and explore the topological properties of graphs associated from the four macroeconomic series, namely, the degree distribution and correlations, the clustering coefficient, the average path length, and community structure. Based on complex network analysis we find degree distributions of associated networks from the growth rates of value-added of three industry series are almost exponential and the degree distributions of associated networks from the growth rates of GDP series are scale free. We also discussed the assortativity and disassortativity of the four associated networks as they are related to the evolutionary process of the original macroeconomic series. All the constructed networks have “small-world” features. The community structures of associated networks suggest dynamic changes of the original macroeconomic series. We also detected the relationship among government policy changes, community structures of associated networks and macroeconomic dynamics. We find great influences of government policies in China on the changes of dynamics of GDP and the three industries adjustment. The work in our paper provides a new way to understand the dynamics of economic development.

Changes in structure and function of fungal community in cow manure composting.

PubMed

Wang, Ke; Yin, Xiangbo; Mao, Hailong; Chu, Chu; Tian, Yu

2018-05-01

In this study, dynamic changes in fungal communities, trophic modes and effect factors in 60 days composting of cow manure were analyzed by using high throughput sequencing, FUNGuild and Biolog FF MicroPlate, respectively. Orpinomyces (relative abundance >10.85%) predominated in feedstock, and Mycothermus became the dominating genus (relative abundance >75%) during the active phase. Aerobic composting treatment had a significant effect on fungal trophic modes with pathogenic fungi fading away and wood saprotrophs increasing over composting time. Fungal communities had the higher carbon sources utilization capabilities at the thermophilic phase and mature phase than those in the other periods. Oxidation reduction potential (ORP) significantly increased from -180 to 180 mV during the treatment. Redundancy analysis showed that the succession of fungal community during composting had a significant association with ORP (p < .05). This indicated that aerobic composting treatment not only influenced fungal community structure, but also changed fungal trophic modes and metabolic characteristics. Copyright © 2018 Elsevier Ltd. All rights reserved.

Effects of the inoculant strain Sphingomonas paucimobilis 20006FA on soil bacterial community and biodegradation in phenanthrene-contaminated soil.

PubMed

Coppotelli, B M; Ibarrolaza, A; Del Panno, M T; Morelli, I S

2008-02-01

The effects of the inoculant strain Sphingomonas paucimobilis 20006FA (isolated from a phenanthrene-contaminated soil) on the dynamics and structure of microbial communities and phenanthrene elimination rate were studied in soil microcosms artificially contaminated with phenanthrene. The inoculant managed to be established from the first inoculation as it was evidenced by denaturing gradient gel electrophoresis analysis, increasing the number of cultivable heterotrophic and PAH-degrading cells and enhancing phenanthrene degradation. These effects were observed only during the inoculation period. Nevertheless, the soil biological activity (dehydrogenase activity and CO(2) production) showed a late increase. Whereas gradual and successive changes in bacterial community structures were caused by phenanthrene contamination, the inoculation provoked immediate, significant, and stable changes on soil bacterial community. In spite of the long-term establishment of the inoculated strain, at the end of the experiment, the bioaugmentation did not produce significant changes in the residual soil phenanthrene concentration and did not improve the residual effects on the microbial soil community.

Bacterioplankton communities of Crater Lake, OR: Dynamic changes with euphotic zone food web structure and stable deep water populations

USGS Publications Warehouse

Urbach, E.; Vergin, K.L.; Larson, G.L.; Giovannoni, S.J.

2007-01-01

The distribution of bacterial and archaeal species in Crater Lake plankton varies dramatically over depth and with time, as assessed by hybridization of group-specific oligonucleotides to RNA extracted from lakewater. Nonmetric, multidimensional scaling (MDS) analysis of relative bacterial phylotype densities revealed complex relationships among assemblages sampled from depth profiles in July, August and September of 1997 through 1999. CL500-11 green nonsulfur bacteria (Phylum Chloroflexi) and marine Group I crenarchaeota are consistently dominant groups in the oxygenated deep waters at 300 and 500 m. Other phylotypes found in the deep waters are similar to surface and mid-depth populations and vary with time. Euphotic zone assemblages are dominated either by ??-proteobacteria or CL120-10 verrucomicrobia, and ACK4 actinomycetes. MDS analyses of euphotic zone populations in relation to environmental variables and phytoplankton and zooplankton population structures reveal apparent links between Daphnia pulicaria zooplankton population densities and microbial community structure. These patterns may reflect food web interactions that link kokanee salmon population densities to community structure of the bacterioplankton, via fish predation on Daphnia with cascading consequences to Daphnia bacterivory and predation on bacterivorous protists. These results demonstrate a stable bottom-water microbial community. They also extend previous observations of food web-driven changes in euphotic zone bacterioplankton community structure to an oligotrophic setting. ?? 2007 Springer Science+Business Media B.V.

Higher temporal variability of forest breeding bird communities in fragmented landscapes

USGS Publications Warehouse

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

1998-01-01

Understanding the relationship between animal community dynamics and landscape structure has become a priority for biodiversity conservation. In particular, predicting the effects of habitat destruction that confine species to networks of small patches is an important prerequisite to conservation plan development. Theoretical models that predict the occurrence of species in fragmented landscapes, and relationships between stability and diversity do exist. However, reliable empirical investigations of the dynamics of biodiversity have been prevented by differences in species detection probabilities among landscapes. Using long-term data sampled at a large spatial scale in conjunction with a capture-recapture approach, we developed estimates of parameters of community changes over a 22-year period for forest breeding birds in selected areas of the eastern United States. We show that forest fragmentation was associated not only with a reduced number of forest bird species, but also with increased temporal variability in the number of species. This higher temporal variability was associated with higher local extinction and turnover rates. These results have major conservation implications. Moreover, the approach used provides a practical tool for the study of the dynamics of biodiversity.

Persistence and diversification of the Holarctic shrew, Sorex tundrensis (Family Soricidae), in response to climate change

USGS Publications Warehouse

Hope, Andrew G.; Waltari, Eric; Fedorov, Vadim B.; Goropashnaya, Anna V.; Talbot, Sandra; Cook, Joseph A.

2011-01-01

Environmental processes govern demography, species movements, community turnover and diversification and yet in many respects these dynamics are still poorly understood at high latitudes. We investigate the combined effects of climate change and geography through time for a widespread Holarctic shrew, Sorex tundrensis. We include a comprehensive suite of closely related outgroup taxa and three independent loci to explore phylogeographic structure and historical demography. We then explore the implications of these findings for other members of boreal communities. The tundra shrew and its sister species, the Tien Shan shrew (Sorex asper), exhibit strong geographic population structure across Siberia and into Beringia illustrating local centres of endemism that correspond to Late Pleistocene refugia. Ecological niche predictions for both current and historical distributions indicate a model of persistence through time despite dramatic climate change. Species tree estimation under a coalescent process suggests that isolation between populations has been maintained across timeframes deeper than the periodicity of Pleistocene glacial cycling. That some species such as the tundra shrew have a history of persistence largely independent of changing climate, whereas other boreal species shifted their ranges in response to climate change, highlights the dynamic processes of community assembly at high latitudes.

Persistence and diversification of the Holarctic shrew, Sorex tundrensis (Family Soricidae), in response to climate change

USGS Publications Warehouse

Hope, Andrew G.; Waltari, Eric; Fedorov, V.B.; Goropashnaya, A.V.; Talbot, Sandra; Cook, Joseph A.

2014-01-01

Environmental processes govern demography, species movements, community turnover and diversification and yet in many respects these dynamics are still poorly understood at high latitudes. We investigate the combined effects of climate change and geography through time for a widespread Holarctic shrew, Sorex tundrensis. We include a comprehensive suite of closely related outgroup taxa and three independent loci to explore phylogeographic structure and historical demography. We then explore the implications of these findings for other members of boreal communities. The tundra shrew and its sister species, the Tien Shan shrew (Sorex asper), exhibit strong geographic population structure across Siberia and into Beringia illustrating local centres of endemism that correspond to Late Pleistocene refugia. Ecological niche predictions for both current and historical distributions indicate a model of persistence through time despite dramatic climate change. Species tree estimation under a coalescent process suggests that isolation between populations has been maintained across timeframes deeper than the periodicity of Pleistocene glacial cycling. That some species such as the tundra shrew have a history of persistence largely independent of changing climate, whereas other boreal species shifted their ranges in response to climate change, highlights the dynamic processes of community assembly at high latitudes.

Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield.

PubMed

Hubalek, Valerie; Wu, Xiaofen; Eiler, Alexander; Buck, Moritz; Heim, Christine; Dopson, Mark; Bertilsson, Stefan; Ionescu, Danny

2016-10-01

Little research has been conducted on microbial diversity deep under the Earth's surface. In this study, the microbial communities of three deep terrestrial subsurface aquifers were investigated. Temporal community data over 6 years revealed that the phylogenetic structure and community dynamics were highly dependent on the degree of isolation from the earth surface biomes. The microbial community at the shallow site was the most dynamic and was dominated by the sulfur-oxidizing genera Sulfurovum or Sulfurimonas at all-time points. The microbial community in the meteoric water filled intermediate aquifer (water turnover approximately every 5 years) was less variable and was dominated by candidate phylum OD1. Metagenomic analysis of this water demonstrated the occurrence of key genes for nitrogen and carbon fixation, sulfate reduction, sulfide oxidation and fermentation. The deepest water mass (5000 year old waters) had the lowest taxon richness and surprisingly contained Cyanobacteria. The high relative abundance of phylogenetic groups associated with nitrogen and sulfur cycling, as well as fermentation implied that these processes were important in these systems. We conclude that the microbial community patterns appear to be shaped by the availability of energy and nutrient sources via connectivity to the surface or from deep geological processes.

Pleistocene megafaunal interaction networks became more vulnerable after human arrival.

PubMed

Pires, Mathias M; Koch, Paul L; Fariña, Richard A; de Aguiar, Marcus A M; dos Reis, Sérgio F; Guimarães, Paulo R

2015-09-07

The end of the Pleistocene was marked by the extinction of almost all large land mammals worldwide except in Africa. Although the debate on Pleistocene extinctions has focused on the roles of climate change and humans, the impact of perturbations depends on properties of ecological communities, such as species composition and the organization of ecological interactions. Here, we combined palaeoecological and ecological data, food-web models and community stability analysis to investigate if differences between Pleistocene and modern mammalian assemblages help us understand why the megafauna died out in the Americas while persisting in Africa. We show Pleistocene and modern assemblages share similar network topology, but differences in richness and body size distributions made Pleistocene communities significantly more vulnerable to the effects of human arrival. The structural changes promoted by humans in Pleistocene networks would have increased the likelihood of unstable dynamics, which may favour extinction cascades in communities facing extrinsic perturbations. Our findings suggest that the basic aspects of the organization of ecological communities may have played an important role in major extinction events in the past. Knowledge of community-level properties and their consequences to dynamics may be critical to understand past and future extinctions. © 2015 The Author(s).

Pleistocene megafaunal interaction networks became more vulnerable after human arrival

PubMed Central

Pires, Mathias M.; Koch, Paul L.; Fariña, Richard A.; de Aguiar, Marcus A. M.; dos Reis, Sérgio F.; Guimarães, Paulo R.

2015-01-01

The end of the Pleistocene was marked by the extinction of almost all large land mammals worldwide except in Africa. Although the debate on Pleistocene extinctions has focused on the roles of climate change and humans, the impact of perturbations depends on properties of ecological communities, such as species composition and the organization of ecological interactions. Here, we combined palaeoecological and ecological data, food-web models and community stability analysis to investigate if differences between Pleistocene and modern mammalian assemblages help us understand why the megafauna died out in the Americas while persisting in Africa. We show Pleistocene and modern assemblages share similar network topology, but differences in richness and body size distributions made Pleistocene communities significantly more vulnerable to the effects of human arrival. The structural changes promoted by humans in Pleistocene networks would have increased the likelihood of unstable dynamics, which may favour extinction cascades in communities facing extrinsic perturbations. Our findings suggest that the basic aspects of the organization of ecological communities may have played an important role in major extinction events in the past. Knowledge of community-level properties and their consequences to dynamics may be critical to understand past and future extinctions. PMID:26336175

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.

Variability of community interaction networks in marine reserves and adjacent exploited areas

USGS Publications Warehouse

Montano-Moctezuma, G.; Li, H.W.; Rossignol, P.A.

2008-01-01

Regional and small-scale local oceanographic conditions can lead to high variability in community structure even among similar habitats. Communities with identical species composition can depict distinct networks due to different levels of disturbance as well as physical and biological processes. In this study we reconstruct community networks in four different areas off the Oregon Coast by matching simulated communities with observed dynamics. We compared reserves with harvested areas. Simulations suggested that different community networks, but with the same species composition, can represent each study site. Differences were found in predator-prey interactions as well as non-predatory interactions between community members. In addition, each site can be represented as a set of models, creating alternative stages among sites. The set of alternative models that characterize each study area depicts a sequence of functional responses where each specific model or interaction structure creates different species composition patterns. Different management practices, either in the past or of the present, may lead to alternative communities. Our findings suggest that management strategies should be analyzed at a community level that considers the possible consequences of shifting from one community scenario to another. This analysis provides a novel conceptual framework to assess the consequences of different management options for ecological communities. ?? 2008 Elsevier B.V. All rights reserved.

Spatial and temporal distribution of the vibrionaceae in coastal waters of Hawaii, Australia, and France.

PubMed

Jones, B W; Maruyama, A; Ouverney, C C; Nishiguchi, M K

2007-08-01

Relatively little is known about large-scale spatial and temporal fluctuations in bacterioplankton, especially within the bacterial families. In general, however, a number of abiotic factors (namely, nutrients and temperature) appear to influence distribution. Community dynamics within the Vibrionaceae are of particular interest to biologists because this family contains a number of important pathogenic, commensal, and mutualist species. Of special interest to this study is the mutualism between sepiolid squids and Vibrio fischeri and Vibrio logei, where host squids seed surrounding waters daily with their bacterial partners. This study seeks to examine the spatial and temporal distribution of the Vibrionaceae with respect to V. fischeri and V. logei in Hawaii, southeastern Australia, and southern France sampling sites. In particular, we examine how the presence of sepiolid squid hosts influences community population structure within the Vibrionaceae. We found that abiotic (temperature) and biotic (host distribution) factors both influence population dynamics. In Hawaii, three sites within squid host habitat contained communities of Vibrionaceae with higher proportions of V. fischeri. In Australia, V. fischeri numbers at host collection sites were greater than other populations; however, there were no spatial or temporal patterns seen at other sample sites. In France, host presence did not appear to influence Vibrio communities, although sampled populations were significantly greater in the winter than summer sampling periods. Results of this study demonstrate the importance of understanding how both abiotic and biotic factors interact to influence bacterial community structure within the Vibrionaceae.

Dynamics of the Methanogenic Archaeal Community during Plant Residue Decomposition in an Anoxic Rice Field Soil ▿

PubMed Central

Peng, Jingjing; Lü, Zhe; Rui, Junpeng; Lu, Yahai

2008-01-01

Incorporation of plant residues strongly enhances the methane production and emission from flooded rice fields. Temperature and residue type are important factors that regulate residue decomposition and CH4 production. However, the response of the methanogenic archaeal community to these factors in rice field soil is not well understood. In the present experiment, the structure of the archaeal community was determined during the decomposition of rice root and straw residues in anoxic rice field soil incubated at three temperatures (15°C, 30°C, and 45°C). More CH4 was produced in the straw treatment than root treatment. Increasing the temperature from 15°C to 45°C enhanced CH4 production. Terminal restriction fragment length polymorphism analyses in combination with cloning and sequencing of 16S rRNA genes showed that Methanosarcinaceae developed early in the incubations, whereas Methanosaetaceae became more abundant in the later stages. Methanosarcinaceae and Methanosaetaceae seemed to be better adapted at 15°C and 30°C, respectively, while the thermophilic Methanobacteriales and rice cluster I methanogens were significantly enhanced at 45°C. Straw residues promoted the growth of Methanosarcinaceae, whereas the root residues favored Methanosaetaceae. In conclusion, our study revealed a highly dynamic structure of the methanogenic archaeal community during plant residue decomposition. The in situ concentration of acetate (and possibly of H2) seems to be the key factor that regulates the shift of methanogenic community. PMID:18344350

Legacy effects of no-analogue disturbances alter plant community diversity and composition in semi-arid sagebrush steppe

USGS Publications Warehouse

Ripplinger, Julie; Franklin, Janet; Edwards, Thomas C.

2015-01-01

Questions(i) What role does the type of managed disturbance play in structuring sagebrush steppe plant communities? (ii) How does the composition of post-disturbance plant communities change with time since disturbance? (iii) Does plant community diversity change over time following managed disturbance?LocationField study within the sagebrush steppe ecosystem. Rich County, Utah, USA.MethodsWe developed a chronosequence spanning up to 50 yrs post-treatment to study sagebrush steppe vegetation dynamics. Direct ordination was used to examine plant community composition by managed disturbance type and time since disturbance, and factorial analysis of covariance was used to examine diversity dynamics following disturbance. Indicator species values were calculated in order to identify characteristic species for each disturbance type.ResultsPlant communities experienced a shift toward distinct community composition for each of the three managed disturbance types, and gave no indication of returning to untreated community composition or diversity. Small post-disturbance increases in the number of non-native grass species were observed in the treatments relative to reference, with native forb species making the largest contribution to altered composition. On fire- and chemically-treated sites the proportional native forb species richness increased over time since disturbance, while the proportional contribution of non-native forbs to total species richness decreased. For all three treatment types, native grasses contributed less on average to total richness than on reference sites, while non-native grasses made up a higher proportion of total richness.ConclusionsCommon shrubland management techniques have legacy effects on the composition and diversity of sagebrush steppe plant communities, and no-analogue disturbances, such as chemical or mechanical treatments, have more pronounced legacy effects than treatments similar to natural disturbance regimes (fire). This study informs a broader understanding of how management actions affect natural systems by highlighting the importance of long-term management legacies as drivers of plant community structure and function.

Human and Environmental Impacts on River Sediment Microbial Communities

DOE PAGES

Gibbons, Sean M.; Jones, Edwin; Bearquiver, Angelita; ...

2014-05-19

Sediment microbial communities are responsible for a majority of the metabolic activity in river and stream ecosystems. Understanding the dynamics in community structure and function across freshwater environments will help us to predict how these ecosystems will change in response to human land-use practices. Here we present a spatiotemporal study of sediments in the Tongue River (Montana, USA), comprising six sites along 134 km of river sampled in both spring and fall for two years. Sequencing of 16S rRNA amplicons and shotgun metagenomes revealed that these sediments are the richest (~65,000 microbial ‘species’ identified) and most novel (93% of OTUsmore » do not match known microbial diversity) ecosystems analyzed by the Earth Microbiome Project to date, and display more functional diversity than was detected in a recent review of global soil metagenomes. Community structure and functional potential have been significantly altered by anthropogenic drivers, including increased pathogenicity and antibiotic metabolism markers near towns and metabolic signatures of coal and coalbed methane extraction byproducts. The core (OTUs shared across all samples) and the overall microbial community exhibited highly similar structure, and phylogeny was weakly coupled with functional potential. Together, these results suggest that microbial community structure is shaped by environmental drivers and niche filtering, though stochastic assembly processes likely play a role as well. These results indicate that sediment microbial communities are highly complex and sensitive to changes in land use practices.« less

Silver nanoparticles uptake by salt marsh plants - Implications for phytoremediation processes and effects in microbial community dynamics.

PubMed

Fernandes, Joana P; Mucha, Ana P; Francisco, Telmo; Gomes, Carlos Rocha; Almeida, C Marisa R

2017-06-15

This study investigated the uptake of silver nanoparticles (AgNPs) by a salt marsh plant, Phragmites australis, as well as AgNPs effects on rhizospheric microbial community, evaluating the implications for phytoremediation processes. Experiments were carried out with elutriate solution doped with Ag, either in ionic form or in NP form. Metal uptake was evaluated in plant tissues, elutriate solutions and sediments (by AAS) and microbial community was characterized in terms of bacterial community structure (evaluated by ARISA). Results showed Ag accumulation but only in plant belowground tissues and only in the absence of rhizosediment, the presence of sediment reducing Ag availability. But in plant roots Ag accumulation was higher when Ag was in NP form. Multivariate analysis of ARISA profiles showed significant effect of the absence/presence of Ag either in ionic or NP form on microbial community structure, although without significant differences among bacterial richness and diversity. Overall, P. australis can be useful for phytoremediation of medium contaminated with Ag, including with AgNPs. However, the presence of Ag in either forms affected the microbial community structure, which may cause disturbances in ecosystems function and compromise phytoremediation processes. Such considerations need to be address regarding environmental management strategies applied to the very important estuarine areas. The form in which the metal was added affected metal uptake by Phragmites australis and rhizosediment microbial community structure, which can affect phytoremediation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Four types of interference competition and their impacts on the ecology and evolution of size-structured populations and communities.

PubMed

Zhang, Lai; Andersen, Ken H; Dieckmann, Ulf; Brännström, Åke

2015-09-07

We investigate how four types of interference competition - which alternatively affect foraging, metabolism, survival, and reproduction - impact the ecology and evolution of size-structured populations. Even though all four types of interference competition reduce population biomass, interference competition at intermediate intensity sometimes significantly increases the abundance of adult individuals and the population׳s reproduction rate. We find that foraging and metabolic interference evolutionarily favor smaller maturation size when interference is weak and larger maturation size when interference is strong. The evolutionary response to survival interference and reproductive interference is always larger maturation size. We also investigate how the four types of interference competition impact the evolutionary dynamics and resultant diversity and trophic structure of size-structured communities. Like other types of trait-mediated competition, all four types of interference competition can induce disruptive selection and thus promote initial diversification. Even though foraging interference and reproductive interference are more potent in promoting initial diversification, they catalyze the formation of diverse communities with complex trophic structure only at high levels of interference intensity. By contrast, survival interference does so already at intermediate levels, while reproductive interference can only support relatively smaller communities with simpler trophic structure. Taken together, our results show how the type and intensity of interference competition jointly affect coexistence patterns in structured population models. Copyright © 2015 Elsevier Ltd. All rights reserved.

Plant DNA barcodes and assessment of phylogenetic community structure of a tropical mixed dipterocarp forest in Brunei Darussalam (Borneo)

PubMed Central

Abu Salim, Kamariah; Chase, Mark W.; Dexter, Kyle G.; Pennington, R. Toby; Tan, Sylvester; Kaye, Maria Ellen; Samuel, Rosabelle

2017-01-01

DNA barcoding is a fast and reliable tool to assess and monitor biodiversity and, via community phylogenetics, to investigate ecological and evolutionary processes that may be responsible for the community structure of forests. In this study, DNA barcodes for the two widely used plastid coding regions rbcL and matK are used to contribute to identification of morphologically undetermined individuals, as well as to investigate phylogenetic structure of tree communities in 70 subplots (10 × 10m) of a 25-ha forest-dynamics plot in Brunei (Borneo, Southeast Asia). The combined matrix (rbcL + matK) comprised 555 haplotypes (from ≥154 genera, 68 families and 25 orders sensu APG, Angiosperm Phylogeny Group, 2016), making a substantial contribution to tree barcode sequences from Southeast Asia. Barcode sequences were used to reconstruct phylogenetic relationships using maximum likelihood, both with and without constraining the topology of taxonomic orders to match that proposed by the Angiosperm Phylogeny Group. A third phylogenetic tree was reconstructed using the program Phylomatic to investigate the influence of phylogenetic resolution on results. Detection of non-random patterns of community assembly was determined by net relatedness index (NRI) and nearest taxon index (NTI). In most cases, community assembly was either random or phylogenetically clustered, which likely indicates the importance to community structure of habitat filtering based on phylogenetically correlated traits in determining community structure. Different phylogenetic trees gave similar overall results, but the Phylomatic tree produced greater variation across plots for NRI and NTI values, presumably due to noise introduced by using an unresolved phylogenetic tree. Our results suggest that using a DNA barcode tree has benefits over the traditionally used Phylomatic approach by increasing precision and accuracy and allowing the incorporation of taxonomically unidentified individuals into analyses. PMID:29049301

Ecological succession reveals potential signatures of marine–terrestrial transition in salt marsh fungal communities

PubMed Central

Dini-Andreote, Francisco; Pylro, Victor Satler; Baldrian, Petr; van Elsas, Jan Dirk; Salles, Joana Falcão

2016-01-01

Marine-to-terrestrial transition represents one of the most fundamental shifts in microbial life. Understanding the distribution and drivers of soil microbial communities across coastal ecosystems is critical given the roles of microbes in soil biogeochemistry and their multifaceted influence on landscape succession. Here, we studied the fungal community dynamics in a well-established salt marsh chronosequence that spans over a century of ecosystem development. We focussed on providing high-resolution assessments of community composition, diversity and ecophysiological shifts that yielded patterns of ecological succession through soil formation. Notably, despite containing 10- to 100-fold lower fungal internal transcribed spacer abundances, early-successional sites revealed fungal richnesses comparable to those of more mature soils. These newly formed sites also exhibited significant temporal variations in β-diversity that may be attributed to the highly dynamic nature of the system imposed by the tidal regime. The fungal community compositions and ecophysiological assignments changed substantially along the successional gradient, revealing a clear signature of ecological replacement and gradually transforming the environment from a marine into a terrestrial system. Moreover, distance-based linear modelling revealed soil physical structure and organic matter to be the best predictors of the shifts in fungal β-diversity along the chronosequence. Taken together, our study lays the basis for a better understanding of the spatiotemporally determined fungal community dynamics in salt marshes and highlights their ecophysiological traits and adaptation in an evolving ecosystem. PMID:26824176

Ecological succession reveals potential signatures of marine-terrestrial transition in salt marsh fungal communities.

PubMed

Dini-Andreote, Francisco; Pylro, Victor Satler; Baldrian, Petr; van Elsas, Jan Dirk; Salles, Joana Falcão

2016-08-01

Marine-to-terrestrial transition represents one of the most fundamental shifts in microbial life. Understanding the distribution and drivers of soil microbial communities across coastal ecosystems is critical given the roles of microbes in soil biogeochemistry and their multifaceted influence on landscape succession. Here, we studied the fungal community dynamics in a well-established salt marsh chronosequence that spans over a century of ecosystem development. We focussed on providing high-resolution assessments of community composition, diversity and ecophysiological shifts that yielded patterns of ecological succession through soil formation. Notably, despite containing 10- to 100-fold lower fungal internal transcribed spacer abundances, early-successional sites revealed fungal richnesses comparable to those of more mature soils. These newly formed sites also exhibited significant temporal variations in β-diversity that may be attributed to the highly dynamic nature of the system imposed by the tidal regime. The fungal community compositions and ecophysiological assignments changed substantially along the successional gradient, revealing a clear signature of ecological replacement and gradually transforming the environment from a marine into a terrestrial system. Moreover, distance-based linear modelling revealed soil physical structure and organic matter to be the best predictors of the shifts in fungal β-diversity along the chronosequence. Taken together, our study lays the basis for a better understanding of the spatiotemporally determined fungal community dynamics in salt marshes and highlights their ecophysiological traits and adaptation in an evolving ecosystem.

Microbiota Dynamics Associated with Environmental Conditions and Potential Roles of Cellulolytic Communities in Traditional Chinese Cereal Starter Solid-State Fermentation.

PubMed

Li, Pan; Liang, Hebin; Lin, Wei-Tie; Feng, Feng; Luo, Lixin

2015-08-01

Traditional Chinese solid-state fermented cereal starters contain highly complex microbial communities and enzymes. Very little is known, however, about the microbial dynamics related to environmental conditions, and cellulolytic communities have never been proposed to exist during cereal starter fermentation. In this study, we performed Illumina MiSeq sequencing combined with PCR-denaturing gradient gel electrophoresis to investigate microbiota, coupled with clone library construction to trace cellulolytic communities in both fermentation stages. A succession of microbial assemblages was observed during the fermentation of starters. Lactobacillales and Saccharomycetales dominated the initial stages, with a continuous decline in relative abundance. However, thermotolerant and drought-resistant Bacillales, Eurotiales, and Mucorales were considerably accelerated during the heating stages, and these organisms dominated until the end of fermentation. Enterobacteriales were consistently ubiquitous throughout the process. For the cellulolytic communities, only the genera Sanguibacter, Beutenbergia, Agrobacterium, and Erwinia dominated the initial fermentation stages. In contrast, stages at high incubation temperature induced the appearance and dominance of Bacillus, Aspergillus, and Mucor. The enzymatic dynamics of amylase and glucoamylase also showed a similar trend, with the activities clearly increased in the first 7 days and subsequently decreased until the end of fermentation. Furthermore, β-glucosidase activity continuously and significantly increased during the fermentation process. Evidently, cellulolytic potential can adapt to environmental conditions by changes in the community structure during the fermentation of starters. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Stressed but Stable: Canopy Loss Decreased Species Synchrony and Metabolic Variability in an Intertidal Hard-Bottom Community

PubMed Central

Valdivia, Nelson; Golléty, Claire; Migné, Aline; Davoult, Dominique; Molis, Markus

2012-01-01

The temporal stability of aggregate community properties depends on the dynamics of the component species. Since species growth can compensate for the decline of other species, synchronous species dynamics can maintain stability (i.e. invariability) in aggregate properties such as community abundance and metabolism. In field experiments we tested the separate and interactive effects of two stressors associated with storminess–loss of a canopy-forming species and mechanical disturbances–on species synchrony and community respiration of intertidal hard-bottom communities on Helgoland Island, NE Atlantic. Treatments consisted of regular removal of the canopy-forming seaweed Fucus serratus and a mechanical disturbance applied once at the onset of the experiment in March 2006. The level of synchrony in species abundances was assessed from estimates of species percentage cover every three months until September 2007. Experiments at two sites consistently showed that canopy loss significantly reduced species synchrony. Mechanical disturbance had neither separate nor interactive effects on species synchrony. Accordingly, in situ measurements of CO2-fluxes showed that canopy loss, but not mechanical disturbances, significantly reduced net primary productivity and temporal variation in community respiration during emersion periods. Our results support the idea that compensatory dynamics may stabilise aggregate properties. They further suggest that the ecological consequences of the loss of a single structurally important species may be stronger than those derived from smaller-scale mechanical disturbances in natural ecosystems. PMID:22574181

Dynamics of bacterial communities before and after distribution in a full-scale drinking water network.

PubMed

El-Chakhtoura, Joline; Prest, Emmanuelle; Saikaly, Pascal; van Loosdrecht, Mark; Hammes, Frederik; Vrouwenvelder, Hans

2015-05-01

Understanding the biological stability of drinking water distribution systems is imperative in the framework of process control and risk management. The objective of this research was to examine the dynamics of the bacterial community during drinking water distribution at high temporal resolution. Water samples (156 in total) were collected over short time-scales (minutes/hours/days) from the outlet of a treatment plant and a location in its corresponding distribution network. The drinking water is treated by biofiltration and disinfectant residuals are absent during distribution. The community was analyzed by 16S rRNA gene pyrosequencing and flow cytometry as well as conventional, culture-based methods. Despite a random dramatic event (detected with pyrosequencing and flow cytometry but not with plate counts), the bacterial community profile at the two locations did not vary significantly over time. A diverse core microbiome was shared between the two locations (58-65% of the taxa and 86-91% of the sequences) and found to be dependent on the treatment strategy. The bacterial community structure changed during distribution, with greater richness detected in the network and phyla such as Acidobacteria and Gemmatimonadetes becoming abundant. The rare taxa displayed the highest dynamicity, causing the major change during water distribution. This change did not have hygienic implications and is contingent on the sensitivity of the applied methods. The concept of biological stability therefore needs to be revised. Biostability is generally desired in drinking water guidelines but may be difficult to achieve in large-scale complex distribution systems that are inherently dynamic. Copyright © 2015 Elsevier Ltd. All rights reserved.

Models of Metabolic Community Structure in Martian Habitable Environments: Constraints from a Terrestrial Analog Acid-Sulfate Fumarole Environment, Cerro Negro Volcano, Nicaragua

NASA Astrophysics Data System (ADS)

Rogers, K. L.; McCollom, T. M.; Hynek, B. M.

2014-12-01

Microbial habitability in extreme environments on Earth is described by microscale geochemical conditions that constrain metabolic niches in concert with long-term habitat stability that is governed by dynamic geologic processes. Using terrestrial analogs to identify habitable martian environments requires correlating microscale geochemical constraints with reconstructions of past martian environments that are based on global-scale observations. While past martian environments can be characterized by primary parameters (e.g. pH, redox, mineralogy, thermal history), microbial habitability on Earth is a complex function of both primary and derived parameters (e.g. metabolic reaction energetics, chemical & thermal gradients, flow dynamics). In recent years we have been investigating acid-sulfate fumaroles at the Mars analog site, Cerro Negro Volcano, Nicaragua, where habitability is constrained by steep thermal gradients, spatially- and temporally-variable vent dynamics, and limited water and nutrient availability. The most common niche identified thus far is found in fumaroles that host mixed photosynthetic and chemosynthetic endolithic microbial communities. One such endolith is dominated by acidic red algae (Cyanidiales), aerobic bacterial heterotrophs (Ktedonobacteria), and archaeal thermoacidophiles (Hyperthermus, Caldisphaera, and Thermofilum). An analysis of the metabolic structure suggests that primary production by the red algae supports the growth of heterotrophic thermoacidophiles. Diversification among the chemoheterotrophs with respect to temperature and oxygen tolerance suggests community adaptation to environmental gradients or variable venting dynamics. Furthermore, individual cells within the endolith are silica-encrusted, providing the possibility for biosignature formation and preservation. Putative hydrothermal environments on early Mars with similar conditions could have supported endolithic communities with comparable metabolic strategies. Even on a generally cold and dry Mars, volcanic craters likely provided long-lived warm and wet conditions that could have supported diverse assemblages of thermoacidophilic organisms with various metabolic strategies adapted to environmental conditions of acid-sulfate fumaroles.

Coevolutionary diversification creates nested-modular structure in phage–bacteria interaction networks

PubMed Central

Beckett, Stephen J.; Williams, Hywel T. P.

2013-01-01

Phage and their bacterial hosts are the most diverse and abundant biological entities in the oceans, where their interactions have a major impact on marine ecology and ecosystem function. The structure of interaction networks for natural phage–bacteria communities offers insight into their coevolutionary origin. At small phylogenetic scales, observed communities typically show a nested structure, in which both hosts and phages can be ranked by their range of resistance and infectivity, respectively. A qualitatively different multi-scale structure is seen at larger phylogenetic scales; a natural assemblage sampled from the Atlantic Ocean displays large-scale modularity and local nestedness within each module. Here, we show that such ‘nested-modular’ interaction networks can be produced by a simple model of host–phage coevolution in which infection depends on genetic matching. Negative frequency-dependent selection causes diversification of hosts (to escape phages) and phages (to track their evolving hosts). This creates a diverse community of bacteria and phage, maintained by kill-the-winner ecological dynamics. When the resulting communities are visualized as bipartite networks of who infects whom, they show the nested-modular structure characteristic of the Atlantic sample. The statistical significance and strength of this observation varies depending on whether the interaction networks take into account the density of the interacting strains, with implications for interpretation of interaction networks constructed by different methods. Our results suggest that the apparently complex community structures associated with marine bacteria and phage may arise from relatively simple coevolutionary origins. PMID:24516719

Eco-evolutionary feedbacks drive species interactions

PubMed Central

Andrade-Domínguez, Andrés; Salazar, Emmanuel; del Carmen Vargas-Lagunas, María; Kolter, Roberto; Encarnación, Sergio

2014-01-01

In the biosphere, many species live in close proximity and can thus interact in many different ways. Such interactions are dynamic and fall along a continuum between antagonism and cooperation. Because interspecies interactions are the key to understanding biological communities, it is important to know how species interactions arise and evolve. Here, we show that the feedback between ecological and evolutionary processes has a fundamental role in the emergence and dynamics of species interaction. Using a two-species artificial community, we demonstrate that ecological processes and rapid evolution interact to influence the dynamics of the symbiosis between a eukaryote (Saccharomyces cerevisiae) and a bacterium (Rhizobium etli). The simplicity of our experimental design enables an explicit statement of causality. The niche-constructing activities of the fungus were the key ecological process: it allowed the establishment of a commensal relationship that switched to ammensalism and provided the selective conditions necessary for the adaptive evolution of the bacteria. In this latter state, the bacterial population radiates into more than five genotypes that vary with respect to nutrient transport, metabolic strategies and global regulation. Evolutionary diversification of the bacterial populations has strong effects on the community; the nature of interaction subsequently switches from ammensalism to antagonism where bacteria promote yeast extinction. Our results demonstrate the importance of the evolution-to-ecology pathway in the persistence of interactions and the stability of communities. Thus, eco-evolutionary dynamics have the potential to transform the structure and functioning of ecosystems. Our results suggest that these dynamics should be considered to improve our understanding of beneficial and detrimental host–microbe interactions. PMID:24304674

Spatial and temporal dynamics of the microbial community in the Hanford unconfined aquifer

PubMed Central

Lin, Xueju; McKinley, James; Resch, Charles T; Kaluzny, Rachael; Lauber, Christian L; Fredrickson, James; Knight, Rob; Konopka, Allan

2012-01-01

Pyrosequencing analysis of 16S rRNA genes was used to study temporal dynamics of groundwater bacteria and archaea over 10 months within three well clusters separated by ∼30 m and located 250 m from the Columbia River on the Hanford Site, WA. Each cluster contained three wells screened at different depths ranging from 10 to 17 m that differed in hydraulic conductivities. Representative samples were selected for analyses of prokaryotic 16S and eukaryotic 18S rRNA gene copy numbers. Temporal changes in community composition occurred in all nine wells over the 10-month sampling period. However, there were particularly strong effects near the top of the water table when the seasonal rise in the Columbia River caused river water intrusion at the top of the aquifer. The occurrence and disappearance of some microbial assemblages (such as Actinobacteria ACK-M1) were correlated with river water intrusion. This seasonal impact on microbial community structure was greater in the shallow saturated zone than deeper zone in the aquifer. Spatial and temporal patterns for several 16S rRNA gene operational taxonomic units associated with particular physiological functions (for example, methane oxidizers and metal reducers) suggests dynamic changes in fluxes of electron donors and acceptors over an annual cycle. In addition, temporal dynamics in eukaryotic 18S rRNA gene copies and the dominance of protozoa in 18S clone libraries suggest that bacterial community dynamics could be affected not only by the physical and chemical environment but also by top-down biological control. PMID:22456444

Spatial and temporal dynamics of the microbial community in the Hanford unconfined aquifer.

PubMed

Lin, Xueju; McKinley, James; Resch, Charles T; Kaluzny, Rachael; Lauber, Christian L; Fredrickson, James; Knight, Rob; Konopka, Allan

2012-09-01

Pyrosequencing analysis of 16S rRNA genes was used to study temporal dynamics of groundwater bacteria and archaea over 10 months within three well clusters separated by ~30 m and located 250 m from the Columbia River on the Hanford Site, WA. Each cluster contained three wells screened at different depths ranging from 10 to 17 m that differed in hydraulic conductivities. Representative samples were selected for analyses of prokaryotic 16S and eukaryotic 18S rRNA gene copy numbers. Temporal changes in community composition occurred in all nine wells over the 10-month sampling period. However, there were particularly strong effects near the top of the water table when the seasonal rise in the Columbia River caused river water intrusion at the top of the aquifer. The occurrence and disappearance of some microbial assemblages (such as Actinobacteria ACK-M1) were correlated with river water intrusion. This seasonal impact on microbial community structure was greater in the shallow saturated zone than deeper zone in the aquifer. Spatial and temporal patterns for several 16S rRNA gene operational taxonomic units associated with particular physiological functions (for example, methane oxidizers and metal reducers) suggests dynamic changes in fluxes of electron donors and acceptors over an annual cycle. In addition, temporal dynamics in eukaryotic 18S rRNA gene copies and the dominance of protozoa in 18S clone libraries suggest that bacterial community dynamics could be affected not only by the physical and chemical environment but also by top-down biological control.

Use of 16S rRNA sequencing and quantitative PCR to correlate venous leg ulcer bacterial bioburden dynamics with wound expansion, antibiotic therapy, and healing

PubMed Central

Sprockett, Daniel D.; Ammons, Christine G.; Tuttle, Marie S.

2016-01-01

Clinical diagnosis of infection in chronic wounds is currently limited to subjective clinical signs and culture-based methods that underestimate the complexity of wound microbial bioburden as revealed by DNA-based microbial identification methods. Here, we use 16S rRNA next generation sequencing and quantitative polymerase chain reaction to characterize weekly changes in bacterial load, community structure, and diversity associated with a chronic venous leg ulcer over the 15-week course of treatment and healing. Our DNA-based methods and detailed sampling scheme reveal that the bacterial bioburden of the wound is unexpectedly dynamic, including changes in the bacterial load and community structure that correlate with wound expansion, antibiotic therapy, and healing. We demonstrate that these multidimensional changes in bacterial bioburden can be summarized using swabs taken prior to debridement, and therefore, can be more easily collected serially than debridement or biopsy samples. Overall, this case illustrates the importance of detailed clinical indicators and longitudinal sampling to determine the pathogenic significance of chronic wound microbial dynamics and guide best use of antimicrobials for improvement of healing outcomes. PMID:25902876

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.

Impact of non-ionic surfactant on the long-term development of lab-scale-activated sludge bacterial communities.

PubMed

Lozada, Mariana; Basile, Laura; Erijman, Leonardo

2007-01-01

The development of bacterial communities in replicate lab-scale-activated sludge reactors degrading a non-ionic surfactant was evaluated by statistical analysis of denaturing gradient gel electrophoresis (DGGE) fingerprints. Four sequential batch reactors were fed with synthetic sewage, two of which received, in addition, 0.01% of nonylphenol ethoxylates (NPE). The dynamic character of bacterial community structure was confirmed by the differences in species composition among replicate reactors. Measurement of similarities between reactors was obtained by pairwise similarity analysis using the Bray Curtis coefficient. The group of NPE-amended reactors exhibited the highest similarity values (Sjk=0.53+/-0.03), indicating that the bacterial community structure of NPE-amended reactors was better replicated than control reactors (Sjk=0.36+/-0.04). Replicate NPE-amended reactors taken at different times of operation clustered together, whereas analogous relations within the control reactor cluster were not observed. The DGGE pattern of isolates grown in conditioned media prepared with media taken at the end of the aeration cycle grouped separately from other conditioned and synthetic media regardless of the carbon source amendment, suggesting that NPE degradation residuals could have a role in the shaping of the community structure.

The relationship between species diversity and genetic structure in the rare Picea chihuahuana tree species community, Mexico.

PubMed

Simental-Rodríguez, Sergio Leonel; Quiñones-Pérez, Carmen Zulema; Moya, Daniel; Hernández-Tecles, Enrique; López-Sánchez, Carlos Antonio; Wehenkel, Christian

2014-01-01

Species diversity and genetic diversity, the most basic elements of biodiversity, have long been treated as separate topics, although populations evolve within a community context. Recent studies on community genetics and ecology have suggested that genetic diversity is not completely independent of species diversity. The Mexican Picea chihuahuana Martínez is an endemic species listed as "Endangered" on the Red List. Forty populations of Chihuahua spruce have been identified. This species is often associated with tree species of eight genera in gallery forests. This rare Picea chihuahuana tree community covers an area no more than 300 ha and has been subject of several studies involving different topics such as ecology, genetic structure and climate change. The overall aim of these studies was to obtain a dataset for developing management tools to help decision makers implement preservation and conservation strategies. However, this unique forest tree community may also represent an excellent subject for helping us to understand the interplay between ecological and evolutionary processes in determining community structure and dynamics. The AFLP technique and species composition data were used together to test the hypothesis that species diversity is related to the adaptive genetic structure of some dominant tree species (Picea chihuahuana, Pinus strobiformis, Pseudotsuga menziesii and Populus tremuloides) of the Picea chihuahuana tree community at fourteen locations. The Hill numbers were used as a diversity measure. The results revealed a significant correlation between tree species diversity and genetic structure in Populus tremuloides. Because the relationship between the two levels of diversity was found to be positive for the putative adaptive AFLP detected, genetic and species structures of the tree community were possibly simultaneously adapted to a combination of ecological or environmental factors. The present findings indicate that interactions between genetic variants and species diversity may be crucial in shaping tree communities.

Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function

PubMed Central

Singh, Baneshwar; Minick, Kevan J.; Strickland, Michael S.; Wickings, Kyle G.; Crippen, Tawni L.; Tarone, Aaron M.; Benbow, M. Eric; Sufrin, Ness; Tomberlin, Jeffery K.; Pechal, Jennifer L.

2018-01-01

As vertebrate carrion decomposes, there is a release of nutrient-rich fluids into the underlying soil, which can impact associated biological community structure and function. How these changes alter soil biogeochemical cycles is relatively unknown and may prove useful in the identification of carrion decomposition islands that have long lasting, focal ecological effects. This study investigated the spatial (0, 1, and 5 m) and temporal (3–732 days) dynamics of human cadaver decomposition on soil bacterial and arthropod community structure and microbial function. We observed strong evidence of a predictable response to cadaver decomposition that varies over space for soil bacterial and arthropod community structure, carbon (C) mineralization and microbial substrate utilization patterns. In the presence of a cadaver (i.e., 0 m samples), the relative abundance of Bacteroidetes and Firmicutes was greater, while the relative abundance of Acidobacteria, Chloroflexi, Gemmatimonadetes, and Verrucomicrobia was lower when compared to samples at 1 and 5 m. Micro-arthropods were more abundant (15 to 17-fold) in soils collected at 0 m compared to either 1 or 5 m, but overall, micro-arthropod community composition was unrelated to either bacterial community composition or function. Bacterial community structure and microbial function also exhibited temporal relationships, whereas arthropod community structure did not. Cumulative precipitation was more effective in predicting temporal variations in bacterial abundance and microbial activity than accumulated degree days. In the presence of the cadaver (i.e., 0 m samples), the relative abundance of Actinobacteria increased significantly with cumulative precipitation. Furthermore, soil bacterial communities and C mineralization were sensitive to the introduction of human cadavers as they diverged from baseline levels and did not recover completely in approximately 2 years. These data are valuable for understanding ecosystem function surrounding carrion decomposition islands and can be applicable to environmental bio-monitoring and forensic sciences. PMID:29354106

Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function.

PubMed

Singh, Baneshwar; Minick, Kevan J; Strickland, Michael S; Wickings, Kyle G; Crippen, Tawni L; Tarone, Aaron M; Benbow, M Eric; Sufrin, Ness; Tomberlin, Jeffery K; Pechal, Jennifer L

2017-01-01

As vertebrate carrion decomposes, there is a release of nutrient-rich fluids into the underlying soil, which can impact associated biological community structure and function. How these changes alter soil biogeochemical cycles is relatively unknown and may prove useful in the identification of carrion decomposition islands that have long lasting, focal ecological effects. This study investigated the spatial (0, 1, and 5 m) and temporal (3-732 days) dynamics of human cadaver decomposition on soil bacterial and arthropod community structure and microbial function. We observed strong evidence of a predictable response to cadaver decomposition that varies over space for soil bacterial and arthropod community structure, carbon (C) mineralization and microbial substrate utilization patterns. In the presence of a cadaver (i.e., 0 m samples), the relative abundance of Bacteroidetes and Firmicutes was greater, while the relative abundance of Acidobacteria, Chloroflexi, Gemmatimonadetes, and Verrucomicrobia was lower when compared to samples at 1 and 5 m. Micro-arthropods were more abundant (15 to 17-fold) in soils collected at 0 m compared to either 1 or 5 m, but overall, micro-arthropod community composition was unrelated to either bacterial community composition or function. Bacterial community structure and microbial function also exhibited temporal relationships, whereas arthropod community structure did not. Cumulative precipitation was more effective in predicting temporal variations in bacterial abundance and microbial activity than accumulated degree days. In the presence of the cadaver (i.e., 0 m samples), the relative abundance of Actinobacteria increased significantly with cumulative precipitation. Furthermore, soil bacterial communities and C mineralization were sensitive to the introduction of human cadavers as they diverged from baseline levels and did not recover completely in approximately 2 years. These data are valuable for understanding ecosystem function surrounding carrion decomposition islands and can be applicable to environmental bio-monitoring and forensic sciences.

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

Landscape matrix mediates occupancy dynamics of Neotropical avian insectivores

USGS Publications Warehouse

Kennedy, Christina M.; Campbell Grant, Evan H.; Neel, Maile C.; Fagan, William F.; Marpa, Peter P.

2011-01-01

In addition to patch-level attributes (i.e., area and isolation), the nature of land cover between habitat patches (the matrix) may drive colonization and extinction dynamics in fragmented landscapes. Despite a long-standing recognition of matrix effects in fragmented systems, an understanding of the relative impacts of different types of land cover on patterns and dynamics of species occurrence remains limited. We employed multi-season occupancy models to determine the relative influence of patch area, patch isolation, within-patch vegetation structure, and landscape matrix on occupancy dynamics of nine Neotropical nsectivorous birds in 99 forest patches embedded in four matrix types (agriculture, suburban evelopment, bauxite mining, and forest) in central Jamaica. We found that within-patch vegetation structure and the matrix type between patches were more important than patch area and patch isolation in determining local colonization and local extinction probabilities, and that the effects of patch area, isolation, and vegetation structure on occupancy dynamics tended to be matrix and species dependent. Across the avian community, the landscape matrix influenced local extinction more than local colonization, indicating that extinction processes, rather than movement, likely drive interspecific differences in occupancy dynamics. These findings lend crucial empirical support to the hypothesis that species occupancy dynamics in fragmented systems may depend greatly upon the landscape context.

The Conversion of Social Capital into Community Development: an intervention in Australia's outback.

PubMed

Onyx, Jenny; Leonard, Rosemary

2010-01-01

The research presented in this article employed a deliberate intervention to mobilize social capital and then studied the dynamics of the way in which it influenced community development. Whether or not social capital is able to facilitate development depends on the specific context in which it occurs. Although the general context of this study was that of small rural towns in Australia's outback that are experiencing decline, each of the four towns studied had unique features which could influence the mobilization of social capital. Rural communities have the willingness and capacity to mobilize but whether this capacity is actualized may well depend on the presence of other mobilizing factors. Specifically the intervention study found that a structure needs to be in place which can take the initiative and work across the community - engaging a range of organizations. Second, the structure needs to be supported, but not controlled, by local government. Third, it needs the kind of social entrepreneurship that can sustain a community-wide vision and bring together the diverse groups within the community.

Ant-Plant Interaction in a Tropical Savanna: May the Network Structure Vary over Time and Influence on the Outcomes of Associations?

PubMed Central

Lange, Denise; Del-Claro, Kleber

2014-01-01

Plant-animal interactions occur in a community context of dynamic and complex ecological interactive networks. The understanding of who interacts with whom is a basic information, but the outcomes of interactions among associates are fundamental to draw valid conclusions about the functional structure of the network. Ecological networks studies in general gave little importance to know the true outcomes of interactions and how they may change over time. We evaluate the dynamic of an interaction network between ants and plants with extrafloral nectaries, by verifying the temporal variation in structure and outcomes of mutualism for the plant community (leaf herbivory). To reach this goal, we used two tools: bipartite network analysis and experimental manipulation. The networks exhibited the same general pattern as other mutualistic networks: nestedness, asymmetry and low specialization and this pattern was maintained over time, but with internal changes (species degree, connectance and ant abundance). These changes influenced the protection effectiveness of plants by ants, which varied over time. Our study shows that interaction networks between ants and plants are dynamic over time, and that these alterations affect the outcomes of mutualisms. In addition, our study proposes that the set of single systems that shape ecological networks can be manipulated for a greater understanding of the entire system. PMID:25141007

Diatom community structure on in-service cruise ship hulls.

PubMed

Hunsucker, Kelli Zargiel; Koka, Abhishek; Lund, Geir; Swain, Geoffrey

2014-10-01

Diatoms are an important component of marine biofilms found on ship hulls. However, there are only a few published studies that describe the presence and abundance of diatoms on ships, and none that relate to modern ship hull coatings. This study investigated the diatom community structure on two in-service cruise ships with the same cruise cycles, one coated with an antifouling (AF) system (copper self-polishing copolymer) and the other coated with a silicone fouling-release (FR) system. Biofilm samples were collected during dry docking from representative areas of the ship and these provided information on the horizontal and vertical zonation of the hull, and intact and damaged coating and niche areas. Diatoms from the genera Achnanthes, Amphora and Navicula were the most common, regardless of horizontal ship zonation and coating type. Other genera were abundant, but their presence was more dependent on the ship zonation and coating type. Samples collected from damaged areas of the hull coating had a similar community composition to undamaged areas, but with higher diatom abundance. Diatom fouling on the niche areas differed from that of the surrounding ship hull and paralleled previous studies that investigated differences in diatom community structure on static and dynamically exposed coatings; niche areas were similar to static immersion and the hull to dynamic immersion. Additionally, diatom richness was greater on the ship with the FR coating, including the identification of several new genera to the biofouling literature, viz. Lampriscus and Thalassiophysa. These results are the first to describe diatom community composition on in-service ship hulls coated with a FR system. This class of coatings appears to have a larger diatom community compared to copper-based AF systems, with new diatom genera that have the ability to stick to ship hulls and withstand hydrodynamic forces, thus creating the potential for new problematic species in the biofilm.

Multiscale patterns and drivers of arbuscular mycorrhizal fungal communities in the roots and root-associated soil of a wild perennial herb.

PubMed

Rasmussen, Pil U; Hugerth, Luisa W; Blanchet, F Guillaume; Andersson, Anders F; Lindahl, Björn D; Tack, Ayco J M

2018-03-24

Arbuscular mycorrhizal (AM) fungi form diverse communities and are known to influence above-ground community dynamics and biodiversity. However, the multiscale patterns and drivers of AM fungal composition and diversity are still poorly understood. We sequenced DNA markers from roots and root-associated soil from Plantago lanceolata plants collected across multiple spatial scales to allow comparison of AM fungal communities among neighbouring plants, plant subpopulations, nearby plant populations, and regions. We also measured soil nutrients, temperature, humidity, and community composition of neighbouring plants and nonAM root-associated fungi. AM fungal communities were already highly dissimilar among neighbouring plants (c. 30 cm apart), albeit with a high variation in the degree of similarity at this small spatial scale. AM fungal communities were increasingly, and more consistently, dissimilar at larger spatial scales. Spatial structure and environmental drivers explained a similar percentage of the variation, from 7% to 25%. A large fraction of the variation remained unexplained, which may be a result of unmeasured environmental variables, species interactions and stochastic processes. We conclude that AM fungal communities are highly variable among nearby plants. AM fungi may therefore play a major role in maintaining small-scale variation in community dynamics and biodiversity. © 2018 The Authors New Phytologist © 2018 New Phytologist Trust.

Scaling Coastal Ecosystems to Oceanographic and Climatic Drivers: Making Sense of Community Variation on Rocky Shores Using the Comparative-Experimental Approach in Upwelling and Downwelling Systems

NASA Astrophysics Data System (ADS)

Menge, B. A.; Gouhier, T.; Chan, F.; Hacker, S.; Menge, D.; Nielsen, K. J.

2016-02-01

Ecology focuses increasingly on the issue of matching spatial and temporal scales responsible for ecosystem pattern and dynamics. Benthic coastal communities traditionally were studied at local scales using mostly short-term research, while environmental (oceanographic, climatic) drivers were investigated at large scales (e.g., regional to oceanic, mostly offshore) using combined snapshot and monitoring (time series) research. The comparative-experimental approach combines local-scale studies at multiple sites spanning large-scale environmental gradients in combination with monitoring of inner shelf oceanographic conditions including upwelling/downwelling wind forcing and their consequences (e.g., temperature), and inputs of subsidies (larvae, phytoplankton, detritus). Temporal scale varies depending on the questions, but can extend from years to decades. We discuss two examples of rocky intertidal ecosystem dynamics, one at a regional scale (California Current System, CCS) and one at an interhemispheric scale. In the upwelling-dominated CCS, 52% and 32% of the variance in local community structure (functional group abundances at 13 sites across 725 km) was explained by external factors (ecological subsidies, oceanographic conditions, geographic location), and species interactions, respectively. The interhemispheric study tested the intermittent upwelling hypothesis (IUH), which predicts that key ecological processes will vary unimodally along a persistent downwelling to persistent upwelling gradient. Using 14-22 sites, unimodal relationships between ecological subsidies (phytoplankton, prey recruitment), prey responses (barnacle colonization, mussel growth) and species interactions (competition rate, predation rate and effect) and the Bakun upwelling index calculated at each site accounted for 50% of the variance. Hence, external factors can account for about half of locally-expressed community structure and dynamics.

SCOR Working Group 137: "Global Patterns of Phytoplankton Dynamics in Coastal Ecosystems": An introduction to the special issue of Estuarine, Coastal and Shelf Science

NASA Astrophysics Data System (ADS)

Paerl, Hans W.; Yin, Kedong; O'Brien, Todd D.

2015-09-01

Phytoplankton form the base of most aquatic food webs and play a central role in assimilation and processing of carbon and nutrients, including nitrogen, phosphorus, silicon, iron and a wide range of trace elements (Reynolds, 2006). In the marine environment, estuarine and coastal ecosystems (jointly termed coastal here) are among the most productive, resourceful and dynamic habitats on Earth (Malone et al., 1999; Day et al., 2012). These ecosystems constitute only ∼10% of the global oceans' surface, but account for over 30% of its primary production (Day et al., 2012). They process vast amounts of nutrients, sediments, carbonaceous, and xenobiotic compounds generated in coastal watersheds, in which approximately 70% of the world's human population resides (Nixon, 1995; Vitousek et al., 1997; NOAA, 2013). Estuarine and coastal ecosystems are also strongly influenced by localized nutrient enrichment from coastal upwelling, with major impacts on the structure and function of phytoplankton communities and the food webs they support (Legendre and Rassoulzadegan, 2012; Paerl and Justić, 2012). In addition, introductions and invasions of exotic plant and animal species have led to significant "top down" mediated changes in phytoplankton community structure and function (Carlton, 1999; Thompson, 2005). Lastly, the coastal zone is the "front line" of climatically-induced environmental change, including warming, altered rainfall patterns, intensities and magnitudes (Trenberth, 2005; IPCC, 2012), which jointly impact phytoplankton community structure and function (Cloern and Jassby, 2012; Hall et al., 2013). The combined effects of these pressures translate into a myriad of changes in phytoplankton production and community structure along geomorphological and geographic gradients (Fig. 1), with cascading quantitative and qualitative impacts on biogeochemical cycling, food web structure and function, water quality and overall resourcefulness and sustainability of these systems (Cloern, 2001; Paerl et al., 2014).

Where Do Community Colleges Stand?

ERIC Educational Resources Information Center

Pietak, Raymond

1971-01-01

Traditional clubs and structures continue to serve needs of interested students. However, more socially aware students must have operational vehicles to meet their dynamic needs. The identification of problem areas and the creation of ad hoc interest groups should be added to the college activity programs. (Author)

Dormancy contributes to the maintenance of microbial diversity.

PubMed

Jones, Stuart E; Lennon, Jay T

2010-03-30

Dormancy is a bet-hedging strategy used by a variety of organisms to overcome unfavorable environmental conditions. By entering a reversible state of low metabolic activity, dormant individuals become members of a seed bank, which can determine community dynamics in future generations. Although microbiologists have documented dormancy in both clinical and natural settings, the importance of seed banks for the diversity and functioning of microbial communities remains untested. Here, we develop a theoretical model demonstrating that microbial communities are structured by environmental cues that trigger dormancy. A molecular survey of lake ecosystems revealed that dormancy plays a more important role in shaping bacterial communities than eukaryotic microbial communities. The proportion of dormant bacteria was relatively low in productive ecosystems but accounted for up to 40% of taxon richness in nutrient-poor systems. Our simulations and empirical data suggest that regional environmental cues and dormancy synchronize the composition of active communities across the landscape while decoupling active microbes from the total community at local scales. Furthermore, we observed that rare bacterial taxa were disproportionately active relative to common bacterial taxa, suggesting that microbial rank-abundance curves are more dynamic than previously considered. We propose that repeated transitions to and from the seed bank may help maintain the high levels of microbial biodiversity that are observed in nearly all ecosystems.

Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input

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

Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste

The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more importantmore » than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.« less

Predation and resource fluctuations drive eco-evolutionary dynamics of a bacterial community

NASA Astrophysics Data System (ADS)

Hiltunen, Teppo; Friman, Ville-Petri; Kaitala, Veijo; Mappes, Johanna; Laakso, Jouni

2012-01-01

Predation and temporal resource availability are among the most important factors determining prey community dynamics and composition. Both factors have been shown to affect prey diversity, but less is known about their interactive effects, especially in rapidly evolving prey communities. In a laboratory microcosm experiment, we manipulated the presence of the predatory protozoan Tetrahymena thermophila and the temporal patterns in the availability of resources for a bacterial prey community. We found that both predation and temporal fluctuations in prey resources resulted in a more even prey community, and these factors also interacted so that the effect of predation was only seen in a fluctuating environment. One possible explanation for this finding could be differences in prey species grazing resistance and resource use abilities, which likely had the greatest effect on prey community structure in fluctuating environments with periodical resource limitation. We also found that prey communities evolved to be more grazing-resistant during the experiment, and that this effect was due to a clear increase in the grazing resistance of the bacterium Serratia marcescens. Our results demonstrate that temporal variability in prey resources and predation can promote more even prey species proportions by allowing the existence of both defensive and competitive prey life-history strategies.

Environmental drivers of differences in microbial community structure in crude oil reservoirs across a methanogenic gradient

USGS Publications Warehouse

Shelton, Jenna L.; Akob, Denise M.; McIntosh, Jennifer C.; Fierer, Noah; Spear, John R.; Warwick, Peter D.; McCray, John E.

2016-01-01

Stimulating in situ microbial communities in oil reservoirs to produce natural gas is a potentially viable strategy for recovering additional fossil fuel resources following traditional recovery operations. Little is known about what geochemical parameters drive microbial population dynamics in biodegraded, methanogenic oil reservoirs. We investigated if microbial community structure was significantly impacted by the extent of crude oil biodegradation, extent of biogenic methane production, and formation water chemistry. Twenty-two oil production wells from north central Louisiana, USA, were sampled for analysis of microbial community structure and fluid geochemistry. Archaea were the dominant microbial community in the majority of the wells sampled. Methanogens, including hydrogenotrophic and methylotrophic organisms, were numerically dominant in every well, accounting for, on average, over 98% of the total Archaea present. The dominant Bacteria groups were Pseudomonas, Acinetobacter, Enterobacteriaceae, and Clostridiales, which have also been identified in other microbially-altered oil reservoirs. Comparing microbial community structure to fluid (gas, water, and oil) geochemistry revealed that the relative extent of biodegradation, salinity, and spatial location were the major drivers of microbial diversity. Archaeal relative abundance was independent of the extent of methanogenesis, but closely correlated to the extent of crude oil biodegradation; therefore, microbial community structure is likely not a good sole predictor of methanogenic activity, but may predict the extent of crude oil biodegradation. However, when the shallow, highly biodegraded, low salinity wells were excluded from the statistical analysis, no environmental parameters could explain the differences in microbial community structure. This suggests that the microbial community structure of the 5 shallow, up-dip wells was different than the 17 deeper, down-dip wells. Also, the 17 down-dip wells had statistically similar microbial communities despite significant changes in environmental parameters between oil fields. Together, this implies that no single microbial population is a reliable indicator of a reservoir's ability to degrade crude oil to methane, and that geochemistry may be a more important indicator for selecting a reservoir suitable for microbial enhancement of natural gas generation.

Tracking dynamics of plant biomass composting by changes in substrate structure, microbial community, and enzyme activity

PubMed Central

2012-01-01

Background Understanding the dynamics of the microbial communities that, along with their secreted enzymes, are involved in the natural process of biomass composting may hold the key to breaking the major bottleneck in biomass-to-biofuels conversion technology, which is the still-costly deconstruction of polymeric biomass carbohydrates to fermentable sugars. However, the complexity of both the structure of plant biomass and its counterpart microbial degradation communities makes it difficult to investigate the composting process. Results In this study, a composter was set up with a mix of yellow poplar (Liriodendron tulipifera) wood-chips and mown lawn grass clippings (85:15 in dry-weight) and used as a model system. The microbial rDNA abundance data obtained from analyzing weekly-withdrawn composted samples suggested population-shifts from bacteria-dominated to fungus-dominated communities. Further analyses by an array of optical microscopic, transcriptional and enzyme-activity techniques yielded correlated results, suggesting that such population shifts occurred along with early removal of hemicellulose followed by attack on the consequently uncovered cellulose as the composting progressed. Conclusion The observed shifts in dominance by representative microbial groups, along with the observed different patterns in the gene expression and enzymatic activities between cellulases, hemicellulases, and ligninases during the composting process, provide new perspectives for biomass-derived biotechnology such as consolidated bioprocessing (CBP) and solid-state fermentation for the production of cellulolytic enzymes and biofuels. PMID:22490508

Tracking Dynamics of Plant Biomass Composting by Changes in Substrate Structure, Microbial Community, and Enzyme Activity

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

Wei, H.; Tucker, M. P.; Baker, J. O.

2012-04-01

Understanding the dynamics of the microbial communities that, along with their secreted enzymes, are involved in the natural process of biomass composting may hold the key to breaking the major bottleneck in biomass-to-biofuels conversion technology, which is the still-costly deconstruction of polymeric biomass carbohydrates to fermentable sugars. However, the complexity of both the structure of plant biomass and its counterpart microbial degradation communities makes it difficult to investigate the composting process. In this study, a composter was set up with a mix of yellow poplar (Liriodendron tulipifera) wood-chips and mown lawn grass clippings (85:15 in dry-weight) and used as amore » model system. The microbial rDNA abundance data obtained from analyzing weekly-withdrawn composted samples suggested population-shifts from bacteria-dominated to fungus-dominated communities. Further analyses by an array of optical microscopic, transcriptional and enzyme-activity techniques yielded correlated results, suggesting that such population shifts occurred along with early removal of hemicellulose followed by attack on the consequently uncovered cellulose as the composting progressed. The observed shifts in dominance by representative microbial groups, along with the observed different patterns in the gene expression and enzymatic activities between cellulases, hemicellulases, and ligninases during the composting process, provide new perspectives for biomass-derived biotechnology such as consolidated bioprocessing (CBP) and solid-state fermentation for the production of cellulolytic enzymes and biofuels.« less

Bacterial community dynamics and activity in relation to dissolved organic matter availability during sea-ice formation in a mesocosm experiment.

PubMed

Eronen-Rasimus, Eeva; Kaartokallio, Hermanni; Lyra, Christina; Autio, Riitta; Kuosa, Harri; Dieckmann, Gerhard S; Thomas, David N

2014-02-01

The structure of sea-ice bacterial communities is frequently different from that in seawater. Bacterial entrainment in sea ice has been studied with traditional microbiological, bacterial abundance, and bacterial production methods. However, the dynamics of the changes in bacterial communities during the transition from open water to frozen sea ice is largely unknown. Given previous evidence that the nutritional status of the parent water may affect bacterial communities during ice formation, bacterial succession was studied in under ice water and sea ice in two series of mesocosms: the first containing seawater from the North Sea and the second containing seawater enriched with algal-derived dissolved organic matter (DOM). The composition and dynamics of bacterial communities were investigated with terminal restriction fragment length polymorphism (T-RFLP), and cloning alongside bacterial production (thymidine and leucine uptake) and abundance measurements (measured by flow cytometry). Enriched and active sea-ice bacterial communities developed in ice formed in both unenriched and DOM-enriched seawater (0-6 days). γ-Proteobacteria dominated in the DOM-enriched samples, indicative of their capability for opportunistic growth in sea ice. The bacterial communities in the unenriched waters and ice consisted of the classes Flavobacteria, α- and γ-Proteobacteria, which are frequently found in natural sea ice in polar regions. Furthermore, the results indicate that seawater bacterial communities are able to adapt rapidly to sudden environmental changes when facing considerable physicochemical stress such as the changes in temperature, salinity, nutrient status, and organic matter supply during ice formation. © 2014 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Community ecology in a changing environment: Perspectives from the Quaternary

NASA Astrophysics Data System (ADS)

Jackson, Stephen T.; Blois, Jessica L.

2015-04-01

Community ecology and paleoecology are both concerned with the composition and structure of biotic assemblages but are largely disconnected. Community ecology focuses on existing species assemblages and recently has begun to integrate history (phylogeny and continental or intercontinental dispersal) to constrain community processes. This division has left a "missing middle": Ecological and environmental processes occurring on timescales from decades to millennia are not yet fully incorporated into community ecology. Quaternary paleoecology has a wealth of data documenting ecological dynamics at these timescales, and both fields can benefit from greater interaction and articulation. We discuss ecological insights revealed by Quaternary terrestrial records, suggest foundations for bridging between the disciplines, and identify topics where the disciplines can engage to mutual benefit.

Community ecology in a changing environment: Perspectives from the Quaternary

PubMed Central

Jackson, Stephen T.; Blois, Jessica L.

2015-01-01

Community ecology and paleoecology are both concerned with the composition and structure of biotic assemblages but are largely disconnected. Community ecology focuses on existing species assemblages and recently has begun to integrate history (phylogeny and continental or intercontinental dispersal) to constrain community processes. This division has left a “missing middle”: Ecological and environmental processes occurring on timescales from decades to millennia are not yet fully incorporated into community ecology. Quaternary paleoecology has a wealth of data documenting ecological dynamics at these timescales, and both fields can benefit from greater interaction and articulation. We discuss ecological insights revealed by Quaternary terrestrial records, suggest foundations for bridging between the disciplines, and identify topics where the disciplines can engage to mutual benefit. PMID:25901314

Community ecology in a changing environment: Perspectives from the Quaternary

USGS Publications Warehouse

Jackson, Stephen T.; Blois, Jessica L.

2015-01-01

Community ecology and paleoecology are both concerned with the composition and structure of biotic assemblages but are largely disconnected. Community ecology focuses on existing species assemblages and recently has begun to integrate history (phylogeny and continental or intercontinental dispersal) to constrain community processes. This division has left a “missing middle”: Ecological and environmental processes occurring on timescales from decades to millennia are not yet fully incorporated into community ecology. Quaternary paleoecology has a wealth of data documenting ecological dynamics at these timescales, and both fields can benefit from greater interaction and articulation. We discuss ecological insights revealed by Quaternary terrestrial records, suggest foundations for bridging between the disciplines, and identify topics where the disciplines can engage to mutual benefit.

Community evolution mining and analysis in social network

NASA Astrophysics Data System (ADS)

Liu, Hongtao; Tian, Yuan; Liu, Xueyan; Jian, Jie

2017-03-01

With the development of digital and network technology, various social platforms emerge. These social platforms have greatly facilitated access to information, attracting more and more users. They use these social platforms every day to work, study and communicate, so every moment social platforms are generating massive amounts of data. These data can often be modeled as complex networks, making large-scale social network analysis possible. In this paper, the existing evolution classification model of community has been improved based on community evolution relationship over time in dynamic social network, and the Evolution-Tree structure is proposed which can show the whole life cycle of the community more clearly. The comparative test result shows that the improved model can excavate the evolution relationship of the community well.

Community ecology in a changing environment: Perspectives from the Quaternary.

PubMed

Jackson, Stephen T; Blois, Jessica L

2015-04-21

Community ecology and paleoecology are both concerned with the composition and structure of biotic assemblages but are largely disconnected. Community ecology focuses on existing species assemblages and recently has begun to integrate history (phylogeny and continental or intercontinental dispersal) to constrain community processes. This division has left a "missing middle": Ecological and environmental processes occurring on timescales from decades to millennia are not yet fully incorporated into community ecology. Quaternary paleoecology has a wealth of data documenting ecological dynamics at these timescales, and both fields can benefit from greater interaction and articulation. We discuss ecological insights revealed by Quaternary terrestrial records, suggest foundations for bridging between the disciplines, and identify topics where the disciplines can engage to mutual benefit.

Bacterial community dynamics in long-term operation of a pilot plant using aerobic granular sludge to treat pig slurry.

PubMed

Fra-Vázquez, A; Morales, N; Figueroa, M; Val Del Río, A; Regueiro, L; Campos, J L; Mosquera-Corral, A

2016-09-01

Aerobic granular sludge represents an interesting approach for simultaneous organic matter and nitrogen removal in wastewater treatment plants. However, the information about microbial communities in aerobic granular systems dealing with industrial wastewater like pig slurry is limited. Herein, bacterial diversity and dynamics were assessed in a pilot scale plant using aerobic granular sludge for organic matter and nitrogen elimination from swine slurry during more than 300 days. Results indicated that bacterial composition evolved throughout the operational period from flocculent activated sludge, used as inoculum, to mature aerobic granules. Bacterial diversity increased at the beginning of the granulation process and then declined due to the application of transient organic matter and nitrogen loads. The operational conditions of the pilot plant and the degree of granulation determined the microbial community of the aerobic granules. Brachymonas, Zoogloea and Thauera were attributed with structural function as they are able to produce extracellular polymeric substances to maintain the granular structure. Nitrogen removal was justified by partial nitrification (Nitrosomonas) and denitrification (Thauera and Zoogloea), while Comamonas was identified as the main organic matter oxidizing bacteria. Overall, clear links between bacterial dynamics and composition with process performance were found and will help to predict their biological functions in wastewater ecosystems improving the future control of the process. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1212-1221, 2016. © 2016 American Institute of Chemical Engineers.

Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time

PubMed Central

Sheik, Cody S.; Stevenson, Emily I.; Den Uyl, Paul A.; Arendt, Carli A.; Aciego, Sarah M.; Dick, Gregory J.

2015-01-01

Glaciers are geologically important yet transient ecosystems that support diverse, biogeochemically significant microbial communities. During the melt season glaciers undergo dramatic physical, geochemical, and biological changes that exert great influence on downstream biogeochemical cycles. Thus, we sought to understand the temporal melt-season dynamics of microbial communities and associated geochemistry at the terminus of Lemon Creek Glacier (LCG) in coastal southern Alaska. Due to late season snowfall, sampling of LCG occurred in three interconnected areas: proglacial Lake Thomas, the lower glacial outflow stream, and the glacier’s terminus. LCG associated microbial communities were phylogenetically diverse and varied by sampling location. However, Betaproteobacteria, Alphaproteobacteria, and Bacteroidetes dominated communities at all sampling locations. Strict anaerobic groups such as methanogens, SR1, and OP11 were also recovered from glacier outflows, indicating anoxic conditions in at least some portions of the LCG subglacial environment. Microbial community structure was significantly correlated with sampling location and sodium concentrations. Microbial communities sampled from terminus outflow waters exhibited day-to-day fluctuation in taxonomy and phylogenetic similarity. However, these communities were not significantly different from randomly constructed communities from all three sites. These results indicate that glacial outflows share a large proportion of phylogenetic overlap with downstream environments and that the observed significant shifts in community structure are driven by changes in relative abundance of different taxa, and not complete restructuring of communities. We conclude that LCG glacial discharge hosts a diverse and relatively stable microbiome that shifts at fine taxonomic scales in response to geochemistry and likely water residence time. PMID:26042114

Polar ecosystem dynamics: recovery of communities from organic enrichment in McMurdo Sound, Antarctica.

PubMed

Kim, Stacy; Hammerstom, Kamille K; Conlan, Kathleen E; Thurber, Andrew R

2010-12-01

Community structure and diversity are influenced by patterns of disturbance and input of food. In Antarctica, the marine ecosystem undergoes highly seasonal changes in availability of light and in primary production. Near research stations, organic input from human activities can disturb the regular productivity regime with a consistent input of sewage. McMurdo Sound has both high-productivity and low-productivity habitats, thereby providing an ideal test bed for community recovery dynamics under polar conditions. We used experimental manipulations of the subtidal communities to test the hypotheses that (1) benthic communities respond differently to disturbance from organic enrichment versus burial and (2) community response also varies in areas with different natural patterns of food supply. Both in low- and high-food habitats, the strongest community response was to organic enrichment and resulted in dominance of typical organic-enrichment specialists. In habitats with highly seasonal productivity, community response was predictable and recovery was rapid. In habitats with low productivity, community variability was high and caging treatments suggested that inconsistencies were due to patchy impacts by scavengers. In areas normally subject to regular organic enrichment, either from primary production or from further up the food web (defecation by marine mammals), recovery of benthic communities takes only years even in a polar system. However, a low-productivity regime is as common in near shore habitats around the continent; under these conditions, recovery of benthic communities from disturbance is likely to be much slower and follow a variable ecological trajectory.

Soil Viral Communities Vary Temporally and along a Land Use Transect as Revealed by Virus-Like Particle Counting and a Modified Community Fingerprinting Approach (fRAPD)

PubMed Central

Narr, Anja; Nawaz, Ali; Wick, Lukas Y.; Harms, Hauke; Chatzinotas, Antonis

2017-01-01

Environmental surveys on soil viruses are still rare and mostly anecdotal, i. e., they mostly report on viruses at one location or for only a few sampling dates. Detailed time-series analysis with multiple samples can reveal the spatio-temporal dynamics of viral communities and provide important input as to how viruses interact with their potential hosts and the environment. Such surveys, however, require fast, easy-to-apply and reliable methods. In the present study we surveyed monthly across 13 months the abundance of virus-like particles (VLP) and the structure of the viral communities in soils along a land use transect (i.e., forest, pasture, and cropland). We evaluated 32 procedures to extract VLP from soil using different buffers and mechanical methods. The most efficient extraction was achieved with 1× saline magnesium buffer in combination with 20 min vortexing. For community structure analysis we developed an optimized fingerprinting approach (fluorescent RAPD-PCR; fRAPD) by combining RAPD-PCR with fluorescently labeled primers in order to size the obtained fragments on a capillary sequencing machine. With the concomitantly collected data of soil specific factors and weather data, we were able to find correlations of viral abundance and community structure with environmental variables and sampling site. More specifically, we found that soil specific factors such as pH and total nitrogen content played a significant role in shaping both soil viral abundance and community structure. The fRAPD analysis revealed high temporal changes and clustered the viral communities according to sampling sites. In particular we observed that temperature and rainfall shaped soil viral communities in non-forest sites. In summary our findings suggest that sampling site was a key factor for shaping the abundance and community structure of soil viruses, and when site vegetation was reduced, temperature and rainfall were also important factors. PMID:29067022

Local structural mechanism for frozen-in dynamics in metallic glasses

NASA Astrophysics Data System (ADS)

Liu, X. J.; Wang, S. D.; Wang, H.; Wu, Y.; Liu, C. T.; Li, M.; Lu, Z. P.

2018-04-01

The nature of the glass transition is a fundamental and long-standing intriguing issue in the condensed-matter physics and materials science community. In particular, the structural response by which a liquid is arrested dynamically to form a glass or amorphous solid upon approaching its freezing temperature [the glass transition temperature (Tg)] remains unclear. Various structural scenarios in terms of the percolation theory have been proposed recently to understand such a phenomenon; however, there is still no consensus on what the general percolation entity is and how the entity responds to the sudden slowdown dynamics during the glass transition. In this paper, we demonstrate that one-dimensional local linear ordering (LLO) is a universal structural motif associated with the glass transition for various metallic glasses. The quantitative evolution of LLO with temperature indicates that a percolating LLO network forms to serve as the backbone of the rigid glass solid when the temperature approaches the freezing point, resulting in the frozen-in dynamics accompanying the glass transition. The percolation transition occurs by pinning different LLO networks together, which only needs the introduction of a small number of "joint" atoms between them, and therefore the energy expenditure is very low.

The impact of resource dependence of the mechanisms of life on the spatial population dynamics of an in silico microbial community

NASA Astrophysics Data System (ADS)

Daly, Aisling J.; Baetens, Jan M.; De Baets, Bernard

2016-12-01

Biodiversity has a critical impact on ecosystem functionality and stability, and thus the current biodiversity crisis has motivated many studies of the mechanisms that sustain biodiversity, a notable example being non-transitive or cyclic competition. We therefore extend existing microscopic models of communities with cyclic competition by incorporating resource dependence in demographic processes, characteristics of natural systems often oversimplified or overlooked by modellers. The spatially explicit nature of our individual-based model of three interacting species results in the formation of stable spatial structures, which have significant effects on community functioning, in agreement with experimental observations of pattern formation in microbial communities.

Developing Tomorrow's Integrated Community Health Systems: A Leadership Challenge for Public Health and Primary Care

PubMed Central

Welton, William E.; Kantner, Theodore A.; Katz, Sheila Moriber

1997-01-01

As the nation's health system moves away from earlier models to one grounded in population health and market-based systems of care, new challenges arise for public health professionals, primary care practitioners, health plan and institutional managers, and community leaders. Among the challenges are the need to develop creative concepts of organization and accountability and to assure that dynamic, system-oriented structures support the new kind of leadership that is required. Developing tomorrow's integrated community health systems will challenge the leadership skills and integrative abilities of public health professionals, primary care practitioners, and managers. These leaders and their new organizations must, in turn, assume increased accountability for improving community health. PMID:9184684

Using Grand Challenges For Innovative Teaching in Structural Geology, Geophysics, and Tectonics

NASA Astrophysics Data System (ADS)

McDaris, J. R.; Tewksbury, B. J.; Wysession, M. E.

2012-12-01

An innovative approach to teaching involves using the "Big Ideas" or "Grand Challenges" of a field, as determined by the research community in that area, as the basis for classroom activities. There have been several recent efforts in the areas of structural geology, tectonics, and geophysics to determine these Grand Challenges, including the areas of seismology ("Seismological Grand Challenges in Understanding Earth's Dynamic Systems"), mineral physics ("Unlocking the Building Blocks of the Planet"), EarthScope-related science ("Unlocking the Secrets of the North American Continent: An EarthScope Science Plan for 2010-2020"), and structural geology and tectonics (at the Structural Geology and Tectonics Forum held at Williams College in June, 2012). These research community efforts produced frameworks of the essential information for their fields with the aim of guiding future research. An integral part of this, however, is training the next generation of scientists, and using these Big Ideas as the basis for course structures and activities is a powerful way to make this happen. When activities, labs, and homeworks are drawn from relevant and cutting-edge research topics, students can find the material more fascinating and engaging, and can develop a better sense of the dynamic process of scientific discovery. Many creative ideas for incorporating the Grand Challenges of structural geology, tectonics, and geophysics in the classroom were developed at a Cutting Edge workshop on "Teaching Structural Geology, Geophysics, and Tectonics in the 21st Century" held at the University of Tennessee in July, 2012.

Science, School Science, and School: Looking at Science Learning in Classrooms from the Perspective of Basil Bernstein's Theory of the Structure of Pedagogic Discourse

NASA Astrophysics Data System (ADS)

Campbell, Ralph Ian

This analytic paper asks one question: How does Basil Bernstein's concept of the structure of pedagogic discourse (SPD) contribute to our understanding of the role of teacher-student interactions in science learning in the classroom? Applying Bernstein's theory of the SPD to an analysis of current research in science education explores the structure of Bernstein's theory as a tool for understanding the challenges and questions related to current concerns about classroom science learning. This analysis applies Bernstein's theory of the SPD as a heuristic through a secondary reading of selected research from the past fifteen years and prompts further consideration of Bernstein's ideas. This leads to a reevaluation of the categories of regulative discourse (RD) and instructional discourse (ID) as structures that frame learning environments and the dynamics of student-teacher interactions, which determine learning outcomes. The SPD becomes a simple but flexible heuristic, offering a useful deconstruction of teaching and learning dynamics in three different classroom environments. Understanding the framing interactions of RD and ID provides perspectives on the balance of agency and expectation, suggesting some causal explanations for the student learning outcomes described by the authors. On one hand, forms of open inquiry and student-driven instruction may lack the structure to ensure the appropriation of desired forms of scientific thinking. On the other hand, well-designed pathways towards the understanding of fundamental concepts in science may lack the forms of more open-ended inquiry that develop transferable understanding. Important ideas emerge about the complex dynamics of learning communities, the materials of learning, and the dynamic role of the teacher as facilitator and expert. Simultaneously, the SPD as a flexible heuristic proves ambiguous, prompting a reevaluation of Bernstein's organization of RD and ID. The hierarchical structure of pedagogic discourse becomes a problematic distinction. Regulative discourse is often more instructional and instructional discourse more instrumental in shaping roles and relationships within the learning community. This analysis suggests an agenda for future classroom research and the education of teachers, capitalizing on the SPD as heuristic and reevaluating the ways that social dynamics and structures for domain-specific learning interact in the realization of classroom learning.

RELATIONSHIP OF MICROBIAL COMMUNITY STRUCTURE AND CARBON DYNAMICS IN SOILS FROM BRAZILIAN SAVANNAS

EPA Science Inventory

Fertilization is a widespread management practice in savanna areas of central Brazil (Cerrado) that are undergoing rapid agricultural land use changes. We conducted field and laboratory studies in soils with added fertilizers to determine the effect that fertilization of native a...

Dynamics of Alliances.

ERIC Educational Resources Information Center

Hubbard, James; And Others

To encourage the involvement of the community in mathematics, science, and technology education, some states and localities have formed alliances. This book outlines four key components of alliance building: process, environment, structure, and outcomes; and describes how changes in one component affect the others. It is designed to serve as a…

Measuring succession: methods for establishing long term vegetation monitoring sites

USDA-ARS?s Scientific Manuscript database

Successional stages are often characterized by dominant plant species (species with the highest cover) and their effect on the structure and function of an area through time. However, the plant species determining the ecosystem properties and plant community dynamics may not be the dominant, especia...

Farm-scale variation of soil quality indices and association with edaphic properties

USDA-ARS?s Scientific Manuscript database

Soil organisms are indicators of dynamic soil quality because their community structure and population density are sensitive to management changes. However, edaphic properties can also affect soil organisms and high spatial variability can confound their utility for soil evaluation. In the present...

Mythical Structures in Community Vision.

ERIC Educational Resources Information Center

Burke, Ken

To negotiate a balance between an ideological concern for society's historical-economic development and an understanding of the individual's need for a sense of self-realization, social theory researchers should look to B. Dervin's "gap theory model" of communication. Adapted from Kenneth Burke, it offers a dynamic means of understanding…

Recruitment dynamics of two ecosystem engineers could drive shellfish populations in U.S. west coast estuaries

EPA Science Inventory

Two species of burrowing shrimp, Neotrypaea californiensis and Upogebia pugettensis are important members of intertidal mudflat communities in US West coast estuaries. Both species act as ecosystem engineers and influence the presence of other structured habitats and suspension ...

Dominance of Endozoicomonas bacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosa microbiome.

PubMed

Pogoreutz, Claudia; Rädecker, Nils; Cárdenas, Anny; Gärdes, Astrid; Wild, Christian; Voolstra, Christian R

2018-02-01

The importance of Symbiodinium algal endosymbionts and a diverse suite of bacteria for coral holobiont health and functioning are widely acknowledged. Yet, we know surprisingly little about microbial community dynamics and the stability of host-microbe associations under adverse environmental conditions. To gain insight into the stability of coral host-microbe associations and holobiont structure, we assessed changes in the community structure of Symbiodinium and bacteria associated with the coral Pocillopora verrucosa under excess organic nutrient conditions. Pocillopora -associated microbial communities were monitored over 14 days in two independent experiments. We assessed the effect of excess dissolved organic nitrogen (DON) and excess dissolved organic carbon (DOC). Exposure to excess nutrients rapidly affected coral health, resulting in two distinct stress phenotypes: coral bleaching under excess DOC and severe tissue sloughing (>90% tissue loss resulting in host mortality) under excess DON. These phenotypes were accompanied by structural changes in the Symbiodinium community. In contrast, the associated bacterial community remained remarkably stable and was dominated by two Endozoicomonas phylotypes, comprising on average 90% of 16S rRNA gene sequences. This dominance of Endozoicomonas even under conditions of coral bleaching and mortality suggests the bacterial community of P. verrucosa may be rather inflexible and thereby unable to respond or acclimatize to rapid changes in the environment, contrary to what was previously observed in other corals. In this light, our results suggest that coral holobionts might occupy structural landscapes ranging from a highly flexible to a rather inflexible composition with consequences for their ability to respond to environmental change.

Structure of Infaunal Communities on the Beaufort Sea Shelf and Slope: Insights from Morphological and Environmental DNA Sequencing Approaches

NASA Astrophysics Data System (ADS)

Hardy, S. M.; Bik, H.; Walker, A.; Sharma, J.; Blanchard, A.

2016-02-01

Rapid change is occurring in the Arctic concurrently with increased human activity, yet our knowledge of the structure and function of high-Arctic sediment communities is still rudimentary. The Beaufort Sea is particularly poorly sampled, and largely unexplored at slope depths, providing little information with which to assess the impacts of petroleum exploration activities now beginning in this area. We are investigating diversity and community structure of meio- and macrobenthic infauna on the continental shelf and slope of the Beaufort Sea across a range of depths (50 to 1000 m) using traditional taxonomic and environmental DNA sequencing approaches, and comparing results to additional sites in the adjacent NE Chukchi Sea petroleum lease-sale area. The Beaufort slope is topographically complex and characterized by an east-west gradient in benthic habitat characteristics, with heavy input of terrestrial organic matter particularly in the region of the Mackenzie River delta. Warmer, saltier subsurface Atlantic water masses impact benthic communities at mid-slope depths, likely influencing turnover in community structure observed with depth. Food resources are variable across the region, with very high sediment chlorophyll concentrations at 350 m depth in some areas. Differences in nematode assemblages were detected across the Beaufort Sea shelf/slope, across depths within the Beaufort Sea, and between the Beaufort and adjacent NE Chukchi Sea. These differences were apparent in both morphological and environmental sequencing data. Macrofaunal communities showed variable community structure among transects, with high abundance and high dominance in polychaete assemblages coincident with the chlorophyll maximum. Sequencing data also revealed an abundance of protists in sediments which have been mostly ignored in studies of ecosystem dynamics in this region, and may represent an important component of the food web.

Evolutionary method for finding communities in bipartite networks.

PubMed

Zhan, Weihua; Zhang, Zhongzhi; Guan, Jihong; Zhou, Shuigeng

2011-06-01

An important step in unveiling the relation between network structure and dynamics defined on networks is to detect communities, and numerous methods have been developed separately to identify community structure in different classes of networks, such as unipartite networks, bipartite networks, and directed networks. Here, we show that the finding of communities in such networks can be unified in a general framework-detection of community structure in bipartite networks. Moreover, we propose an evolutionary method for efficiently identifying communities in bipartite networks. To this end, we show that both unipartite and directed networks can be represented as bipartite networks, and their modularity is completely consistent with that for bipartite networks, the detection of modular structure on which can be reformulated as modularity maximization. To optimize the bipartite modularity, we develop a modified adaptive genetic algorithm (MAGA), which is shown to be especially efficient for community structure detection. The high efficiency of the MAGA is based on the following three improvements we make. First, we introduce a different measure for the informativeness of a locus instead of the standard deviation, which can exactly determine which loci mutate. This measure is the bias between the distribution of a locus over the current population and the uniform distribution of the locus, i.e., the Kullback-Leibler divergence between them. Second, we develop a reassignment technique for differentiating the informative state a locus has attained from the random state in the initial phase. Third, we present a modified mutation rule which by incorporating related operations can guarantee the convergence of the MAGA to the global optimum and can speed up the convergence process. Experimental results show that the MAGA outperforms existing methods in terms of modularity for both bipartite and unipartite networks.

Vegetative community control of freshwater availability: Phoenix Islands case study

NASA Astrophysics Data System (ADS)

Engels, M.; Heinse, R.

2014-12-01

On small low islands with limited freshwater resources, terrestrial plant communities play a large role in moderating freshwater availability. Freshwater demands of vegetative communities are variable depending on the composition of the community. Hence, changes to community structure from production crop introductions, non-native species invasions, and climate change, may have significant implications for freshwater availability. Understanding how vegetative community changes impact freshwater availability will allow for better management and forecasting of limited freshwater supplies. To better understand these dynamics, we investigated three small tropical atolls in the Phoenix Island Protected Area, Kiribati. Despite their close proximity, these islands receive varying amounts of rainfall, are host to different plant communities and two of the islands have abandoned coconut plantations. Using electromagnetic induction, ground penetrating radar, soil samples, climate and satellite data, we present preliminary estimates of vegetative water demand for different tropical plant communities.

Effects of potentization in aqueous solutions.

PubMed

Schulte, J

1999-10-01

Over the past two decades, research into structure formation and structure conservation in water has created a significant interest among the homeopathy research community. The formation of sustained static and dynamic structures in aqueous solutions is thought to be synonymous with the possible storage of information in associated liquids. Prominent models and experiments considering this possibility are presented in this paper, and some of their subtleties, which were not given much room in the respective original publications, will be elucidated in more detail here.

Structure of local interactions in complex financial dynamics

PubMed Central

Jiang, X. F.; Chen, T. T.; Zheng, B.

2014-01-01

With the network methods and random matrix theory, we investigate the interaction structure of communities in financial markets. In particular, based on the random matrix decomposition, we clarify that the local interactions between the business sectors (subsectors) are mainly contained in the sector mode. In the sector mode, the average correlation inside the sectors is positive, while that between the sectors is negative. Further, we explore the time evolution of the interaction structure of the business sectors, and observe that the local interaction structure changes dramatically during a financial bubble or crisis. PMID:24936906

Social contagions on time-varying community networks

NASA Astrophysics Data System (ADS)

Liu, Mian-Xin; Wang, Wei; Liu, Ying; Tang, Ming; Cai, Shi-Min; Zhang, Hai-Feng

2017-05-01

Time-varying community structures exist widely in real-world networks. However, previous studies on the dynamics of spreading seldom took this characteristic into account, especially those on social contagions. To study the effects of time-varying community structures on social contagions, we propose a non-Markovian social contagion model on time-varying community networks based on the activity-driven network model. A mean-field theory is developed to analyze the proposed model. Through theoretical analyses and numerical simulations, two hierarchical features of the behavior adoption processes are found. That is, when community strength is relatively large, the behavior can easily spread in one of the communities, while in the other community the spreading only occurs at higher behavioral information transmission rates. Meanwhile, in spatial-temporal evolution processes, hierarchical orders are observed for the behavior adoption. Moreover, under different information transmission rates, three distinctive patterns are demonstrated in the change of the whole network's final adoption proportion along with the growing community strength. Within a suitable range of transmission rate, an optimal community strength can be found that can maximize the final adoption proportion. Finally, compared with the average activity potential, the promoting or inhibiting of social contagions is much more influenced by the number of edges generated by active nodes.

Fish and Phytoplankton Exhibit Contrasting Temporal Species Abundance Patterns in a Dynamic North Temperate Lake

PubMed Central

Hansen, Gretchen J. A.; Carey, Cayelan C.

2015-01-01

Temporal patterns of species abundance, although less well-studied than spatial patterns, provide valuable insight to the processes governing community assembly. We compared temporal abundance distributions of two communities, phytoplankton and fish, in a north temperate lake. We used both 17 years of observed relative abundance data as well as resampled data from Monte Carlo simulations to account for the possible effects of non-detection of rare species. Similar to what has been found in other communities, phytoplankton and fish species that appeared more frequently were generally more abundant than rare species. However, neither community exhibited two distinct groups of “core” (common occurrence and high abundance) and “occasional” (rare occurrence and low abundance) species. Both observed and resampled data show that the phytoplankton community was dominated by occasional species appearing in only one year that exhibited large variation in their abundances, while the fish community was dominated by core species occurring in all 17 years at high abundances. We hypothesize that the life-history traits that enable phytoplankton to persist in highly dynamic environments may result in communities dominated by occasional species capable of reaching high abundances when conditions allow. Conversely, longer turnover times and broad environmental tolerances of fish may result in communities dominated by core species structured primarily by competitive interactions. PMID:25651399

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.

Effects of sedimentary sulfide on community structure, population dynamics, and colonization depth of macrozoobenthos in organic-rich estuarine sediments.

PubMed

Kanaya, Gen; Uehara, Tadayasu; Kikuchi, Eisuke

2016-08-15

An annual field survey and in situ recolonization experiment revealed the effects of sedimentary sulfide (H2S) on macrozoobenthos in a eutrophic brackish lagoon. Species diversity was much lower throughout the year in muddy opportunist-dominant sulfidic areas. Mass mortality occurred during warmer months under elevated H2S levels. An enclosure experiment demonstrated that sedimentary H2S modified community composition, size structure, and colonization depth of macrozoobenthos. Species-specific responses to each sediment type (sand, sulfidic mud, and mud with H2S removed) resulted in changes in the established community structure. Dominant polychaetes (Hediste spp., Pseudopolydora spp., and Capitella teleta) occurred predominantly in a thin surface layer in the presence of H2S. On the other hand, organic-rich mud facilitated settlement of polychaete larvae if it does not contain H2S. These results demonstrate that sediment characteristics, including H2S level and organic content, were key structuring factors for the macrozoobenthic assemblage in organically polluted estuarine sediments. Copyright © 2016 Elsevier Ltd. All rights reserved.

[Rapid ecological assessment of tropical fish communities in a gold mine area of Costa Rica].

PubMed

Espinoza Mendiola, Mario

2008-12-01

Gold mining impacts have generated a great concern regarding aquatic systems and habitat fragmentation. Anthropogenic disturbances on the structure and heterogeneity of a system can have an important effect on aquatic community stability. Ecological rapid assessments (1996, 2002, and 2007) were employed to determine the structure, composition and distribution of tropical fish communities in several rivers and smaller creeks from a gold mining area in Cerro Crucitas, Costa Rica. In addition, species composition and relative abundance were related with habitat structure. A total of 35 species were registered, among which sardine Astyanax aeneus (Characidae) and livebearer Alfaro cultratus (Poeciliidae) were the most abundant fish (71%). The highest species richness was observed in Caño Crucitas (s=19) and Minas Creek (s=18). Significant differences in fish communities structure and composition from Infiernillo river and Minas creek were observed (lamda = 0.0, F(132, 66) = 2.24, p < 0.001). Presence and/or absence of certain species such as Dormitor gobiomorus, Rhamdia nicaraguensis, Parachromis loiseillei and Atractosteus tropicus explained most of the spatial variation among sites. Habitat structure also contributed to explain differences among sites (lamda = 0.004, F(60.183) = 5.52, p < 0.001). Substratum (soft and hard bottom types) and habitat attributes (elevation, width and depth) explained most of the variability observed in Infiernillo River, Caño Crucitas and Tamagá Creek. In addition, a significant association between fish species and habitat structure was observed. This study reveals a high complexity in tropical fish communities that inhabit a gold mine area. Furthermore, it highlights the importance of habitat heterogeneity in fish community dynamics. The loss and degradation of aquatic systems in Cerro Crucitas can have a strong negative effect on fish community structure and composition of local species. A better understanding of the use of specific habitats that serve as essential fish habitats can improve tropical fish conservation and management strategies, thus increasing local diversity, and thereby, the biological importance of the area.

Atoll-scale patterns in coral reef community structure: Human signatures on Ulithi Atoll, Micronesia.

PubMed

Crane, Nicole L; Nelson, Peter; Abelson, Avigdor; Precoda, Kristin; Rulmal, John; Bernardi, Giacomo; Paddack, Michelle

2017-01-01

The dynamic relationship between reefs and the people who utilize them at a subsistence level is poorly understood. This paper characterizes atoll-scale patterns in shallow coral reef habitat and fish community structure, and correlates these with environmental characteristics and anthropogenic factors, critical to conservation efforts for the reefs and the people who depend on them. Hierarchical clustering analyses by site for benthic composition and fish community resulted in the same 3 major clusters: cluster 1-oceanic (close proximity to deep water) and uninhabited (low human impact); cluster 2-oceanic and inhabited (high human impact); and cluster 3-lagoonal (facing the inside of the lagoon) and inhabited (highest human impact). Distance from village, reef exposure to deep water and human population size had the greatest effect in predicting the fish and benthic community structure. Our study demonstrates a strong association between benthic and fish community structure and human use across the Ulithi Atoll (Yap State, Federated States of Micronesia) and confirms a pattern observed by local people that an 'opportunistic' scleractinian coral (Montipora sp.) is associated with more highly impacted reefs. Our findings suggest that small human populations (subsistence fishing) can nevertheless have considerable ecological impacts on reefs due, in part, to changes in fishing practices rather than overfishing per se, as well as larger global trends. Findings from this work can assist in building local capacity to manage reef resources across an atoll-wide scale, and illustrates the importance of anthropogenic impact even in small communities.

Molecular Dynamics Simulation Reveals Correlated Inter-Lobe Motion in Protein Lysine Methyltransferase SMYD2.

PubMed

Spellmon, Nicholas; Sun, Xiaonan; Sirinupong, Nualpun; Edwards, Brian; Li, Chunying; Yang, Zhe

2015-01-01

SMYD proteins are an exciting field of study as they are linked to many types of cancer-related pathways. Cardiac and skeletal muscle development and function also depend on SMYD proteins opening a possible avenue for cardiac-related treatment. Previous crystal structure studies have revealed that this special class of protein lysine methyltransferases have a bilobal structure, and an open-closed motion may regulate substrate specificity. Here we use the molecular dynamics simulation to investigate the still-poorly-understood SMYD2 dynamics. Cross-correlation analysis reveals that SMYD2 exhibits a negative correlated inter-lobe motion. Principle component analysis suggests that this correlated dynamic is contributed to by a twisting motion of the C-lobe with respect to the N-lobe and a clamshell-like motion between the lobes. Dynamical network analysis defines possible allosteric paths for the correlated dynamics. There are nine communities in the dynamical network with six in the N-lobe and three in the C-lobe, and the communication between the lobes is mediated by a lobe-bridging β hairpin. This study provides insight into the dynamical nature of SMYD2 and could facilitate better understanding of SMYD2 substrate specificity.

Habitat structure mediates biodiversity effects on ecosystem properties

PubMed Central

Godbold, J. A.; Bulling, M. T.; Solan, M.

2011-01-01

Much of what we know about the role of biodiversity in mediating ecosystem processes and function stems from manipulative experiments, which have largely been performed in isolated, homogeneous environments that do not incorporate habitat structure or allow natural community dynamics to develop. Here, we use a range of habitat configurations in a model marine benthic system to investigate the effects of species composition, resource heterogeneity and patch connectivity on ecosystem properties at both the patch (bioturbation intensity) and multi-patch (nutrient concentration) scale. We show that allowing fauna to move and preferentially select patches alters local species composition and density distributions, which has negative effects on ecosystem processes (bioturbation intensity) at the patch scale, but overall positive effects on ecosystem functioning (nutrient concentration) at the multi-patch scale. Our findings provide important evidence that community dynamics alter in response to localized resource heterogeneity and that these small-scale variations in habitat structure influence species contributions to ecosystem properties at larger scales. We conclude that habitat complexity forms an important buffer against disturbance and that contemporary estimates of the level of biodiversity required for maintaining future multi-functional systems may need to be revised. PMID:21227969

Self-organization of bacterial communities against environmental pH variation: Controlled chemotactic motility arranges cell population structures in biofilms

PubMed Central

Nakayama, Madoka; Shoji, Wataru

2017-01-01

As with many living organisms, bacteria often live on the surface of solids, such as foods, organisms, buildings and soil. Compared with dispersive behavior in liquid, bacteria on surface environment exhibit significantly restricted mobility. They have access to only limited resources and cannot be liberated from the changing environment. Accordingly, appropriate collective strategies are necessarily required for long-term growth and survival. However, in spite of our deepening knowledge of the structure and characteristics of individual cells, strategic self-organizing dynamics of their community is poorly understood and therefore not yet predictable. Here, we report a morphological change in Bacillus subtilis biofilms due to environmental pH variations, and present a mathematical model for the macroscopic spatio-temporal dynamics. We show that an environmental pH shift transforms colony morphology on hard agar media from notched ‘volcano-like’ to round and front-elevated ‘crater-like’. We discover that a pH-dependent dose-response relationship between nutritional resource level and quantitative bacterial motility at the population level plays a central role in the mechanism of the spatio-temporal cell population structure design in biofilms. PMID:28253348

Habitat structure mediates biodiversity effects on ecosystem properties.

PubMed

Godbold, J A; Bulling, M T; Solan, M

2011-08-22

Much of what we know about the role of biodiversity in mediating ecosystem processes and function stems from manipulative experiments, which have largely been performed in isolated, homogeneous environments that do not incorporate habitat structure or allow natural community dynamics to develop. Here, we use a range of habitat configurations in a model marine benthic system to investigate the effects of species composition, resource heterogeneity and patch connectivity on ecosystem properties at both the patch (bioturbation intensity) and multi-patch (nutrient concentration) scale. We show that allowing fauna to move and preferentially select patches alters local species composition and density distributions, which has negative effects on ecosystem processes (bioturbation intensity) at the patch scale, but overall positive effects on ecosystem functioning (nutrient concentration) at the multi-patch scale. Our findings provide important evidence that community dynamics alter in response to localized resource heterogeneity and that these small-scale variations in habitat structure influence species contributions to ecosystem properties at larger scales. We conclude that habitat complexity forms an important buffer against disturbance and that contemporary estimates of the level of biodiversity required for maintaining future multi-functional systems may need to be revised.

Self-organization of bacterial communities against environmental pH variation: Controlled chemotactic motility arranges cell population structures in biofilms.

PubMed

Tasaki, Sohei; Nakayama, Madoka; Shoji, Wataru

2017-01-01

As with many living organisms, bacteria often live on the surface of solids, such as foods, organisms, buildings and soil. Compared with dispersive behavior in liquid, bacteria on surface environment exhibit significantly restricted mobility. They have access to only limited resources and cannot be liberated from the changing environment. Accordingly, appropriate collective strategies are necessarily required for long-term growth and survival. However, in spite of our deepening knowledge of the structure and characteristics of individual cells, strategic self-organizing dynamics of their community is poorly understood and therefore not yet predictable. Here, we report a morphological change in Bacillus subtilis biofilms due to environmental pH variations, and present a mathematical model for the macroscopic spatio-temporal dynamics. We show that an environmental pH shift transforms colony morphology on hard agar media from notched 'volcano-like' to round and front-elevated 'crater-like'. We discover that a pH-dependent dose-response relationship between nutritional resource level and quantitative bacterial motility at the population level plays a central role in the mechanism of the spatio-temporal cell population structure design in biofilms.

Bacterial community dynamic associated with autochthonous bioaugmentation for enhanced Cu phytoremediation of salt-marsh sediments.

PubMed

Almeida, C Marisa R; Oliveira, Tânia; Reis, Izabela; Gomes, Carlos R; Mucha, Ana P

2017-12-01

Autochthonous bioaugmentation for metal phytoremediation is still little explored, particularly its application to estuarine salt marshes, but results obtained so far are promising. Nevertheless, understanding the behaviour of the microbial communities in the process of bioaugmentation and their role in improving metal phytoremediation is very important to fully validate the application of this biological technology. This study aimed to characterize the bacterial community dynamic associated with the application of autochthonous bioaugmentation in an experimentation which showed that Phragmites australis rhizosphere microorganisms could increase this salt marsh plant potential to phytoremediate Cu contaminated sediments. Bacterial communities present in the autochthonous microbial consortium resistant to Cu added to the medium and in the sediment at the beginning and at the end of the experiment were characterized by ARISA. Complementarily, the consortium and the sediment used for its production were characterized by next generation sequencing using the pyrosequencing platform 454. The microbial consortium resistant to Cu obtained from non-vegetated sediment was dominated by the genus Lactococcus (46%), Raoultella (25%), Bacillus (12%) and Acinetobacter (11%), whereas the one obtained form rhizosediment was dominated by the genus Gluconacetobacter (77%), Bacillus (17%) and Dyella (3%). Results clearly showed that, after two months of experiment, Cu caused a shift in the bacterial community structure of sediments, an effect that was observed either with or without addition of the metal resistant microbial consortium. Therefore, bioaugmentation application improved the process of phytoremediation (metal translocation by the plant was increased) without inducing long term changes in the bacterial community structure of the sediments. So, phytoremediation combined with autochthonous bioaugmentation can be a suitable technology for the recovery of estuarine areas, contributing for an efficient risk management strategy of these coastal zones. Copyright © 2017. Published by Elsevier Ltd.

A study of lagoonal and estuarine processes in the area of Merritt Island encompassing the space center

NASA Technical Reports Server (NTRS)

1974-01-01

A study was conducted to determine the marine biology and dynamic oceanographic properties of the Indian River in Florida. One of the major areas of concentration involved the compilation of a taxonomic list of marine animals in the river. An important conclusion of the study is that diversity of the benthic community is substantially higher than expected. The effect of major climatic factors on the diversity and structure of the benthic community is analyzed.

Temperate Snake Community in South America: Is Diet Determined by Phylogeny or Ecology?

PubMed Central

Etchepare, Eduardo G.

2015-01-01

Communities are complex and dynamic systems that change with time. The first attempts to explain how they were structured involve contemporary phenomena like ecological interactions between species (e.g., competition and predation) and led to the competition-predation hypothesis. Recently, the deep history hypothesis has emerged, which suggests that profound differences in the evolutionary history of organisms resulted in a number of ecological features that remain largely on species that are part of existing communities. Nevertheless, both phylogenetic structure and ecological interactions can act together to determine the structure of a community. Because diet is one of the main niche axes, in this study we evaluated, for the first time, the impact of ecological and phylogenetic factors on the diet of Neotropical snakes from the subtropical-temperate region of South America. Additionally, we studied their relationship with morphological and environmental aspects to understand the natural history and ecology of this community. A canonical phylogenetical ordination analysis showed that phylogeny explained most of the variation in diet, whereas ecological characters explained very little of this variation. Furthermore, some snakes that shared the habitat showed some degree of diet convergence, in accordance with the competition-predation hypothesis, although phylogeny remained the major determinant in structuring this community. The clade with the greatest variability was the subfamily Dipsadinae, whose members had a very different type of diet, based on soft-bodied invertebrates. Our results are consistent with the deep history hypothesis, and we suggest that the community under study has a deep phylogenetic effect that explains most of the variation in the diet. PMID:25945501

No association between the use of Bti for mosquito control and the dynamics of non-target aquatic invertebrates in French coastal and continental wetlands.

PubMed

Lagadic, Laurent; Schäfer, Ralf B; Roucaute, Marc; Szöcs, Eduard; Chouin, Sébastien; de Maupeou, Jérôme; Duchet, Claire; Franquet, Evelyne; Le Hunsec, Benoit; Bertrand, Céline; Fayolle, Stéphanie; Francés, Benoît; Rozier, Yves; Foussadier, Rémi; Santoni, Jean-Baptiste; Lagneau, Christophe

2016-05-15

The environmental safety of Bacillus thuringiensis subsp. israelensis (Bti) is still controversial, mainly because most of the previous field studies on its undesired effects were spatially limited and did not address the relationship between community similarity and application time and frequency. No general statement can therefore be drawn on the usage conditions of Bti that insure protection of non-target organisms. The present study was conducted in eight sites distributed over the main geographical sectors where mosquito control is implemented in mainland France and Corsica. Changes in non-target aquatic invertebrates were followed at elapsed time after repeated applications of two Bti formulations (VectoBac® WDG or 12AS) up to four consecutive years. We examined the influence of both larvicide treatments and environmental variables on community dynamics and dissimilarity between treated and control areas. As it can be argued that chironomids are the most vulnerable group of non-target invertebrates, we scrutinised potential Bti-related effects on the dynamics of their community. The use of VectoBac® WDG and 12AS in coastal and continental wetlands had no immediate or long-term detectable effect on the taxonomic structure and taxa abundance of non-target aquatic invertebrate communities, including chironomids. This applied to the main habitats where mosquito larvae occur, regardless of their geographic location. Flooding, whose frequency and duration depend on local meteorological and hydrological conditions, was identified as the main environmental driver of invertebrate community dynamics. Our findings add support to the environmental safety of currently available Bti formulations when following recommended application rates and best mosquito control practices. Copyright © 2016 Elsevier B.V. All rights reserved.

Community dynamics drive punctuated engraftment of the fecal microbiome following transplantation using freeze-dried, encapsulated fecal microbiota.

PubMed

Staley, Christopher; Vaughn, Byron P; Graiziger, Carolyn T; Singroy, Stephanie; Hamilton, Matthew J; Yao, Dan; Chen, Chi; Khoruts, Alexander; Sadowsky, Michael J

2017-05-04

Fecal microbiota transplantation (FMT) is a highly effective treatment of recurrent and recalcitrant Clostridium difficile infection (rCDI). In a recent study oral-delivery of encapsulated, freeze-dried donor material, resulted in comparable rates of cure to colonoscopic approaches. Here we characterize shifts in the fecal bacterial community structure of patients treated for rCDI using encapsulated donor material. Prior to FMT, patient fecal samples showed declines in diversity and abundance of Firmicutes and Bacteroidetes, with concurrent increases in members of the Proteobacteria, specifically Enterobacteriaceae. Moreover, patients who experienced recurrence of CDI within the 2-month clinical follow-up had greater abundances of Enterobacteriaceae and did not show resolution of dysbioses. Despite resolution of rCDI following oral-administration of encapsulated fecal microbiota, community composition was slow to return to a normal donor-like assemblage. Post-FMT taxa within the Firmicutes showed rapid increases in relative abundance and did not vary significantly over time. Conversely, Bacteroidetes taxa only showed significant increases in abundance after one month post-FMT, corresponding to significant increases in the community attributable to the donors. Changes in the associations among dominant OTUs were observed at days, weeks, and months post-FMT, suggesting shifts in community dynamics may be related to the timing of increases in abundance of specific taxa. Administration of encapsulated, freeze-dried, fecal microbiota to rCDI patients resulted in restoration of bacterial diversity and resolution of dysbiosis. However, shifts in the fecal microbiome were incremental rather than immediate, and may be driven by changes in community dynamics reflecting changes in the host environment.

Biogeography and body size shuffling of aquatic salamander communities on a shifting refuge

PubMed Central

Bonett, Ronald M.; Trujano-Alvarez, Ana Lilia; Williams, Michael J.; Timpe, Elizabeth K.

2013-01-01

Freshwater habitats of coastal plains are refugia for many divergent vertebrate lineages, yet these environments are highly vulnerable to sea-level fluctuations, which suggest that resident communities have endured dynamic histories. Using the fossil record and a multi-locus nuclear phylogeny, we examine divergence times, biogeography, body size evolution and patterns of community assembly of aquatic salamanders from North American coastal plains since the Late Cretaceous. At least five salamander families occurred on the extensive Western Interior Coastal Plain (WICP), which existed from the Late Cretaceous through the Eocene. Four of these families subsequently colonized the emergent Southeastern Coastal Plain (SECP) by the Early Oligocene to Late Miocene. Three families ultimately survived and underwent extensive body size evolution in situ on the SECP. This included at least two major size reversals in recent taxa that are convergent with confamilial WICP ancestors. Dynamics of the coastal plain, major lineage extinctions and frequent extreme changes in body size have resulted in significant shuffling of the size structure of aquatic salamander communities on this shifting refuge since the Cretaceous. PMID:23466988

The dynamic changes and interactional networks of prokaryotic community between co-digestion and mono-digestions of corn stalk and pig manure.

PubMed

Wang, Min; Zhang, Xueying; Zhou, Jun; Yuan, Yuexiang; Dai, Yumei; Li, Dong; Li, Zhidong; Liu, Xiaofeng; Yan, Zhiying

2017-02-01

Anaerobic co-digestion is considered to be an efficient way to improve the biogas production. The abundance, dynamic and interactional networks of prokaryotic community were investigated between co-digestion and mono-digestions of corn stalk and pig manure in mesophilic batch test. Co-digestion showed higher methane production, and contributed to suitable microenvironment as well as stable prokaryotic community structure. The highest methane production was achieved with the highest relative abundance of Methanosaeta. Prokaryotic community in mono-digestions might inhibited by FA or FVFA. The functional modules in co-digestion and mono-digestion of pig manure clustered together with bigger size and higher degree, and the connections of metabolic functions were better-organized, which means high-efficient utilization of substrate and prevention of the two digestion systems crash. The partial mantel tests showed the functional modules were significantly affected by environmental factors. These results further explained that why co-digestion was more efficient than mono-digestion owing to suitable microenvironment. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

The vesicomyid bivalve habitat at cold seeps supports heterogeneous and dynamic macrofaunal assemblages

NASA Astrophysics Data System (ADS)

Guillon, Erwan; Menot, Lénaïck; Decker, Carole; Krylova, Elena; Olu, Karine

2017-02-01

The high biodiversity found at cold seeps, despite elevated concentrations of methane and hydrogen sulfide, is attributed to multiple sources of habitat heterogeneity. In addition to geological and geochemical processes, biogenic habitats formed by large symbiont-bearing taxa, such as bivalves and siboglinid tubeworms, or by microbial mats drive the biodiversity of small-sized fauna. However, because these habitat-forming species also depend on geochemical gradients, the respective influence of abiotic and biotic factors in structuring associated macrofaunal communities is often unresolved. The giant pockmark Regab located at 3200 m depth on the Congo margin is characterized by different fluid-flow regimes, providing a mosaic of the most common biogenic habitats encountered at seeps: microbial mats, mussel beds, and vesicomyid clam beds; the latter being distributed along a gradient of environmental conditions from the center to the periphery of the pockmark. Here, we examined the structure of macrofaunal communities in biogenic habitats formed in soft sediment to (1) determine the influence of the habitats on the associated macrofaunal communities (inter-habitat comparison), (2) describe how macrofaunal communities vary among vesicomyid clam beds (intra-habitat comparison) and (3) assess the inter-annual variation in vesicomyid beds based on repeated sampling at a three-year interval. The highest densities were found in the microbial mat communities in intermediate fluid-flow areas, but they had low diversity - also observed in the sediment close to mussel beds. In contrast, vesicomyid beds harbored the highest diversity. The vesicomyid beds did not show a homogeneous macrofaunal community across sampled areas; instead, density and composition of macrofauna varied according to the location of the beds inside the pockmark. The clam bed sampled in the most active, central part of the pockmark resembled bacterial mat communities by the presence of highly sulfide-tolerant species living at the sediment surface, along with vesicomyid juveniles. This similarity suggests a gradual change in community composition from mats to clam beds. Inter-annual comparisons of the different clam beds highlighted that the most active central site had a more variable community than its peripheral counterparts. Finally, a rapid shift in community structure, particularly in polychaete families, in experimentally reduced oxygen concentrations in the central part of Regab, suggests that high beta-diversity communities can withstand intense variation in geochemical conditions. These community dynamics are likely related to the diversity and to the plasticity of the vesicomyids themselves, because they can cope with high spatial and temporal environmental variability at a very local scale.

A Functional Cartography of Cognitive Systems

PubMed Central

Mattar, Marcelo G.; Cole, Michael W.; Thompson-Schill, Sharon L.; Bassett, Danielle S.

2015-01-01

One of the most remarkable features of the human brain is its ability to adapt rapidly and efficiently to external task demands. Novel and non-routine tasks, for example, are implemented faster than structural connections can be formed. The neural underpinnings of these dynamics are far from understood. Here we develop and apply novel methods in network science to quantify how patterns of functional connectivity between brain regions reconfigure as human subjects perform 64 different tasks. By applying dynamic community detection algorithms, we identify groups of brain regions that form putative functional communities, and we uncover changes in these groups across the 64-task battery. We summarize these reconfiguration patterns by quantifying the probability that two brain regions engage in the same network community (or putative functional module) across tasks. These tools enable us to demonstrate that classically defined cognitive systems—including visual, sensorimotor, auditory, default mode, fronto-parietal, cingulo-opercular and salience systems—engage dynamically in cohesive network communities across tasks. We define the network role that a cognitive system plays in these dynamics along the following two dimensions: (i) stability vs. flexibility and (ii) connected vs. isolated. The role of each system is therefore summarized by how stably that system is recruited over the 64 tasks, and how consistently that system interacts with other systems. Using this cartography, classically defined cognitive systems can be categorized as ephemeral integrators, stable loners, and anything in between. Our results provide a new conceptual framework for understanding the dynamic integration and recruitment of cognitive systems in enabling behavioral adaptability across both task and rest conditions. This work has important implications for understanding cognitive network reconfiguration during different task sets and its relationship to cognitive effort, individual variation in cognitive performance, and fatigue. PMID:26629847

Jellyfish modulate bacterial dynamic and community structure.

PubMed

Tinta, Tinkara; Kogovšek, Tjaša; Malej, Alenka; Turk, Valentina

2012-01-01

Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into possible changes in bacterial population dynamics and nutrient pathways following jellyfish blooms which have important implications for ecology of coastal waters.

Seasonal variability in airborne bacterial communities at a high elevation site and their relationship to other air studies and to potential sources

NASA Astrophysics Data System (ADS)

Bowers, R. M.; Mccubbin, I. B.; Hallar, A. G.; Fierer, N.

2012-12-01

Airborne bacteria are a large component of the near-surface atmospheric aerosol; however we know surprisingly little about their spatiotemporal dynamics and even less about their distributions at high-elevation. With this work, we describe seasonal shifts in bacterial abundances, total particle abundances, and bacterial community structure at a high-elevation research station located in Colorado, USA. In addition, we describe the unique composition of these high-elevation airborne bacterial communities as compared to the bacteria commonly observed throughout the lower elevation atmosphere as well as bacteria common to major sources such as leaf surfaces, soils, water bodies and various other surfaces. To address these knowledge gaps, we collected aerosol samples on the rooftop of Storm Peak Laboratory (3200 m ASL) over the course of 2-3 week periods during each of the four calendar seasons. Total bacterial abundances were assessed via flow cytometry, total particle abundances were calculated with an aerodynamic particle sizer, and bacterial communities were characterized using a high-throughput barcoded DNA sequencing approach. The airborne bacterial communities at Storm Peak Lab were then used in a meta-analysis comparing Storm Peak bacteria to other near-surface (lower elevation) bacterial communities and to the communities of likely source environments. Bacterial abundances varied by season, which was similar but not identical to the changes in total particle abundances across the same sampling period. Airborne bacterial community structure varied significantly by season, with the summer communities being the most distinct. Season specific bacterial groups were identified, suggesting that a large proportion of the airborne community may be derived from nearby sources. However following a multi-environment meta-analysis using several air and source derived bacterial community datasets, the high-elevation air communities were the most distinct as compared to the other airborne communities used in the analysis. Furthermore, a very low proportion of the Storm Peak airborne community could be explained by the source environments used in the meta-analysis, suggesting a unique airborne community at high-elevation. High-alpine bacterial communities appear to make up a large fraction of the total atmospheric aerosol, however the different seasonal patterns between bacterial counts and total particle counts suggest that distinct factors control the quantities of different particles making it into the atmosphere. Furthermore, the characteristics of local terrestrial sources that undergo seasonal cycles seem to have a large influence on the airborne communities, but these sources could not explain the occurrence of all airborne bacterial taxa. As airborne bacteria are more commonly being recognized as a ubiquitous component of the atmosphere, a better understanding of their temporal dynamics in the high-alpine environment may give us insight into their many potential roles in atmospheric dynamics, free troposphere atmospheric dispersal patterns, and their role in human and environmental health.

Elevated enzyme activities in soils under the invasive nitrogen-fixing tree Falcataria moluccana

Treesearch

Steven D. Allison; Caroline Nielsen; R. Flint Hughes

2006-01-01

Like other N-fixing invasive species in Hawaii, Falcataria moluccana dramatically alters forest structure, litterfall quality and quantity, and nutrient dynamics. We hypothesized that these biogeochemical changes would also affect the soil microbial community and the extracellular enzymes responsible for carbon and nutrient mineralization. Across...

Influences of environment and disturbance on forest patterns in coastal Oregon watersheds.

Treesearch

Michael C. Wimberly; Thomas A. Spies

2001-01-01

Modern ecology often emphasizes the distinction between traditional theories of stable, environmentally structured communities and a new paradigm of disturbance driven, nonequilibrium dynamics. However, multiple hypotheses for observed vegetation patterns have seldom been explicitly tested. We used multivariate statistics and variation partitioning methods to assess...

Evaluation of Participatory Research in Developing Community Leadership Skills.

ERIC Educational Resources Information Center

Karim, Wazir-Jahan B.

1982-01-01

This paper attempts to evaluate and explain the dynamic processes of decision-making and leadership development through participatory research, using the Malaysian experience as a case study. The focus is on the structural and situational constraints in the Malaysian rural society, the formal political machinery and the implementation of…

Socioecological disparities in New Orleans following Hurricane Katrina

Treesearch

Joshua A. Lewis; Wayne C. Zipperer; Henrik Ernstson; Brittany Bernik; Rebecca Hazen; Thomas Elmqvist; Michael J. Blum

2017-01-01

Despite growing interest in urban resilience, remarkably little is known about vegetation dynamics in the aftermath of disasters. In this study, we examined the composition and structure of plant communities across New Orleans (Louisiana, USA) following catastrophic flooding triggered by levee failures during Hurricane Katrina in 2005. Focusing on eight...

Wetlands for Wastewater: a Visual Approach to Microbial Dynamics

NASA Astrophysics Data System (ADS)

Joubert, L.; Wolfaardt, G.; Du Plessis, K.

2007-12-01

The complex character of distillery wastewater comprises high concentrations of sugars, lignins, hemicelluloses, dextrans, resins, polyphenols and organic acids which are recalcitrant to biodegradation. Microorganisms play a key role in the production and degradation of organic matter, environmental pollutants, and cycling of nutrients and metals. Due to their short life cycles microbes respond rapidly to external nutrient loading, with major consequences for the stability of biological systems. We evaluated the feasibility of wetlands to treat winery and distillery effluents in experimental systems based on constructed wetlands, including down-scaled on-site distillery wetlands, small-scale controlled greenhouse systems, and bench-scale mesocosms. Chemical, visual and molecular fingerprinting (t-RFLP) techniques were applied to study the dynamics of planktonic and attached (biofilm) communities at various points in wetlands of different size, retention time and geological substrate, and under influence of shock nutrient loadings. Variable- Pressure Scanning Electron Microscopy (VP-SEM) was applied to visualize microbial colonization, morphotype diversity and distribution, and 3D biofilm architecture. Cross-taxon and predator-prey interactions were markedly influenced by organic loading, while the presence of algae affected microbial community composition and biofilm structure. COD removal varied with geological substrate, and was positively correlated with retention time in gravel wetlands. Planktonic and biofilm communities varied markedly in different regions of the wetland and over time, as indicated by whole-community t-RFLP and VP-SEM. An integrative visual approach to community dynamics enhanced data retrieval not afforded by molecular techniques alone. The high microbial diversity along spatial and temporal gradients, and responsiveness to the physico-chemical environment, suggest that microbial communities maintain metabolic function by modifying species composition in response to fluctuations in their environment. It seems apparent that microbial community plasticity may indeed be the distinguishing characteristic of a successful wetland system.

Rapid changes and long-term cycles in the benthic megafaunal community observed over 24 years in the abyssal northeast Pacific

NASA Astrophysics Data System (ADS)

Kuhnz, Linda A.; Ruhl, Henry A.; Huffard, Christine L.; Smith, Kenneth L.

2014-05-01

The abyssal seafloor community in the NE Pacific (Station M, ∼4000 m depth) was studied between 2006 and 2012 using remotely operated vehicles (ROVs) as part of a continuing 24-year time-series study. New patterns continue to emerge showing that the deep-sea can be dynamic on short time scales, rather than static over long periods. In just over 2 years the community shifted from a sessile, suspension-feeding, sponge-dominated community to a mobile, detritus-feeding, sea cucumber-dominated assemblage. In 2006 megafaunal diversity (Simpson’s Diversity Index, SDI) was high, yet the community was depauperate in terms of density compared to later periods. Over an 18-month period beginning in spring 2011, the densities of mobile organisms increased by nearly an order of magnitude while diversity decreased below 2006 levels. In late 2012 four sea cucumbers (two Peniagone spp., Elpidia sp. A, and Scotoplanes globosa) were at the highest densities recorded since investigations began at Station M in 1989. For a group of 10 echinoderms investigated over the entire study period, we saw evidence of a long-term cycle spanning 2 decades. These changes can be tied to a variable food supply originating in shallow water. Large variations over decadal-scales indicate that remote abyssal communities are dynamic and likely subject to impacts from anthropogenic changes like ocean warming, acidification, and pollution manifested in the upper ocean. The degree of dynamism indicates that one-time or short-term investigations are not sufficient for assessing biological community structure in conservation or exploitation studies in the deep sea.

Health Disparity and Structural Violence: How Fear Undermines Health Among Immigrants at Risk for Diabetes

PubMed Central

Page-Reeves, Janet; Niforatos, Joshua; Mishra, Shiraz; Regino, Lidia; Gingrich, Andrew; Bulten, Robert

2013-01-01

Diabetes is a national health problem, and the burden of the disease and its consequences particularly affect Hispanics. While social determinants of health models have improved our conceptualization of how certain contexts and environments influence an individual's ability to make healthy choices, a structural violence framework transcends traditional uni-dimensional analysis. Thus, a structural violence approach is capable of revealing dynamics of social practices that operate across multiple dimensions of people's lives in ways that may not immediately appear related to health. Working with a Hispanic immigrant community in Albuquerque, New Mexico, we demonstrate how structural forces simultaneously directly inhibit access to appropriate healthcare services and create fear among immigrants, acting to further undermine health and nurture disparity. Although fear is not normally directly associated with diabetes health outcomes, in the community where we conducted this study participant narratives discussed fear and health as interconnected. PMID:24052924

A 454 Survey Reveals the Community Composition and Core Microbiome of the Common Bed Bug (Cimex lectularius) across an Urban Landscape

PubMed Central

Meriweather, Matthew; Matthews, Sara; Rio, Rita; Baucom, Regina S.

2013-01-01

Elucidating the spatial dynamic and core constituents of the microbial communities found in association with arthropod hosts is of crucial importance for insects that may vector human or agricultural pathogens. The hematophagous Cimex lectularius (Hemiptera: Cimicidae), known as the human bed bug, has made a recent resurgence in North America, as well as worldwide, potentially owing to increased travel, climate change and resistance to insecticides. A comprehensive survey of the bed bug microbiome has not been performed to date, nor has an assessment of the spatial dynamics of its microbiome. Here we present a survey of internal and external bed bug microbial communities by amplifying the V4–V6 hypervariable region of the 16S rDNA gene region followed by 454 Titanium sequencing using 31 individuals from eight distinct collection locations obtained from residences in Cincinnati, OH. Across all samples, 97% of the microbial community is made up of two dominant OTUs, previously identified as the α-proteobacterium Wolbachia and an unnamed γ-proteobacterium from the Enterobacteriaceae. Microbial communities varied among host locations for measures of community diversity and exhibited structure according to collection location. This broad survey represents the most in-depth assessment, to date, of the microbes that associate with bed bugs. PMID:23585900

A 454 survey reveals the community composition and core microbiome of the common bed bug (Cimex lectularius) across an Urban Landscape.

PubMed

Meriweather, Matthew; Matthews, Sara; Rio, Rita; Baucom, Regina S

2013-01-01

Elucidating the spatial dynamic and core constituents of the microbial communities found in association with arthropod hosts is of crucial importance for insects that may vector human or agricultural pathogens. The hematophagous Cimex lectularius (Hemiptera: Cimicidae), known as the human bed bug, has made a recent resurgence in North America, as well as worldwide, potentially owing to increased travel, climate change and resistance to insecticides. A comprehensive survey of the bed bug microbiome has not been performed to date, nor has an assessment of the spatial dynamics of its microbiome. Here we present a survey of internal and external bed bug microbial communities by amplifying the V4-V6 hypervariable region of the 16S rDNA gene region followed by 454 Titanium sequencing using 31 individuals from eight distinct collection locations obtained from residences in Cincinnati, OH. Across all samples, 97% of the microbial community is made up of two dominant OTUs, previously identified as the α-proteobacterium Wolbachia and an unnamed γ-proteobacterium from the Enterobacteriaceae. Microbial communities varied among host locations for measures of community diversity and exhibited structure according to collection location. This broad survey represents the most in-depth assessment, to date, of the microbes that associate with bed bugs.

Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate‐reducing benthic microbial populations

PubMed Central

Saad, Sainab; Bhatnagar, Srijak; Tegetmeyer, Halina E.; Geelhoed, Jeanine S.; Strous, Marc

2017-01-01

Summary For the anaerobic remineralization of organic matter in marine sediments, sulfate reduction coupled to fermentation plays a key role. Here, we enriched sulfate‐reducing/fermentative communities from intertidal sediments under defined conditions in continuous culture. We transiently exposed the cultures to oxygen or nitrate twice daily and investigated the community response. Chemical measurements, provisional genomes and transcriptomic profiles revealed trophic networks of microbial populations. Sulfate reducers coexisted with facultative nitrate reducers or aerobes enabling the community to adjust to nitrate or oxygen pulses. Exposure to oxygen and nitrate impacted the community structure, but did not suppress fermentation or sulfate reduction as community functions, highlighting their stability under dynamic conditions. The most abundant sulfate reducer in all cultures, related to Desulfotignum balticum, appeared to have coupled both acetate‐ and hydrogen oxidation to sulfate reduction. We describe a novel representative of the widespread uncultured candidate phylum Fermentibacteria (formerly candidate division Hyd24‐12). For this strictly anaerobic, obligate fermentative bacterium, we propose the name ‘USabulitectum silens’ and identify it as a partner of sulfate reducers in marine sediments. Overall, we provide insights into the function of fermentative, as well as sulfate‐reducing microbial communities and their adaptation to a dynamic environment. PMID:28836729

Proposed military handbook for dynamic data acquisition and analysis - An invitation to review

NASA Technical Reports Server (NTRS)

Himelblau, Harry; Wise, James H.; Piersol, Allan G.; Grundvig, Max R.

1990-01-01

A draft Military Handbook prepared under the sponsorship of the USAF Space Division is presently being distributed throughout the U.S. for review by the aerospace community. This comprehensive document provides recommended guidelines for the acquisition and analysis of structural dynamics and aeroacoustic data, and is intended to reduce the errors and variability commonly found in flight, ground and laboratory dynamic test measurements. In addition to the usual variety of measurement problems encountered in the definition of dynamic loads, the development of design and test criteria, and the analysis of failures, special emphasis is given to certain state-of-the-art topics, such as pyroshock data acquisition and nonstationary random data analysis.

Succession and regulation factors of small eukaryote community composition in a lacustrine ecosystem (Lake Pavin).

PubMed

Lepère, Cécile; Boucher, Delphine; Jardillier, Ludwig; Domaizon, Isabelle; Debroas, Didier

2006-04-01

The structure and dynamics of small eukaryotes (cells with a diameter less than 5 microm) were studied over two consecutive years in an oligomesotrophic lake (Lake Pavin in France). Water samples were collected at 5 and 30 m below the surface; when the lake was stratified, these depths corresponded to the epilimnion and hypolimnion. Changes in small-eukaryote structure were analyzed using terminal restriction fragment length polymorphism (T-RFLP) and cloning and sequencing of the 18S rRNA genes. Terminal restriction fragments from clones were used to reveal the dominant taxa in T-RFLP profiles of the environmental samples. Spumella-like cells (Chrysophyceae) did not dominate the small eukaryote community identified by molecular techniques in lacustrine ecosystems. Small eukaryotes appeared to be dominated by heterotrophic cells, particularly Cercozoa, which represented nearly half of the identified phylotypes, followed by the Fungi-LKM11 group (25%), choanoflagellates (10.3%) and Chrysophyceae (8.9%). Bicosoecida, Cryptophyta, and ciliates represented less than 9% of the community studied. No seasonal reproducibility in temporal evolution of the small-eukaryote community was observed from 1 year to the next. The T-RFLP patterns were related to bottom-up (resources) and top-down (grazing) variables using canonical correspondence analysis. The results showed a strong top-down regulation of small eukaryotes by zooplankton, more exactly, by cladocerans at 5 m and copepods at 30 m. Among bottom-up factors, temperature had a significant effect at both depths. The concentrations of nitrogenous nutrients and total phosphorus also had an effect on small-eukaryote dynamics at 5 m, whereas bacterial abundance and dissolved oxygen played a more important structuring role in the deeper zone.

Rotary-Balance Testing for Aircraft Dynamics (Les Essais sur Balance Rotative pour l’Etude de la Dynamique du Vol de l’Avion)

DTIC Science & Technology

1990-01-01

critical examination of the rotary-balance techniques used in the AGARD community for the analysis of high-angle-of-attack dynamic behavior of aircraft. It...aircraft. It was felt that sudi a critical examination should encompass both the experimental techniques used to obtain rotary-flow aerodynamic data and the...monitor the vibrational and critical structural characteristies of the apparatus and tunnel support system. Many of these systems are integrated directly

The effects of hydrological dynamics on benthic diatom community structure in a highly stratified estuary: The case of the Ebro Estuary (Catalonia, Spain)

NASA Astrophysics Data System (ADS)

Rovira, L.; Trobajo, R.; Leira, M.; Ibáñez, C.

2012-04-01

This study of the distribution of benthic diatom assemblages and their relationship with environmental factors in a highly stratified Mediterranean estuary, i.e. the Ebro Estuary, shows the importance of hydrological dynamics to explain the features of the diatom community in such an estuary, where river flow magnitude and fluctuations imply strong physicochemical variability especially in sites close to the sea. Eight sites along the estuary were sampled during 2007-2008 both at superficial and deep water layers, in order to gather both horizontal and vertical estuarine physicochemical and hydrological gradients. Canonical Variates Analysis and Hierarchical Cluster Analysis segregated diatom community in two assemblages depending on the dynamics of the salt-wedge. The diatom assemblages of riverine conditions (i.e. without salt-wedge influence) where characterised by high abundances of Cocconeis placentula var. euglypta and Amphora pediculus, meanwhile high abundances of Nizschia frustulum and Nitzschia inconspicua were characteristic of estuarine conditions (i.e. under salt-wedge influence). Redundancy Analysis showed that both diatom assemblages responded seasonally to Ebro River flows, especially in estuarine conditions, where fluctuating conditions affected diatom assemblages both at spatial and temporal scale.

Rice root-associated bacteria – insights in community structures across ten cultivars

PubMed Central

Hardoim, Pablo Rodrigo; Andreote, Fernando Dini; Reinhold-Hurek, Barbara; Sessitsch, Angela; van Overbeek, Leonard Simon; van Elsas, Jan Dirk

2015-01-01

In this study, the effect of plant genotype, soil type and nutrient use efficiency on the composition of different bacterial communities associated with rice roots were investigated. Thus, total bacteria, Alpha- and Beta-proteobacteria, Pseudomonas and Actinobacteria were studied using PCR followed by denaturing gradient gel electrophoresis (PCR-DGGE). Rice genotype determined to a large extent the composition of the different bacterial communities across cultivars. Several cultivars belonging to Oryza sativa subspecies indica tended to select similar bacterial communities, whereas those belonging to subspecies japonica and aromatica selected ones with divergent community structures. An effect of soil type was pronounced for the Actinobacteria communities, while a small effect of ‘improved’ and ‘traditional’ plants was noted for all communities analysed. A few dominant bands in PCR-DGGE, affiliated with Rhizobium radiobacter, Dickeya zeae, Mycobacterium bolletii and with members of the Rhizobiales, Rhodospirillaceae and Paenibacillaceae were spread across cultivars. In contrast, a majority of bands (e.g. affiliated with Enterobacter cloacae or Burkholderia kururiensis) was only present in particular cultivars or was erratically distributed amongst rice replicates. The data suggested that both bacterial adaptation and plant genotype contribute to the shaping of the dynamic bacterial communities associated with roots of rice plants. PMID:21426364

Community structures and population dynamics of "Candidatus Accumulibacter" in activated sludges of wastewater treatment plants using ppk1 as phylogenetic marker.

PubMed

Zeng, Wei; Zhang, Limin; Fan, Pengchao; Guo, Jingjing; Peng, Yongzhen

2018-05-01

Candidatus Accumulibacter has been identified as dominant polyphosphate-accumulating organisms (PAOs) in enhanced biological phosphorus (P) removal (EBPR) from wastewater. This study revealed the relevance of community structure, abundance and seasonal population dynamics of Candidatus Accumulibacter to process operation of wastewater treatment plants (WWTPs) in China using ppk1 gene as phylogenetic marker. All sludge samples had properties of denitrifying P removal using nitrate as an electron acceptor. Accumulibacter abundance in the anaerobic-anoxic-oxic (A 2 O) process was the highest (26% of total bacteria), and higher in winter than in summer with a better EBPR performance. Type-II was the dominant Accumulibacter in all processes, and type-I accounted for a small proportion of total Accumulibacter. The abundance of Clade-IIC as the most dominant clade reached 2.59×10 9 cells/g MLSS and accounted for 87.3% of total Accumulibacter. Clade IIC mainly contributed to denitrifying P removal. Clades IIA, IIC and IID were found in all processes, while clade-IIF was only found in oxidation ditch process through phylogenetic analysis. High proportion of clade IID to total Accumulibacter led to poor performance of aerobic P-uptake in inverted A 2 O process. Therefore, Accumulibacter clades in WWTPs were diverse, and EBPR performance was closely related to the clade-level community structures and abundances of Accumulibacter. Copyright © 2017. Published by Elsevier B.V.

Hydrology Affects Environmental and Spatial Structuring of Microalgal Metacommunities in Tropical Pacific Coast Wetlands.

PubMed

Rojo, Carmen; Mesquita-Joanes, Francesc; Monrós, Juan S; Armengol, Javier; Sasa, Mahmood; Bonilla, Fabián; Rueda, Ricardo; Benavent-Corai, José; Piculo, Rubén; Segura, M Matilde

2016-01-01

The alternating climate between wet and dry periods has important effects on the hydrology and therefore on niche-based processes of water bodies in tropical areas. Additionally, assemblages of microorganism can show spatial patterns, in the form of a distance decay relationship due to their size or life form. We aimed to test spatial and environmental effects, modulated by a seasonal flooding climatic pattern, on the distribution of microalgae in 30 wetlands of a tropical dry forest region: the Pacific coast of Costa Rica and Nicaragua. Three surveys were conducted corresponding to the beginning, the highest peak, and the end of the hydrological year during the wet season, and species abundance and composition of planktonic and benthic microalgae was determined. Variation partitioning analysis (as explained by spatial distance or environmental factors) was applied to each seasonal dataset by means of partial redundancy analysis. Our results show that microalgal assemblages were structured by spatial and environmental factors depending on the hydrological period of the year. At the onset of hydroperiod and during flooding, neutral effects dominated community dynamics, but niche-based local effects resulted in more structured algal communities at the final periods of desiccating water bodies. Results suggest that climate-mediated effects on hydrology can influence the relative role of spatial and environmental factors on metacommunities of microalgae. Such variability needs to be accounted in order to describe accurately community dynamics in tropical coastal wetlands.

Hydrology Affects Environmental and Spatial Structuring of Microalgal Metacommunities in Tropical Pacific Coast Wetlands

PubMed Central

Rojo, Carmen; Mesquita-Joanes, Francesc; Monrós, Juan S.; Armengol, Javier; Sasa, Mahmood; Bonilla, Fabián; Rueda, Ricardo; Benavent-Corai, José; Piculo, Rubén; Segura, M. Matilde

2016-01-01

The alternating climate between wet and dry periods has important effects on the hydrology and therefore on niche-based processes of water bodies in tropical areas. Additionally, assemblages of microorganism can show spatial patterns, in the form of a distance decay relationship due to their size or life form. We aimed to test spatial and environmental effects, modulated by a seasonal flooding climatic pattern, on the distribution of microalgae in 30 wetlands of a tropical dry forest region: the Pacific coast of Costa Rica and Nicaragua. Three surveys were conducted corresponding to the beginning, the highest peak, and the end of the hydrological year during the wet season, and species abundance and composition of planktonic and benthic microalgae was determined. Variation partitioning analysis (as explained by spatial distance or environmental factors) was applied to each seasonal dataset by means of partial redundancy analysis. Our results show that microalgal assemblages were structured by spatial and environmental factors depending on the hydrological period of the year. At the onset of hydroperiod and during flooding, neutral effects dominated community dynamics, but niche-based local effects resulted in more structured algal communities at the final periods of desiccating water bodies. Results suggest that climate-mediated effects on hydrology can influence the relative role of spatial and environmental factors on metacommunities of microalgae. Such variability needs to be accounted in order to describe accurately community dynamics in tropical coastal wetlands. PMID:26900916

Noah’s Ark Conservation Will Not Preserve Threatened Ecological Communities under Climate Change

PubMed Central

Harris, Rebecca Mary Bernadette; Carter, Oberon; Gilfedder, Louise; Porfirio, Luciana Laura; Lee, Greg; Bindoff, Nathaniel Lee

2015-01-01

Background Effective conservation of threatened ecological communities requires knowledge of where climatically suitable habitat is likely to persist into the future. We use the critically endangered Lowland Grassland community of Tasmania, Australia as a case study to identify options for management in cases where future climatic conditions become unsuitable for the current threatened community. Methods We model current and future climatic suitability for the Lowland Themeda and the Lowland Poa Grassland communities, which make up the listed ecological community. We also model climatic suitability for the structurally dominant grass species of these communities, and for closely related grassland and woodland communities. We use a dynamically downscaled regional climate model derived from six CMIP3 global climate models, under the A2 SRES emissions scenario. Results All model projections showed a large reduction in climatically suitable area by mid-century. Outcomes are slightly better if closely related grassy communities are considered, but the extent of suitable area is still substantially reduced. Only small areas within the current distribution are projected to remain climatically suitable by the end of the century, and very little of that area is currently in good condition. Conclusions As the climate becomes less suitable, a gradual change in the species composition, structure and habitat quality of the grassland communities is likely. Conservation management will need to focus on maintaining diversity, structure and function, rather than attempting to preserve current species composition. Options for achieving this include managing related grassland types to maintain grassland species at the landscape-scale, and maximising the resilience of grasslands by reducing further fragmentation, weed invasion and stress from other land uses, while accepting that change is inevitable. Attempting to maintain the status quo by conserving the current structure and composition of Lowland Grassland communities is unlikely to be a viable management option in the long term. PMID:25881302

Noah's Ark conservation will not preserve threatened ecological communities under climate change.

PubMed

Harris, Rebecca Mary Bernadette; Carter, Oberon; Gilfedder, Louise; Porfirio, Luciana Laura; Lee, Greg; Bindoff, Nathaniel Lee

2015-01-01

Effective conservation of threatened ecological communities requires knowledge of where climatically suitable habitat is likely to persist into the future. We use the critically endangered Lowland Grassland community of Tasmania, Australia as a case study to identify options for management in cases where future climatic conditions become unsuitable for the current threatened community. We model current and future climatic suitability for the Lowland Themeda and the Lowland Poa Grassland communities, which make up the listed ecological community. We also model climatic suitability for the structurally dominant grass species of these communities, and for closely related grassland and woodland communities. We use a dynamically downscaled regional climate model derived from six CMIP3 global climate models, under the A2 SRES emissions scenario. All model projections showed a large reduction in climatically suitable area by mid-century. Outcomes are slightly better if closely related grassy communities are considered, but the extent of suitable area is still substantially reduced. Only small areas within the current distribution are projected to remain climatically suitable by the end of the century, and very little of that area is currently in good condition. As the climate becomes less suitable, a gradual change in the species composition, structure and habitat quality of the grassland communities is likely. Conservation management will need to focus on maintaining diversity, structure and function, rather than attempting to preserve current species composition. Options for achieving this include managing related grassland types to maintain grassland species at the landscape-scale, and maximising the resilience of grasslands by reducing further fragmentation, weed invasion and stress from other land uses, while accepting that change is inevitable. Attempting to maintain the status quo by conserving the current structure and composition of Lowland Grassland communities is unlikely to be a viable management option in the long term.

Ontogenetic functional diversity: size structure of a keystone predator drives functioning of a complex ecosystem.

PubMed

Rudolf, Volker H W; Rasmussen, Nick L

2013-05-01

A central challenge in community ecology is to understand the connection between biodiversity and the functioning of ecosystems. While traditional approaches have largely focused on species-level diversity, increasing evidence indicates that there exists substantial ecological diversity among individuals within species. By far, the largest source of this intraspecific diversity stems from variation among individuals in ontogenetic stage and size. Although such ontogenetic shifts are ubiquitous in natural communities, whether and how they scale up to influence the structure and functioning of complex ecosystems is largely unknown. Here we take an experimental approach to examine the consequences of ontogenetic niche shifts for the structure of communities and ecosystem processes. In particular we experimentally manipulated the stage structure in a keystone predator, larvae of the dragonfly Anax junius, in complex experimental pond communities to test whether changes in the population stage or size structure of a keystone species scale up to alter community structure and ecosystem processes, and how functional differences scale with relative differences in size among stages. We found that the functional role of A. junius was stage-specific. Altering what stages were present in a pond led to concurrent changes in community structure, primary producer biomass (periphyton and phytoplankton), and ultimately altered ecosystem processes (respiration and net primary productivity), indicating a strong, but stage-specific, trophic cascade. Interestingly, the stage-specific effects did not simply scale with size or biomass of the predator, but instead indicated clear ontogenetic niche shifts in ecological interactions. Thus, functional differences among stages within a keystone species scaled up to alter the functioning of entire ecosystems. Therefore, our results indicate that the classical approach of assuming an average functional role of a species can be misleading because functional roles are dynamic and will change with shifts in the stage structure of the species. In general this emphasizes the importance of accounting for functional diversity below the species level to predict how natural and anthropogenic changes alter the functioning of natural ecosystems.

Dynamics of coral-associated microbiomes during a thermal bleaching event.

PubMed

Pootakham, Wirulda; Mhuantong, Wuttichai; Putchim, Lalita; Yoocha, Thippawan; Sonthirod, Chutima; Kongkachana, Wasitthee; Sangsrakru, Duangjai; Naktang, Chaiwat; Jomchai, Nukoon; Thongtham, Nalinee; Tangphatsornruang, Sithichoke

2018-03-23

Coral-associated microorganisms play an important role in their host fitness and survival. A number of studies have demonstrated connections between thermal tolerance in corals and the type/relative abundance of Symbiodinium they harbor. More recently, the shifts in coral-associated bacterial profiles were also shown to be linked to the patterns of coral heat tolerance. Here, we investigated the dynamics of Porites lutea-associated bacterial and algal communities throughout a natural bleaching event, using full-length 16S rRNA and internal transcribed spacer sequences (ITS) obtained from PacBio circular consensus sequencing. We provided evidence of significant changes in the structure and diversity of coral-associated microbiomes during thermal stress. The balance of the symbiosis shifted from a predominant association between corals and Gammaproteobacteria to a predominance of Alphaproteobacteria and to a lesser extent Betaproteobacteria following the bleaching event. On the contrary, the composition and diversity of Symbiodinium communities remained unaltered throughout the bleaching event. It appears that the switching and/or shuffling of Symbiodinium types may not be the primary mechanism used by P. lutea to cope with increasing seawater temperature. The shifts in the structure and diversity of associated bacterial communities may contribute more to the survival of the coral holobiont under heat stress. © 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

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.

Persistence and diversification of the Holarctic shrew, Sorex tundrensis (Family Soricidae), in response to climate change

USGS Publications Warehouse

Hope, A.G.; Waltari, Eric; Fedorov, V.B.; Goropashnaya, A.V.; Talbot, S.L.; Cook, J.A.

2011-01-01

Environmental processes govern demography, species movements, community turnover and diversification and yet in many respects these dynamics are still poorly understood at high latitudes. We investigate the combined effects of climate change and geography through time for a widespread Holarctic shrew, Sorex tundrensis. We include a comprehensive suite of closely related outgroup taxa and three independent loci to explore phylogeographic structure and historical demography. We then explore the implications of these findings for other members of boreal communities. The tundra shrew and its sister species, the Tien Shan shrew (Sorex asper), exhibit strong geographic population structure across Siberia and into Beringia illustrating local centres of endemism that correspond to Late Pleistocene refugia. Ecological niche predictions for both current and historical distributions indicate a model of persistence through time despite dramatic climate change. Species tree estimation under a coalescent process suggests that isolation between populations has been maintained across timeframes deeper than the periodicity of Pleistocene glacial cycling. That some species such as the tundra shrew have a history of persistence largely independent of changing climate, whereas other boreal species shifted their ranges in response to climate change, highlights the dynamic processes of community assembly at high latitudes. ?? 2011 Blackwell Publishing Ltd.

Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.

PubMed

Haider, Kamran; Cruz, Anthony; Ramsey, Steven; Gilson, Michael K; Kurtzman, Tom

2018-01-09

We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.