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Sample records for niche enabling microbial

  1. A niche for cyanobacteria producing chlorophyll f within a microbial mat.

    Science.gov (United States)

    Ohkubo, Satoshi; Miyashita, Hideaki

    2017-10-01

    Acquisition of additional photosynthetic pigments enables photosynthetic organisms to survive in particular niches. To reveal the ecological significance of chlorophyll (Chl) f, we investigated the distribution of Chl and cyanobacteria within two microbial mats. In a 7-mm-thick microbial mat beneath the running water of the Nakabusa hot spring, Japan, Chl f was only distributed 4.0-6.5 mm below the surface, where the intensity of far-red light (FR) was higher than that of photosynthetically active radiation (PAR). In the same mat, two ecotypes of Synechococcus and two ecotypes of Chl f-producing Leptolyngbya were detected in the upper and deeper layers, respectively. Only the Leptolyngbya strains could grow when FR was the sole light source. These results suggest that the deeper layer of the microbial mat was a habitat for Chl f-producing cyanobacteria, and Chl f enabled them to survive in a habitat with little PAR.

  2. The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader's niche.

    Science.gov (United States)

    Mallon, C A; Le Roux, X; van Doorn, G S; Dini-Andreote, F; Poly, F; Salles, J F

    2018-03-01

    Although many environments like soils are constantly subjected to invasion by alien microbes, invaders usually fail to succeed, succumbing to the robust diversity often found in nature. So far, only successful invasions have been explored, and it remains unknown to what extent an unsuccessful invasion can impact resident communities. Here we hypothesized that unsuccessful invasions can cause impacts to soil functioning by decreasing the diversity and niche breadth of resident bacterial communities, which could cause shifts to community composition and niche structure-an effect that is likely exacerbated when diversity is compromised. To examine this question, diversity gradients of soil microbial communities were subjected to invasion by the frequent, yet oft-unsuccessful soil invader, Escherichia coli, and evaluated for changes to diversity, bacterial community composition, niche breadth, and niche structure. Contrary to expectations, diversity and niche breadth increased across treatments upon invasion. Community composition and niche structure were also altered, with shifts of niche structure revealing an escape by the resident community away from the invader's resources. Importantly, the extent of the escape varied in response to the community's diversity, where less diverse communities experienced larger shifts. Thus, although transient and unsuccessful, the invader competed for resources with resident species and caused tangible impacts that modified both the diversity and functioning of resident communities, which can likely generate a legacy effect that influences future invasion attempts.

  3. Coupling of the chemical niche and microbiome in the rhizosphere: implications from watermelon grafting

    Directory of Open Access Journals (Sweden)

    Yang SONG,Chen ZHU,Waseem RAZA,Dongsheng WANG,Qiwei HUANG,Shiwei GUO,Ning LING,Qirong SHEN

    2016-09-01

    Full Text Available Grafting is commonly used to overcome soil-borne diseases. However, its effects on the rhizodeposits as well as the linkages between the rhizosphere chemical niche and microbiome remained unknown. In this paper, significant negative correlations between the bacterial alpha diversity and both the disease incidence (r = -0.832, P = 0.005 and pathogen population (r = - 0.786, P = 0.012 were detected. Moreover, our results showed that the chemical diversity not only predicts bacterial alpha diversity but also can impact on overall microbial community structure (beta diversity in the rhizosphere. Furthermore, some anti-fungal compounds including heptadecane and hexadecane were identified in the rhizosphere of grafted watermelon. We concluded that grafted watermelon can form a distinct rhizosphere chemical niche and thus recruit microbial communities with high diversity. Furthermore, the diverse bacteria and the antifungal compounds in the rhizosphere can potentially serve as biological and chemical barriers, respectively, to hinder pathogen invasion. These results not only lead us toward broadening the view of disease resistance mechanism of grafting, but also provide clues to control the microbial composition by manipulating the rhizosphere chemical niche.

  4. Electrolyte-Sensing Transistor Decals Enabled by Ultrathin Microbial Nanocellulose

    Science.gov (United States)

    Yuen, Jonathan D.; Walper, Scott A.; Melde, Brian J.; Daniele, Michael A.; Stenger, David A.

    2017-01-01

    We report an ultra-thin electronic decal that can simultaneously collect, transmit and interrogate a bio-fluid. The described technology effectively integrates a thin-film organic electrochemical transistor (sensing component) with an ultrathin microbial nanocellulose wicking membrane (sample handling component). As far as we are aware, OECTs have not been integrated in thin, permeable membrane substrates for epidermal electronics. The design of the biocompatible decal allows for the physical isolation of the electronics from the human body while enabling efficient bio-fluid delivery to the transistor via vertical wicking. High currents and ON-OFF ratios were achieved, with sensitivity as low as 1 mg·L-1.

  5. Microbial ecology and biogeochemistry of continental Antarctic soils.

    Science.gov (United States)

    Cowan, Don A; Makhalanyane, Thulani P; Dennis, Paul G; Hopkins, David W

    2014-01-01

    The Antarctica Dry Valleys are regarded as the coldest hyperarid desert system on Earth. While a wide variety of environmental stressors including very low minimum temperatures, frequent freeze-thaw cycles and low water availability impose severe limitations to life, suitable niches for abundant microbial colonization exist. Antarctic desert soils contain much higher levels of microbial diversity than previously thought. Edaphic niches, including cryptic and refuge habitats, microbial mats and permafrost soils all harbor microbial communities which drive key biogeochemical cycling processes. For example, lithobionts (hypoliths and endoliths) possess a genetic capacity for nitrogen and carbon cycling, polymer degradation, and other system processes. Nitrogen fixation rates of hypoliths, as assessed through acetylene reduction assays, suggest that these communities are a significant input source for nitrogen into these oligotrophic soils. Here we review aspects of microbial diversity in Antarctic soils with an emphasis on functionality and capacity. We assess current knowledge regarding adaptations to Antarctic soil environments and highlight the current threats to Antarctic desert soil communities.

  6. The microbial ecology of permafrost

    DEFF Research Database (Denmark)

    Jansson, Janet; Tas, Neslihan

    2014-01-01

    Permafrost constitutes a major portion of the terrestrial cryosphere of the Earth and is a unique ecological niche for cold-adapted microorganisms. There is a relatively high microbial diversity in permafrost, although there is some variation in community composition across different permafrost......-gas emissions. This Review describes new data on the microbial ecology of permafrost and provides a platform for understanding microbial life strategies in frozen soil as well as the impact of climate change on permafrost microorganisms and their functional roles....

  7. CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline

    OpenAIRE

    Agrawal, Sonia; Arze, Cesar; Adkins, Ricky S.; Crabtree, Jonathan; Riley, David; Vangala, Mahesh; Galens, Kevin; Fraser, Claire M.; Tettelin, Herv?; White, Owen; Angiuoli, Samuel V.; Mahurkar, Anup; Fricke, W. Florian

    2017-01-01

    Background The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuitive, automated, and cloud-enabled analysis pipeline for comparative microbial genomics. Results CloVR-Comparative runs on annotated complete or draft genome sequences that are uploaded by the user or selected via a taxonomic tree-based user interface and downloaded from NCBI. ...

  8. Microbial ecology and biogeochemistry of continental Antarctic soils

    Directory of Open Access Journals (Sweden)

    Don A Cowan

    2014-04-01

    Full Text Available The Antarctica Dry Valleys are regarded as the coldest hyperarid desert system on Earth. While a wide variety of environmental stressors including very low minimum temperatures, frequent freeze-thaw cycles and low water availability impose severe limitations to life, suitable niches for abundant microbial colonization exist. Antarctic desert soils contain much higher levels of microbial diversity than previously thought. Edaphic niches, including cryptic and refuge habitats, microbial mats and permafrost soils all harbour microbial communities which drive key biogeochemical cycling processes. For example, lithobionts (hypoliths and endoliths possess a genetic capacity for nitrogen and carbon cycling, polymer degradation and other system processes. Nitrogen fixation rates of hypoliths, as assessed through acetylene reduction assays, suggest that these communities are a significant input source for nitrogen into these oligotrophic soils. Here we review aspects of microbial diversity in Antarctic soils with an emphasis on functionality and capacity. We assess current knowledge regarding adaptations to Antarctic soil environments and highlight the current threats to Antarctic desert soil communities.

  9. Pre-metastatic niches

    DEFF Research Database (Denmark)

    Peinado, Héctor; Zhang, Haiying; Matei, Irina R.

    2017-01-01

    It is well established that organs of future metastasis are not passive receivers of circulating tumour cells, but are instead selectively and actively modified by the primary tumour before metastatic spread has even occurred. Sowing the 'seeds' of metastasis requires the action of tumour......-secreted factors and tumour-shed extracellular vesicles that enable the 'soil' at distant metastatic sites to encourage the outgrowth of incoming cancer cells. In this Review, we summarize the main processes and new mechanisms involved in the formation of the pre-metastatic niche....

  10. A New Approach to Predict Microbial Community Assembly and Function Using a Stochastic, Genome-Enabled Modeling Framework

    Science.gov (United States)

    King, E.; Brodie, E.; Anantharaman, K.; Karaoz, U.; Bouskill, N.; Banfield, J. F.; Steefel, C. I.; Molins, S.

    2016-12-01

    Characterizing and predicting the microbial and chemical compositions of subsurface aquatic systems necessitates an understanding of the metabolism and physiology of organisms that are often uncultured or studied under conditions not relevant for one's environment of interest. Cultivation-independent approaches are therefore important and have greatly enhanced our ability to characterize functional microbial diversity. The capability to reconstruct genomes representing thousands of populations from microbial communities using metagenomic techniques provides a foundation for development of predictive models for community structure and function. Here, we discuss a genome-informed stochastic trait-based model incorporated into a reactive transport framework to represent the activities of coupled guilds of hypothetical microorganisms. Metabolic pathways for each microbe within a functional guild are parameterized from metagenomic data with a unique combination of traits governing organism fitness under dynamic environmental conditions. We simulate the thermodynamics of coupled electron donor and acceptor reactions to predict the energy available for cellular maintenance, respiration, biomass development, and enzyme production. While `omics analyses can now characterize the metabolic potential of microbial communities, it is functionally redundant as well as computationally prohibitive to explicitly include the thousands of recovered organisms into biogeochemical models. However, one can derive potential metabolic pathways from genomes along with trait-linkages to build probability distributions of traits. These distributions are used to assemble groups of microbes that couple one or more of these pathways. From the initial ensemble of microbes, only a subset will persist based on the interaction of their physiological and metabolic traits with environmental conditions, competing organisms, etc. Here, we analyze the predicted niches of these hypothetical microbes and

  11. Sexual reproduction and the evolution of microbial pathogens.

    Science.gov (United States)

    Heitman, Joseph

    2006-09-05

    Three common systemic human fungal pathogens--Cryptococcus neoformans, Candida albicans and Aspergillus fumigatus--have retained all the machinery to engage in sexual reproduction, and yet their populations are often clonal with limited evidence for recombination. Striking parallels have emerged with four protozoan parasites that infect humans: Toxoplasma gondii, Trypanosoma brucei, Trypanosoma cruzi and Plasmodium falciparum. Limiting sexual reproduction appears to be a common virulence strategy, enabling generation of clonal populations well adapted to host and environmental niches, yet retaining the ability to engage in sexual or parasexual reproduction and respond to selective pressure. Continued investigation of the sexual nature of microbial pathogens should facilitate both laboratory investigation and an understanding of the complex interplay between pathogens, hosts, vectors, and their environments.

  12. Cellular population dynamics control the robustness of the stem cell niche

    Directory of Open Access Journals (Sweden)

    Adam L. MacLean

    2015-11-01

    Full Text Available Within populations of cells, fate decisions are controlled by an indeterminate combination of cell-intrinsic and cell-extrinsic factors. In the case of stem cells, the stem cell niche is believed to maintain ‘stemness’ through communication and interactions between the stem cells and one or more other cell-types that contribute to the niche conditions. To investigate the robustness of cell fate decisions in the stem cell hierarchy and the role that the niche plays, we introduce simple mathematical models of stem and progenitor cells, their progeny and their interplay in the niche. These models capture the fundamental processes of proliferation and differentiation and allow us to consider alternative possibilities regarding how niche-mediated signalling feedback regulates the niche dynamics. Generalised stability analysis of these stem cell niche systems enables us to describe the stability properties of each model. We find that although the number of feasible states depends on the model, their probabilities of stability in general do not: stem cell–niche models are stable across a wide range of parameters. We demonstrate that niche-mediated feedback increases the number of stable steady states, and show how distinct cell states have distinct branching characteristics. The ecological feedback and interactions mediated by the stem cell niche thus lend (surprisingly high levels of robustness to the stem and progenitor cell population dynamics. Furthermore, cell–cell interactions are sufficient for populations of stem cells and their progeny to achieve stability and maintain homeostasis. We show that the robustness of the niche – and hence of the stem cell pool in the niche – depends only weakly, if at all, on the complexity of the niche make-up: simple as well as complicated niche systems are capable of supporting robust and stable stem cell dynamics.

  13. Identifying niche-mediated regulatory factors of stem cell phenotypic state: a systems biology approach.

    Science.gov (United States)

    Ravichandran, Srikanth; Del Sol, Antonio

    2017-02-01

    Understanding how the cellular niche controls the stem cell phenotype is often hampered due to the complexity of variegated niche composition, its dynamics, and nonlinear stem cell-niche interactions. Here, we propose a systems biology view that considers stem cell-niche interactions as a many-body problem amenable to simplification by the concept of mean field approximation. This enables approximation of the niche effect on stem cells as a constant field that induces sustained activation/inhibition of specific stem cell signaling pathways in all stem cells within heterogeneous populations exhibiting the same phenotype (niche determinants). This view offers a new basis for the development of single cell-based computational approaches for identifying niche determinants, which has potential applications in regenerative medicine and tissue engineering. © 2017 The Authors. FEBS Letters published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.

  14. Microbial minorities modulate methane consumption through niche partitioning

    NARCIS (Netherlands)

    Bodelier, P.L.E.; Meima-Franke, M.; Hordijk, C.A.; Steenbergh, A.K.; Hefting, M.M.; Bodrossy, L.; von Bergen, M.; Seifert, J.

    2013-01-01

    Microbes catalyze all major geochemical cycles on earth. However, the role of microbial traits and community composition in biogeochemical cycles is still poorly understood mainly due to the inability to assess the community members that are actually performing biogeochemical conversions in complex

  15. Regulatory System for Stem/Progenitor Cell Niches in the Adult Rodent Pituitary

    Science.gov (United States)

    Yoshida, Saishu; Kato, Takako; Kato, Yukio

    2016-01-01

    The anterior lobe of the pituitary gland is a master endocrine tissue composed of five types of endocrine cells. Although the turnover rate of pituitary endocrine cells is as low as about 1.6% per day, recent studies have demonstrated that Sex-determining region Y-box 2 (SOX2)+-cells exist as pituitary stem/progenitor cells in the adult anterior lobe and contribute to cell regeneration. Notably, SOX2+-pituitary stem/progenitor cells form two types of niches in this tissue: the marginal cell layer (MCL-niche) and the dense cell clusters scattering in the parenchyma (parenchymal-niche). However, little is known about the mechanisms and factors for regulating the pituitary stem/progenitor cell niches, as well as the functional differences between the two types of niches. Elucidation of the regulatory mechanisms in the niches might enable us to understand the cell regeneration system that acts in accordance with physiological demands in the adult pituitary. In this review, so as to reveal the regulatory mechanisms of the two types of niche, we summarize the regulatory factors and their roles in the adult rodent pituitary niches by focusing on three components: soluble factors, cell surface proteins and extracellular matrixes. PMID:26761002

  16. Regulatory System for Stem/Progenitor Cell Niches in the Adult Rodent Pituitary

    Directory of Open Access Journals (Sweden)

    Saishu Yoshida

    2016-01-01

    Full Text Available The anterior lobe of the pituitary gland is a master endocrine tissue composed of five types of endocrine cells. Although the turnover rate of pituitary endocrine cells is as low as about 1.6% per day, recent studies have demonstrated that Sex-determining region Y-box 2 (SOX2+-cells exist as pituitary stem/progenitor cells in the adult anterior lobe and contribute to cell regeneration. Notably, SOX2+-pituitary stem/progenitor cells form two types of niches in this tissue: the marginal cell layer (MCL-niche and the dense cell clusters scattering in the parenchyma (parenchymal-niche. However, little is known about the mechanisms and factors for regulating the pituitary stem/progenitor cell niches, as well as the functional differences between the two types of niches. Elucidation of the regulatory mechanisms in the niches might enable us to understand the cell regeneration system that acts in accordance with physiological demands in the adult pituitary. In this review, so as to reveal the regulatory mechanisms of the two types of niche, we summarize the regulatory factors and their roles in the adult rodent pituitary niches by focusing on three components: soluble factors, cell surface proteins and extracellular matrixes.

  17. Optimization of Femtosecond Laser Polymerized Structural Niches to Control Mesenchymal Stromal Cell Fate in Culture

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    Manuela T. Raimondi

    2014-06-01

    Full Text Available We applied two-photon polymerization to fabricate 3D synthetic niches arranged in complex patterns to study the effect of mechano-topological parameters on morphology, renewal and differentiation of rat mesenchymal stromal cells. Niches were formed in a photoresist with low auto-fluorescence, which enabled the clear visualization of the fluorescence emission of the markers used for biological diagnostics within the internal niche structure. The niches were structurally stable in culture up to three weeks. At three weeks of expansion in the niches, cell density increased by almost 10-fold and was 67% greater than in monolayer culture. Evidence of lineage commitment was observed in monolayer culture surrounding the structural niches, and within cell aggregates, but not inside the niches. Thus, structural niches were able not only to direct stem cell homing and colony formation, but also to guide aggregate formation, providing increased surface-to-volume ratios and space for stem cells to adhere and renew, respectively.

  18. Novel co-culture plate enables growth dynamic-based assessment of contact-independent microbial interactions.

    Directory of Open Access Journals (Sweden)

    Thomas J Moutinho

    Full Text Available Interactions between microbes are central to the dynamics of microbial communities. Understanding these interactions is essential for the characterization of communities, yet challenging to accomplish in practice. There are limited available tools for characterizing diffusion-mediated, contact-independent microbial interactions. A practical and widely implemented technique in such characterization involves the simultaneous co-culture of distinct bacterial species and subsequent analysis of relative abundance in the total population. However, distinguishing between species can be logistically challenging. In this paper, we present a low-cost, vertical membrane, co-culture plate to quantify contact-independent interactions between distinct bacterial populations in co-culture via real-time optical density measurements. These measurements can be used to facilitate the analysis of the interaction between microbes that are physically separated by a semipermeable membrane yet able to exchange diffusible molecules. We show that diffusion across the membrane occurs at a sufficient rate to enable effective interaction between physically separate cultures. Two bacterial species commonly found in the cystic fibrotic lung, Pseudomonas aeruginosa and Burkholderia cenocepacia, were co-cultured to demonstrate how this plate may be implemented to study microbial interactions. We have demonstrated that this novel co-culture device is able to reliably generate real-time measurements of optical density data that can be used to characterize interactions between microbial species.

  19. Microbial co-occurrence relationships in the human microbiome.

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    Karoline Faust

    Full Text Available The healthy microbiota show remarkable variability within and among individuals. In addition to external exposures, ecological relationships (both oppositional and symbiotic between microbial inhabitants are important contributors to this variation. It is thus of interest to assess what relationships might exist among microbes and determine their underlying reasons. The initial Human Microbiome Project (HMP cohort, comprising 239 individuals and 18 different microbial habitats, provides an unprecedented resource to detect, catalog, and analyze such relationships. Here, we applied an ensemble method based on multiple similarity measures in combination with generalized boosted linear models (GBLMs to taxonomic marker (16S rRNA gene profiles of this cohort, resulting in a global network of 3,005 significant co-occurrence and co-exclusion relationships between 197 clades occurring throughout the human microbiome. This network revealed strong niche specialization, with most microbial associations occurring within body sites and a number of accompanying inter-body site relationships. Microbial communities within the oropharynx grouped into three distinct habitats, which themselves showed no direct influence on the composition of the gut microbiota. Conversely, niches such as the vagina demonstrated little to no decomposition into region-specific interactions. Diverse mechanisms underlay individual interactions, with some such as the co-exclusion of Porphyromonaceae family members and Streptococcus in the subgingival plaque supported by known biochemical dependencies. These differences varied among broad phylogenetic groups as well, with the Bacilli and Fusobacteria, for example, both enriched for exclusion of taxa from other clades. Comparing phylogenetic versus functional similarities among bacteria, we show that dominant commensal taxa (such as Prevotellaceae and Bacteroides in the gut often compete, while potential pathogens (e.g. Treponema and

  20. Microbial Co-occurrence Relationships in the Human Microbiome

    Science.gov (United States)

    Izard, Jacques; Segata, Nicola; Gevers, Dirk

    2012-01-01

    The healthy microbiota show remarkable variability within and among individuals. In addition to external exposures, ecological relationships (both oppositional and symbiotic) between microbial inhabitants are important contributors to this variation. It is thus of interest to assess what relationships might exist among microbes and determine their underlying reasons. The initial Human Microbiome Project (HMP) cohort, comprising 239 individuals and 18 different microbial habitats, provides an unprecedented resource to detect, catalog, and analyze such relationships. Here, we applied an ensemble method based on multiple similarity measures in combination with generalized boosted linear models (GBLMs) to taxonomic marker (16S rRNA gene) profiles of this cohort, resulting in a global network of 3,005 significant co-occurrence and co-exclusion relationships between 197 clades occurring throughout the human microbiome. This network revealed strong niche specialization, with most microbial associations occurring within body sites and a number of accompanying inter-body site relationships. Microbial communities within the oropharynx grouped into three distinct habitats, which themselves showed no direct influence on the composition of the gut microbiota. Conversely, niches such as the vagina demonstrated little to no decomposition into region-specific interactions. Diverse mechanisms underlay individual interactions, with some such as the co-exclusion of Porphyromonaceae family members and Streptococcus in the subgingival plaque supported by known biochemical dependencies. These differences varied among broad phylogenetic groups as well, with the Bacilli and Fusobacteria, for example, both enriched for exclusion of taxa from other clades. Comparing phylogenetic versus functional similarities among bacteria, we show that dominant commensal taxa (such as Prevotellaceae and Bacteroides in the gut) often compete, while potential pathogens (e.g. Treponema and Prevotella in the

  1. Toward a Periodic Table of Niches, or Exploring the Lizard Niche Hypervolume.

    Science.gov (United States)

    Pianka, Eric R; Vitt, Laurie J; Pelegrin, Nicolás; Fitzgerald, Daniel B; Winemiller, Kirk O

    2017-11-01

    Widespread niche convergence suggests that species can be organized according to functional trait combinations to create a framework analogous to a periodic table. We compiled ecological data for lizards to examine patterns of global and regional niche diversification, and we used multivariate statistical approaches to develop the beginnings for a periodic table of niches. Data (50+ variables) for five major niche dimensions (habitat, diet, life history, metabolism, defense) were compiled for 134 species of lizards representing 24 of the 38 extant families. Principal coordinates analyses were performed on niche dimensional data sets, and species scores for the first three axes were used as input for a principal components analysis to ordinate species in continuous niche space and for a regression tree analysis to separate species into discrete niche categories. Three-dimensional models facilitate exploration of species positions in relation to major gradients within the niche hypervolume. The first gradient loads on body size, foraging mode, and clutch size. The second was influenced by metabolism and terrestrial versus arboreal microhabitat. The third was influenced by activity time, life history, and diet. Natural dichotomies are activity time, foraging mode, parity mode, and habitat. Regression tree analysis identified 103 cases of extreme niche conservatism within clades and 100 convergences between clades. Extending this approach to other taxa should lead to a wider understanding of niche evolution.

  2. Agriculturally important microbial biofilms: Present status and future prospects.

    Science.gov (United States)

    Velmourougane, Kulandaivelu; Prasanna, Radha; Saxena, Anil Kumar

    2017-07-01

    Microbial biofilms are a fascinating subject, due to their significant roles in the environment, industry, and health. Advances in biochemical and molecular techniques have helped in enhancing our understanding of biofilm structure and development. In the past, research on biofilms primarily focussed on health and industrial sectors; however, lately, biofilms in agriculture are gaining attention due to their immense potential in crop production, protection, and improvement. Biofilms play an important role in colonization of surfaces - soil, roots, or shoots of plants and enable proliferation in the desired niche, besides enhancing soil fertility. Although reports are available on microbial biofilms in general; scanty information is published on biofilm formation by agriculturally important microorganisms (bacteria, fungi, bacterial-fungal) and their interactions in the ecosystem. Better understanding of agriculturally important bacterial-fungal communities and their interactions can have several implications on climate change, soil quality, plant nutrition, plant protection, bioremediation, etc. Understanding the factors and genes involved in biofilm formation will help to develop more effective strategies for sustainable and environment-friendly agriculture. The present review brings together fundamental aspects of biofilms, in relation to their formation, regulatory mechanisms, genes involved, and their application in different fields, with special emphasis on agriculturally important microbial biofilms. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology.

    Science.gov (United States)

    von Bergen, Martin; Jehmlich, Nico; Taubert, Martin; Vogt, Carsten; Bastida, Felipe; Herbst, Florian-Alexander; Schmidt, Frank; Richnow, Hans-Hermann; Seifert, Jana

    2013-10-01

    The recent development of metaproteomics has enabled the direct identification and quantification of expressed proteins from microbial communities in situ, without the need for microbial enrichment. This became possible by (1) significant increases in quality and quantity of metagenome data and by improvements of (2) accuracy and (3) sensitivity of modern mass spectrometers (MS). The identification of physiologically relevant enzymes can help to understand the role of specific species within a community or an ecological niche. Beside identification, relative and absolute quantitation is also crucial. We will review label-free and label-based methods of quantitation in MS-based proteome analysis and the contribution of quantitative proteome data to microbial ecology. Additionally, approaches of protein-based stable isotope probing (protein-SIP) for deciphering community structures are reviewed. Information on the species-specific metabolic activity can be obtained when substrates or nutrients are labeled with stable isotopes in a protein-SIP approach. The stable isotopes ((13)C, (15)N, (36)S) are incorporated into proteins and the rate of incorporation can be used for assessing the metabolic activity of the corresponding species. We will focus on the relevance of the metabolic and phylogenetic information retrieved with protein-SIP studies and for detecting and quantifying the carbon flux within microbial consortia. Furthermore, the combination of protein-SIP with established tools in microbial ecology such as other stable isotope probing techniques are discussed.

  4. Homogeneous versus heterogeneous probes for microbial ecological microarrays.

    Science.gov (United States)

    Bae, Jin-Woo; Park, Yong-Ha

    2006-07-01

    Microbial ecological microarrays have been developed for investigating the composition and functions of microorganism communities in environmental niches. These arrays include microbial identification microarrays, which use oligonucleotides, gene fragments or microbial genomes as probes. In this article, the advantages and disadvantages of each type of probe are reviewed. Oligonucleotide probes are currently useful for probing uncultivated bacteria that are not amenable to gene fragment probing, whereas the functional gene fragments amplified randomly from microbial genomes require phylogenetic and hierarchical categorization before use as microbial identification probes, despite their high resolution for both specificity and sensitivity. Until more bacteria are sequenced and gene fragment probes are thoroughly validated, heterogeneous bacterial genome probes will provide a simple, sensitive and quantitative tool for exploring the ecosystem structure.

  5. Health-Associated Niche Inhabitants as Oral Probiotics: The Case of Streptococcus dentisani

    OpenAIRE

    L?pez-L?pez, Arantxa; Camelo-Castillo, Anny; Ferrer, Mar?a D.; Simon-Soro, ?urea; Mira, Alex

    2017-01-01

    Oral diseases, including dental caries and periodontitis, are among the most prevalent diseases worldwide and develop as a consequence of a microbial dysbiosis. Several bacterial strains are being tested as potential oral health-promoting organisms, but usually they are species isolated from niches other than the site where they must exert its probiotic action, typically from fecal samples. We hypothesize that oral inhabitants associated to health conditions will be more effective than tradit...

  6. Development of biomass power plant technologies in Malaysia: niche development and the formation of innovative capabilities

    DEFF Research Database (Denmark)

    Hansen, Ulrich Elmer

    The objective of this thesis is to contribute to advance further the emerging research agenda on the transfer and diffusion of low-carbon technologies in developing countries by adopting a study of the development of biomass power plant technologies in Malaysia. The main research question addresses...... successive periods of fieldwork in Malaysia. The thesis conceptualises the diffusion of biomass technologies in Malaysia as a niche development process and finds that the development of a palm oil biomass waste-to-energy niche in Malaysia has only made limited progress despite a period of twenty years...... of niche formation. The thesis identifies the reluctance to implement an efficient energy policy as the main limiting factor for niche development in this case. Although a number of donor programs have advocated the introduction of a stronger enabling framework for niche development, they have generally...

  7. Why developmental niche construction is not selective niche construction: and why it matters.

    Science.gov (United States)

    Stotz, Karola

    2017-10-06

    In the last decade, niche construction has been heralded as the neglected process in evolution. But niche construction is just one way in which the organism's interaction with and construction of the environment can have potential evolutionary significance. The constructed environment does not just select for , it also produces new variation. Nearly 3 decades ago, and in parallel with Odling-Smee's article 'Niche-constructing phenotypes', West and King introduced the 'ontogenetic niche' to give the phenomena of exo genetic inheritance a formal name. Since then, a range of fields in the life sciences and medicine has amassed evidence that parents influence their offspring by means other than DNA (parental effects), and proposed mechanisms for how heritable variation can be environmentally induced and developmentally regulated. The concept of 'developmental niche construction' (DNC) elucidates how a diverse range of mechanisms contributes to the transgenerational transfer of developmental resources. My most central of claims is that whereas the selective niche of niche construction theory is primarily used to explain the active role of the organism in its selective environment, DNC is meant to indicate the active role of the organism in its developmental environment. The paper highlights the differences between the construction of the selective and the developmental niche, and explores the overall significance of DNC for evolutionary theory.

  8. Stitch the niche - a practical philosophy and visual schematic for the niche concept

    NARCIS (Netherlands)

    McInerny, Greg J.; Etienne, Rampal S.

    2012-01-01

    By over-focusing on precise definitions, ecology has produced a confused idea of the niche concept. This, our second paper, develops a practical philosophy for the niche that approaches the concept at the correct level of abstraction. We deconstruct the niche into effect and response components and

  9. Periarteriolar Glioblastoma Stem Cell Niches Express Bone Marrow Hematopoietic Stem Cell Niche Proteins

    NARCIS (Netherlands)

    Hira, Vashendriya V. V.; Wormer, Jill R.; Kakar, Hala; Breznik, Barbara; van der Swaan, Britt; Hulsbos, Renske; Tigchelaar, Wikky; Tonar, Zbynek; Khurshed, Mohammed; Molenaar, Remco J.; van Noorden, Cornelis J. F.

    2018-01-01

    In glioblastoma, a fraction of malignant cells consists of therapy-resistant glioblastoma stem cells (GSCs) residing in protective niches that recapitulate hematopoietic stem cell (HSC) niches in bone marrow. We have previously shown that HSC niche proteins stromal cell-derived factor-1α (SDF-1α),

  10. Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion.

    Science.gov (United States)

    Vanwonterghem, Inka; Jensen, Paul D; Rabaey, Korneel; Tyson, Gene W

    2016-09-01

    Our understanding of the complex interconnected processes performed by microbial communities is hindered by our inability to culture the vast majority of microorganisms. Metagenomics provides a way to bypass this cultivation bottleneck and recent advances in this field now allow us to recover a growing number of genomes representing previously uncultured populations from increasingly complex environments. In this study, a temporal genome-centric metagenomic analysis was performed of lab-scale anaerobic digesters that host complex microbial communities fulfilling a series of interlinked metabolic processes to enable the conversion of cellulose to methane. In total, 101 population genomes that were moderate to near-complete were recovered based primarily on differential coverage binning. These populations span 19 phyla, represent mostly novel species and expand the genomic coverage of several rare phyla. Classification into functional guilds based on their metabolic potential revealed metabolic networks with a high level of functional redundancy as well as niche specialization, and allowed us to identify potential roles such as hydrolytic specialists for several rare, uncultured populations. Genome-centric analyses of complex microbial communities across diverse environments provide the key to understanding the phylogenetic and metabolic diversity of these interactive communities. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

  11. Niche Filtering of Bacteria in Soil and Rock Habitats of the Colorado Plateau Desert, Utah, USA.

    Science.gov (United States)

    Lee, Kevin C; Archer, Stephen D J; Boyle, Rachel H; Lacap-Bugler, Donnabella C; Belnap, Jayne; Pointing, Stephen B

    2016-01-01

    A common feature of microbial colonization in deserts is biological soil crusts (BSCs), and these comprise a complex community dominated by Cyanobacteria. Rock substrates, particularly sandstone, are also colonized by microbial communities. These are separated by bare sandy soil that also supports microbial colonization. Here we report a high-throughput sequencing study of BSC and cryptoendolith plus adjacent bare soil communities in the Colorado Plateau Desert, Utah, USA. Bare soils supported a community with low levels of recoverable DNA and high evenness, whilst BSC yielded relatively high recoverable DNA, and reduced evenness compared to bare soil due to specialized crust taxa. The cryptoendolithic community displayed the greatest evenness but the lowest diversity, reflecting the highly specialized nature of these communities. A strong substrate-dependent pattern of community assembly was observed, and in particular cyanobacterial taxa were distinct. Soils were virtually devoid of photoautotrophic signatures, BSC was dominated by a closely related group of Microcoleus/Phormidium taxa, whilst cryptoendolithic colonization in sandstone supported almost exclusively a single genus, Chroococcidiopsis . We interpret this as strong evidence for niche filtering of taxa in communities. Local inter-niche recruitment of photoautotrophs may therefore be limited and so communities likely depend significantly on cyanobacterial recruitment from distant sources of similar substrate. We discuss the implication of this finding in terms of conservation and management of desert microbiota.

  12. The Fluctuation Niche in Plants

    Directory of Open Access Journals (Sweden)

    Jaume Terradas

    2009-01-01

    Full Text Available Classical approaches to niche in coexisting plants have undervalued temporal fluctuations. We propose that fluctuation niche is an important dimension of the total niche and interacts with habitat and life-history niches to provide a better understanding of the multidimensional niche space where ecological interactions occur. To scale a fluctuation niche, it is necessary to relate environmental constrictions or species performance not only to the absolute values of the usual environmental and ecophysiological variables but also to their variances or other measures of variability. We use Mediterranean plant communities as examples, because they present characteristic large seasonal and interannual fluctuations in water and nutrient availabilities, along an episodic-constant gradient, and because the plant responses include a number of syndromes coupled to this gradient.

  13. The Fluctuation Niche in Plants

    International Nuclear Information System (INIS)

    Terradas, J.; Penuelas, J.; Lloret, F.; Penuelas, J.

    2009-01-01

    Classical approaches to niche in coexisting plants have undervalued temporal fluctuations. We propose that fluctuation niche is an important dimension of the total niche and interacts with habitat and life-history niches to provide a better understanding of the multidimensional niche space where ecological interactions occur. To scale a fluctuation niche, it is necessary to relate environmental constrictions or species performance not only to the absolute values of the usual environmental and eco physiological variables but also to their variances or other measures of variability. We use Mediterranean plant communities as examples, because they present characteristic large seasonal and inter annual fluctuations in water and nutrient availabilities, along an episodic-constant gradient, and because the plant responses include a number of syndromes coupled to this gradient.

  14. Novel therapeutic strategies to target leukemic cells that hijack compartmentalized continuous hematopoietic stem cell niches.

    Science.gov (United States)

    Hira, Vashendriya V V; Van Noorden, Cornelis J F; Carraway, Hetty E; Maciejewski, Jaroslaw P; Molenaar, Remco J

    2017-08-01

    Acute myeloid leukemia and acute lymphoblastic leukemia cells hijack hematopoietic stem cell (HSC) niches in the bone marrow and become leukemic stem cells (LSCs) at the expense of normal HSCs. LSCs are quiescent and resistant to chemotherapy and can cause relapse of the disease. HSCs in niches are needed to generate blood cell precursors that are committed to unilineage differentiation and eventually production of mature blood cells, including red blood cells, megakaryocytes, myeloid cells and lymphocytes. Thus far, three types of HSC niches are recognized: endosteal, reticular and perivascular niches. However, we argue here that there is only one type of HSC niche, which consists of a periarteriolar compartment and a perisinusoidal compartment. In the periarteriolar compartment, hypoxia and low levels of reactive oxygen species preserve the HSC pool. In the perisinusoidal compartment, hypoxia in combination with higher levels of reactive oxygen species enables proliferation of progenitor cells and their mobilization into the circulation. Because HSC niches offer protection to LSCs against chemotherapy, we review novel therapeutic strategies to inhibit homing of LSCs in niches for the prevention of dedifferentiation of leukemic cells into LSCs and to stimulate migration of leukemic cells out of niches. These strategies enhance differentiation and proliferation and thus sensitize leukemic cells to chemotherapy. Finally, we list clinical trials of therapies that tackle LSCs in HSC niches to circumvent their protection against chemotherapy. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  15. Niche conservatism and phylogenetic clustering in a tribe of arid-adapted marsupial mice, the Sminthopsini.

    Science.gov (United States)

    García-Navas, Vicente; Westerman, Michael

    2018-05-28

    The progressive expansion of the Australian arid zone during the last 20 Ma appears to have spurred the diversification of several families of plants, vertebrates and invertebrates, yet such taxonomic groups appear to show limited niche radiation. Here, we test whether speciation is associated with niche conservatism (constraints on ecological divergence) or niche divergence in a tribe of marsupial mice (Sminthopsini; 23 taxa) that includes the most speciose genus of living dasyurids, the sminthopsins. To that end, we integrated phylogenetic data with ecological niche modelling, to enable us to reconstruct the evolution of climatic suitability within Sminthopsini. Niche overlap among species was low-moderate (but generally higher than expected given environmental background similarity), and the degree of phylogenetic clustering increased with aridity. Climatic niche reconstruction illustrates that there has been little apparent evolution of climatic tolerance within clades. Accordingly, climatic disparity tends to be accumulated among clades, suggesting considerable niche conservatism. Our results also indicate that evolution of climatic tolerances has been heterogeneous across different dimensions of climate (temperature vs. precipitation) and across phylogenetic clusters (Sminthopsis murina group vs. other groups). Although some results point to the existence of shifts in climatic niches during the speciation of sminthopsins, our study provides evidence for substantial phylogenetic niche conservatism in the group. We conclude that niche diversification had a low impact on the speciation of this tribe of small, but highly mobile marsupials. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

  16. An introduction to niche construction theory.

    Science.gov (United States)

    Laland, Kevin; Matthews, Blake; Feldman, Marcus W

    Niche construction refers to the modification of selective environments by organisms. Theoretical and empirical studies of niche construction are increasing in importance as foci in evolutionary ecology. This special edition presents theoretical and empirical research that illustrates the significance of niche construction to the field. Here we set the scene for the following papers by (1) discussing the history of niche construction research, (2) providing clear definitions that distinguish niche construction from related concepts such as ecosystem engineering and the extended phenotype, (3) providing a brief summary of the findings of niche construction research, (4) discussing the contribution of niche construction and ecological inheritance to (a) expanded notions of inheritance, and (b) the extended evolutionary synthesis, and (5) briefly touching on some of the issues that underlie the controversies over niche construction.

  17. Shotgun microbial profiling of fossil remains

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Ermini, Luca; Jónsson, Hákon

    2014-01-01

    the specimen of interest, but instead reflect environmental organisms that colonized the specimen after death. Here, we characterize the microbial diversity recovered from seven c. 200- to 13 000-year-old horse bones collected from northern Siberia. We use a robust, taxonomy-based assignment approach...... to identify the microorganisms present in ancient DNA extracts and quantify their relative abundance. Our results suggest that molecular preservation niches exist within ancient samples that can potentially be used to characterize the environments from which the remains are recovered. In addition, microbial...... community profiling of the seven specimens revealed site-specific environmental signatures. These microbial communities appear to comprise mainly organisms that colonized the fossils recently. Our approach significantly extends the amount of useful data that can be recovered from ancient specimens using...

  18. Microbial genome-enabled insights into plant-microorganism interactions.

    Science.gov (United States)

    Guttman, David S; McHardy, Alice C; Schulze-Lefert, Paul

    2014-12-01

    Advances in genome-based studies on plant-associated microorganisms have transformed our understanding of many plant pathogens and are beginning to greatly widen our knowledge of plant interactions with mutualistic and commensal microorganisms. Pathogenomics has revealed how pathogenic microorganisms adapt to particular hosts, subvert innate immune responses and change host range, as well as how new pathogen species emerge. Similarly, culture-independent community profiling methods, coupled with metagenomic and metatranscriptomic studies, have provided the first insights into the emerging field of research on plant-associated microbial communities. Together, these approaches have the potential to bridge the gap between plant microbial ecology and plant pathology, which have traditionally been two distinct research fields.

  19. Multitrophic microbial interactions for eco- and agro-biotechnological processes: theory and practice.

    Science.gov (United States)

    Saleem, Muhammad; Moe, Luke A

    2014-10-01

    Multitrophic level microbial loop interactions mediated by protist predators, bacteria, and viruses drive eco- and agro-biotechnological processes such as bioremediation, wastewater treatment, plant growth promotion, and ecosystem functioning. To what extent these microbial interactions are context-dependent in performing biotechnological and ecosystem processes remains largely unstudied. Theory-driven research may advance the understanding of eco-evolutionary processes underlying the patterns and functioning of microbial interactions for successful development of microbe-based biotechnologies for real world applications. This could also be a great avenue to test the validity or limitations of ecology theory for managing diverse microbial resources in an era of altering microbial niches, multitrophic interactions, and microbial diversity loss caused by climate and land use changes. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Ecological allometries and niche use dynamics across Komodo dragon ontogeny

    Science.gov (United States)

    Purwandana, Deni; Ariefiandy, Achmad; Imansyah, M. Jeri; Seno, Aganto; Ciofi, Claudio; Letnic, Mike; Jessop, Tim S.

    2016-04-01

    Ontogenetic allometries in ecological habits and niche use are key responses by which individuals maximize lifetime fitness. Moreover, such allometries have significant implications for how individuals influence population and community dynamics. Here, we examined how body size variation in Komodo dragons ( Varanus komodoensis) influenced ecological allometries in their: (1) prey size preference, (2) daily movement rates, (3) home range area, and (4) subsequent niche use across ontogeny. With increased body mass, Komodo dragons increased prey size with a dramatic switch from small (≤10 kg) to large prey (≥50 kg) in lizards heavier than 20 kg. Rates of foraging movement were described by a non-linear concave down response with lizard increasing hourly movement rates up until ˜20 kg body mass before decreasing daily movement suggesting reduced foraging effort in larger lizards. In contrast, home range area exhibited a sigmoid response with increased body mass. Intrapopulation ecological niche use and overlap were also strongly structured by body size. Thus, ontogenetic allometries suggest Komodo dragon's transition from a highly active foraging mode exploiting small prey through to a less active sit and wait feeding strategy focused on killing large ungulates. Further, our results suggest that as body size increases across ontogeny, the Komodo dragon exhibited marked ontogenetic niche shifts that enabled it to function as an entire vertebrate predator guild by exploiting prey across multiple trophic levels.

  1. Niche energy markets in rural areas

    International Nuclear Information System (INIS)

    Walsh, M.; McCarthy, S.

    1996-01-01

    The objective of this project is the development of a standard methodology for integrating non-food crops in rural areas with niche energy markets. This has involved a number of steps including (i) identification of 3 niche markets for energy crops which are of common interest to the partners, (ii) application of the standard costing methodology to investigate these three niche markets and (iii) comparison of the results from this work in three workshops (one for each market). Three tightly defined niche markets were identified; these were chosen following an examination of the national energy marekts in each of the partners countries (Ireland, Germany, Netherlands, UK, Greece and Portugal). This paper gives an overview of the national energy markets which were examined. The three niche markets are introduced and the reasons for their selection given. The application of the methodology to each of the niche markets is presented along with the conclusions of the partners regarding the niche markets. (Author)

  2. The microbial diversity, distribution, and ecology of permafrost in China: a review.

    Science.gov (United States)

    Hu, Weigang; Zhang, Qi; Tian, Tian; Cheng, Guodong; An, Lizhe; Feng, Huyuan

    2015-07-01

    Permafrost in China mainly located in high-altitude areas. It represents a unique and suitable ecological niche that can be colonized by abundant microbes. Permafrost microbial community varies across geographically separated locations in China, and some lineages are novel and possible endemic. Besides, Chinese permafrost is a reservoir of functional microbial groups involved in key biogeochemical cycling processes. In future, more work is necessary to determine if these phylogenetic groups detected by DNA-based methods are part of the viable microbial community, and their functional roles and how they potentially respond to climate change. This review summaries recent studies describing microbial biodiversity found in permafrost and associated environments in China, and provides a framework for better understanding the microbial ecology of permafrost.

  3. Ecological allometries and niche use dynamics across Komodo dragon ontogeny.

    Science.gov (United States)

    Purwandana, Deni; Ariefiandy, Achmad; Imansyah, M Jeri; Seno, Aganto; Ciofi, Claudio; Letnic, Mike; Jessop, Tim S

    2016-04-01

    Ontogenetic allometries in ecological habits and niche use are key responses by which individuals maximize lifetime fitness. Moreover, such allometries have significant implications for how individuals influence population and community dynamics. Here, we examined how body size variation in Komodo dragons (Varanus komodoensis) influenced ecological allometries in their: (1) prey size preference, (2) daily movement rates, (3) home range area, and (4) subsequent niche use across ontogeny. With increased body mass, Komodo dragons increased prey size with a dramatic switch from small (≤10 kg) to large prey (≥50 kg) in lizards heavier than 20 kg. Rates of foraging movement were described by a non-linear concave down response with lizard increasing hourly movement rates up until ∼20 kg body mass before decreasing daily movement suggesting reduced foraging effort in larger lizards. In contrast, home range area exhibited a sigmoid response with increased body mass. Intrapopulation ecological niche use and overlap were also strongly structured by body size. Thus, ontogenetic allometries suggest Komodo dragon's transition from a highly active foraging mode exploiting small prey through to a less active sit and wait feeding strategy focused on killing large ungulates. Further, our results suggest that as body size increases across ontogeny, the Komodo dragon exhibited marked ontogenetic niche shifts that enabled it to function as an entire vertebrate predator guild by exploiting prey across multiple trophic levels.

  4. Biosynthesis and derivatization of microbial glycolipids and their potential application in tribology

    Science.gov (United States)

    Microbial-produced glycolipids are biobased products with immense potential for commercial applications. Advances in the production process have led to the lowering of production cost and the appearance of commercial products in niche markets. The ability to manipulate the molecular structure by f...

  5. Niche players

    Science.gov (United States)

    Seandel, Marco; Falciatori, Ilaria; Shmelkov, Sergey V.; Kim, Jiyeon; James, Daylon; Rafii, Shahin

    2010-01-01

    The undifferentiated spermatogonia of adult mouse testes are composed of both true stem cells and committed progenitors. It is unclear what normally prevents these adult germ cells from manifesting multipotency. The critical elements of the spermatogonial stem cell niche, while poorly understood, are thought to be composed of Sertoli cells with several other somatic cell types in close proximity. We recently discovered a novel orphan G-protein coupled receptor (GPR125) that is restricted to undifferentiated spermatogonia within the testis. GPR125 expression was maintained when the progenitor cells were extracted from the in vivo niche and propagated under growth conditions that recapitulate key elements of the niche. Such conditions preserved the ability of the cells to generate multipotent derivatives, known as multipotent adult spermatogonial derived progenitor cells (MASCs). Upon differentiation, the latter produced a variety tissues including functional endothelium, illustrating the potential applications of such cells. Thus, GPR125 represents a novel target for purifying adult stem and progenitors from tissues, with the goal of developing autologous multipotent cell lines. PMID:18256534

  6. Microbial Ecology and Evolution in the Acid Mine Drainage Model System.

    Science.gov (United States)

    Huang, Li-Nan; Kuang, Jia-Liang; Shu, Wen-Sheng

    2016-07-01

    Acid mine drainage (AMD) is a unique ecological niche for acid- and toxic-metals-adapted microorganisms. These low-complexity systems offer a special opportunity for the ecological and evolutionary analyses of natural microbial assemblages. The last decade has witnessed an unprecedented interest in the study of AMD communities using 16S rRNA high-throughput sequencing and community genomic and postgenomic methodologies, significantly advancing our understanding of microbial diversity, community function, and evolution in acidic environments. This review describes new data on AMD microbial ecology and evolution, especially dynamics of microbial diversity, community functions, and population genomes, and further identifies gaps in our current knowledge that future research, with integrated applications of meta-omics technologies, will fill. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. Microbial ecology of hot desert edaphic systems.

    Science.gov (United States)

    Makhalanyane, Thulani P; Valverde, Angel; Gunnigle, Eoin; Frossard, Aline; Ramond, Jean-Baptiste; Cowan, Don A

    2015-03-01

    A significant proportion of the Earth's surface is desert or in the process of desertification. The extreme environmental conditions that characterize these areas result in a surface that is essentially barren, with a limited range of higher plants and animals. Microbial communities are probably the dominant drivers of these systems, mediating key ecosystem processes. In this review, we examine the microbial communities of hot desert terrestrial biotopes (including soils, cryptic and refuge niches and plant-root-associated microbes) and the processes that govern their assembly. We also assess the possible effects of global climate change on hot desert microbial communities and the resulting feedback mechanisms. We conclude by discussing current gaps in our understanding of the microbiology of hot deserts and suggest fruitful avenues for future research. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  8. Subsurface microbial habitats on Mars

    Science.gov (United States)

    Boston, P. J.; Mckay, C. P.

    1991-01-01

    We developed scenarios for shallow and deep subsurface cryptic niches for microbial life on Mars. Such habitats could have considerably prolonged the persistence of life on Mars as surface conditions became increasingly inhospitable. The scenarios rely on geothermal hot spots existing below the near or deep subsurface of Mars. Recent advances in the comparatively new field of deep subsurface microbiology have revealed previously unsuspected rich aerobic and anaerobic microbal communities far below the surface of the Earth. Such habitats, protected from the grim surface conditions on Mars, could receive warmth from below and maintain water in its liquid state. In addition, geothermally or volcanically reduced gases percolating from below through a microbiologically active zone could provide the reducing power needed for a closed or semi-closed microbial ecosystem to thrive.

  9. Niche construction game cancer cells play.

    Science.gov (United States)

    Bergman, Aviv; Gligorijevic, Bojana

    2015-10-01

    Niche construction concept was originally defined in evolutionary biology as the continuous interplay between natural selection via environmental conditions and the modification of these conditions by the organism itself. Processes unraveling during cancer metastasis include construction of niches, which cancer cells use towards more efficient survival, transport into new environments and preparation of the remote sites for their arrival. Many elegant experiments were done lately illustrating, for example, the premetastatic niche construction, but there is practically no mathematical modeling done which would apply the niche construction framework. To create models useful for understanding niche construction role in cancer progression, we argue that a) genetic, b) phenotypic and c) ecological levels are to be included. While the model proposed here is phenomenological in its current form, it can be converted into a predictive outcome model via experimental measurement of the model parameters. Here we give an overview of an experimentally formulated problem in cancer metastasis and propose how niche construction framework can be utilized and broadened to model it. Other life science disciplines, such as host-parasite coevolution, may also benefit from niche construction framework adaptation, to satisfy growing need for theoretical considerations of data collected by experimental biology.

  10. Niche construction game cancer cells play

    Science.gov (United States)

    Bergman, Aviv; Gligorijevic, Bojana

    2015-10-01

    Niche construction concept was originally defined in evolutionary biology as the continuous interplay between natural selection via environmental conditions and the modification of these conditions by the organism itself. Processes unraveling during cancer metastasis include construction of niches, which cancer cells use towards more efficient survival, transport into new environments and preparation of the remote sites for their arrival. Many elegant experiments were done lately illustrating, for example, the premetastatic niche construction, but there is practically no mathematical modeling done which would apply the niche construction framework. To create models useful for understanding niche construction role in cancer progression, we argue that a) genetic, b) phenotypic and c) ecological levels are to be included. While the model proposed here is phenomenological in its current form, it can be converted into a predictive outcome model via experimental measurement of the model parameters. Here we give an overview of an experimentally formulated problem in cancer metastasis and propose how niche construction framework can be utilized and broadened to model it. Other life science disciplines, such as host-parasite coevolution, may also benefit from niche construction framework adaptation, to satisfy growing need for theoretical considerations of data collected by experimental biology.

  11. Spatial distributions of niche-constructing populations

    Directory of Open Access Journals (Sweden)

    Xiaozhuo Han

    2015-12-01

    Full Text Available Niche construction theory regards organisms not only as the object of natural selection but also an active subject that can change their own selective pressure through eco-evolutionary feedbacks. Through reviewing the existing works on the theoretical models of niche construction, here we present the progress made on how niche construction influences genetic structure of spatially structured populations and the spatial-temporal dynamics of metapopulations, with special focuses on mathematical models and simulation methods. The majority of results confirmed that niche construction can significantly alter the evolutionary trajectories of structured populations. Organism-environmental interactions induced by niche construction can have profound influence on the dynamics, competition and diversity of metapopulations. It can affect fine-scale spatially distribution of species and spatial heterogeneity of the environment. We further propose a few research directions with potentials, such as applying adaptive dynamics or spatial game theory to explore the effect of niche construction on phenotypic evolution and diversification.

  12. Microbial Ecology of Soil Aggregation in Agroecosystems

    Science.gov (United States)

    Hofmockel, K. S.; Bell, S.; Tfailly, M.; Thompson, A.; Callister, S.

    2017-12-01

    Crop selection and soil texture influence the physicochemical attributes of the soil, which structures microbial communities and influences soil C cycling storage. At the molecular scale, microbial metabolites and necromass alter the soil environment, which creates feedbacks that influence ecosystem functions, including soil C accumulation. By integrating lab to field studies we aim to identify the molecules, organisms and metabolic pathways that control carbon cycling and stabilization in bioenergy soils. We investigated the relative influence of plants, microbes, and minerals on soil aggregate ecology at the Great Lakes Bioenergy Research experiment. Sites in WI and MI, USA have been in corn and switchgrass cropping systems for a decade. By comparing soil aggregate ecology across sites and cropping systems we are able to test the relative importance of plant, microbe, mineral influences on soil aggregate dynamics. Soil microbial communities (16S) differ in diversity and phylogeny among sites and cropping systems. FT-ICR MS revealed differences in the molecular composition of water-soluble fraction of soil organic matter for cropping systems and soil origin for both relative abundance of assigned formulas and biogeochemical classes of compounds. We found the degree of aggregation, measured by mean weighted diameter of aggregate fractions, is influenced by plant-soil interactions. Similarly, the proportion of soil aggregate fractions varied by both soil and plant factors. Differences in aggregation were reflected in differences in bacterial, but not fungal community composition across aggregate fractions, within each soil. Scanning electron microscopy revealed stark differences in mineral-organic interactions that influence the microbial niche and the accessibility of substrates within the soil. The clay soils show greater surface heterogeneity, enabling interactions with organic fraction of the soil. This is consistent with molecular data that reveal differences

  13. Genome-Enabled Modeling of Biogeochemical Processes Predicts Metabolic Dependencies that Connect the Relative Fitness of Microbial Functional Guilds

    Science.gov (United States)

    Brodie, E.; King, E.; Molins, S.; Karaoz, U.; Steefel, C. I.; Banfield, J. F.; Beller, H. R.; Anantharaman, K.; Ligocki, T. J.; Trebotich, D.

    2015-12-01

    with genome-enabled reactive flow and transport we simulated the importance of pore network properties including connectivity in regulating metabolic interdependencies between microbial functional guilds.

  14. Rainwater Harvesting and Social Networks: Visualising Interactions for Niche Governance, Resilience and Sustainability

    Directory of Open Access Journals (Sweden)

    Sarah Ward

    2016-11-01

    Full Text Available Visualising interactions across urban water systems to explore transition and change processes requires the development of methods and models at different scales. This paper contributes a model representing the network interactions of rainwater harvesting (RWH infrastructure innovators and other organisations in the UK RWH niche to identify how resilience and sustainability feature within niche governance in practice. The RWH network interaction model was constructed using a modified participatory social network analysis (SNA. The SNA was further analysed through the application of a two-part analytical framework based on niche management and the safe, resilient and sustainable (‘Safe and SuRe’ framework. Weak interactions between some RWH infrastructure innovators and other organisations highlighted reliance on a limited number of persuaders to influence the regime and landscape, which were underrepresented. Features from niche creation and management were exhibited by the RWH network interaction model, though some observed characteristics were not represented. Additional Safe and SuRe features were identified covering diverse innovation, responsivity, no protection, unconverged expectations, primary influencers, polycentric or adaptive governance and multiple learning-types. These features enable RWH infrastructure innovators and other organisations to reflect on improving resilience and sustainability, though further research in other sectors would be useful to verify and validate observation of the seven features.

  15. A variational approach to niche construction.

    Science.gov (United States)

    Constant, Axel; Ramstead, Maxwell J D; Veissière, Samuel P L; Campbell, John O; Friston, Karl J

    2018-04-01

    In evolutionary biology, niche construction is sometimes described as a genuine evolutionary process whereby organisms, through their activities and regulatory mechanisms, modify their environment such as to steer their own evolutionary trajectory, and that of other species. There is ongoing debate, however, on the extent to which niche construction ought to be considered a bona fide evolutionary force, on a par with natural selection. Recent formulations of the variational free-energy principle as applied to the life sciences describe the properties of living systems, and their selection in evolution, in terms of variational inference. We argue that niche construction can be described using a variational approach. We propose new arguments to support the niche construction perspective, and to extend the variational approach to niche construction to current perspectives in various scientific fields. © 2018 The Authors.

  16. Competition and niche separation of pelagic bacteria in freshwater habitats.

    Science.gov (United States)

    Pernthaler, Jakob

    2017-06-01

    Freshwater bacterioplankton assemblages are composed of sympatric populations that can be delineated, for example, by ribosomal RNA gene relatedness and that differ in key ecophysiological properties. They may be free-living or attached, specialized for particular concentrations or subsets of substrates, or invest a variable amount of their resources in defence traits against protistan predators and viruses. Some may be motile and tactic whereas others are not, with far-reaching implications for their respective life styles and niche partitioning. The co-occurrence of competitors with overlapping growth requirements has profound consequences for the stability of community functions; it can to some extent be explained by habitat factors such as the microscale complexity and spatiotemporal variability of the lacustrine environments. On the other hand, the composition and diversity of freshwater microbial assemblages also reflects non-equilibrium states, dispersal and the stochasticity of community assembly processes. This review synoptically discusses the competition and niche separation of heterotrophic bacterial populations (defined at various levels of phylogenetic resolution) in the pelagic zone of inland surface waters from a variety of angles, focusing on habitat heterogeneity and the resulting biogeographic distribution patterns, the ecophysiological adaptations to the substrate field and the interactions of prokaryotes with predators and viruses. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  17. The United States pork niche market phenomenon.

    Science.gov (United States)

    Honeyman, M S; Pirog, R S; Huber, G H; Lammers, P J; Hermann, J R

    2006-08-01

    After the broad industrialization of the US pork industry, there has been a development of niche markets for export and domestic pork; that is, there is a pork niche market phenomenon. The US pork niche market phenomenon is characterized, and 2 of the major markets are explained in detail. With the Midwest's tradition of a diversified family-based agriculture and record low hog prices of the late 1990s, the conditions were conducive for this phenomenon to develop. Pork niche markets utilize various sales methods including Internet sales, local abattoir sales, direct marketing, farmer networks, and targeting to organized groups. In 2003, there were approximately 35 to 40 active pork niche marketing efforts in Iowa. The Berkshire breed is an example of a swine breed that has had a recent resurgence because of niche markets. Berkshire pork is known for tenderness and excellent quality. Berkshire registrations have increased 4-fold in the last 10 yr. One of the larger niche marketers of "natural pork" is Niman Ranch Pork, which has more than 400 farmer-producers and processes about 2,500 pigs weekly. Many US consumers of pork are interested in issues concerning the environment, food safety, pig welfare, and pig farm ownership and structure. These consumers may be willing to pay more for pork from farmers who are also concerned about these issues. Small- and medium-sized swine farmers are active in pork niche markets. Niche markets claim product differentiation by superior or unique product quality and social attributes. Quality attributes include certain swine breeds, and meat quality, freshness, taste or flavor, and tenderness. Social or credence attributes often are claimed and include freedom from antibiotics and growth promotants; local family farm production; natural, organic, outdoor, or bedded rearing; humane rearing; known origin; environmentally friendly production; and the absence of animal by-products in the feed. Niche pork markets and alternative swine

  18. Microbial biosensors for environmental monitoring

    Directory of Open Access Journals (Sweden)

    David VOGRINC

    2015-12-01

    Full Text Available Microbial biosensors are analytical devices capable of sensing substances in the environment due to the specific biological reaction of the microorganism or its parts. Construction of a microbial biosensor requires knowledge of microbial response to the specific analyte. Linking this response with the quantitative data, using a transducer, is the crucial step in the construction of a biosensor. Regarding the transducer type, biosensors are divided into electrochemical, optical biosensors and microbial fuel cells. The use of the proper configuration depends on the selection of the biosensing element. With the use of transgenic E. coli strains, bioluminescence or fluorescence based biosensors were developed. Microbial fuel cells enable the use of the heterogeneous microbial populations, isolated from wastewater. Different microorganisms are used for different pollutants – pesticides, heavy metals, phenolic compounds, organic waste, etc. Biosensing enables measurement of their concentration and their toxic or genotoxic effects on the microbes. Increasing environmental awareness has contributed to the increase of interest for biomonitoring. Although technologies, such as bioinformatics and genetic engineering, allow us to design complex and efficient microbial biosensors for environmental pollutants, the transfer of the laboratory work to the field still remains a problem to solve.

  19. The quick and the dead: microbial demography at the yeast thermal limit.

    Science.gov (United States)

    Maxwell, Colin S; Magwene, Paul M

    2017-03-01

    The niche of microorganisms is determined by where their populations can expand. Populations can fail to grow because of high death or low birth rates, but these are challenging to measure in microorganisms. We developed a novel technique that enables single-cell measurement of age-structured birth and death rates in the budding yeast, Saccharomyces cerevisiae, and used this method to study responses to heat stress in a genetically diverse panel of strains. We find that individual cells show significant heterogeneity in their rates of birth and death during heat stress. Genotype-by-environment effects on processes that regulate asymmetric cell division contribute to this heterogeneity. These lead to either premature senescence or early life mortality during heat stress, and we find that a mitochondrial inheritance defect explains the early life mortality phenotype of one of the strains we studied. This study demonstrates how the interplay of physiology, genetic variation and environmental variables influence where microbial populations survive and flourish. © 2016 John Wiley & Sons Ltd.

  20. THE NICHE CONSTRUCTION PERSPECTIVE: A CRITICAL APPRAISAL*

    Science.gov (United States)

    Scott-Phillips, Thomas C; Laland, Kevin N; Shuker, David M; Dickins, Thomas E; West, Stuart A

    2014-01-01

    Niche construction refers to the activities of organisms that bring about changes in their environments, many of which are evolutionarily and ecologically consequential. Advocates of niche construction theory (NCT) believe that standard evolutionary theory fails to recognize the full importance of niche construction, and consequently propose a novel view of evolution, in which niche construction and its legacy over time (ecological inheritance) are described as evolutionary processes, equivalent in importance to natural selection. Here, we subject NCT to critical evaluation, in the form of a collaboration between one prominent advocate of NCT, and a team of skeptics. We discuss whether niche construction is an evolutionary process, whether NCT obscures or clarifies how natural selection leads to organismal adaptation, and whether niche construction and natural selection are of equivalent explanatory importance. We also consider whether the literature that promotes NCT overstates the significance of niche construction, whether it is internally coherent, and whether it accurately portrays standard evolutionary theory. Our disagreements reflect a wider dispute within evolutionary theory over whether the neo-Darwinian synthesis is in need of reformulation, as well as different usages of some key terms (e.g., evolutionary process). PMID:24325256

  1. The niche party concept and its measurement

    OpenAIRE

    Meyer, Thomas M; Miller, Bernhard

    2015-01-01

    The concept of the niche party has become increasingly popular in analyses of party competition. Yet, existing approaches vary in their definitions and their measurement approaches. We propose using a minimal definition that allows us to compare political parties in terms of their ?nicheness?. We argue that the conceptual core of the niche party concept is based on issue emphasis and that a niche party emphasizes policy areas neglected by its rivals. Based on this definition, we propose a con...

  2. Does niche divergence accompany allopatric divergence in Aphelocoma jays as predicted under ecological speciation? Insights from tests with niche models.

    Science.gov (United States)

    McCormack, John E; Zellmer, Amanda J; Knowles, L Lacey

    2010-05-01

    The role of ecology in the origin of species has been the subject of long-standing interest to evolutionary biologists. New sources of spatially explicit ecological data allow for large-scale tests of whether speciation is associated with niche divergence or whether closely related species tend to be similar ecologically (niche conservatism). Because of the confounding effects of spatial autocorrelation of environmental variables, we generate null expectations for niche divergence for both an ecological-niche modeling and a multivariate approach to address the question: do allopatrically distributed taxa occupy similar niches? In a classic system for the study of niche evolution--the Aphelocoma jays--we show that there is little evidence for niche divergence among Mexican Jay (A. ultramarina) lineages in the process of speciation, contrary to previous results. In contrast, Aphelocoma species that exist in partial sympatry in some regions show evidence for niche divergence. Our approach is widely applicable to the many cases of allopatric lineages in the beginning stages of speciation. These results do not support an ecological speciation model for Mexican Jay lineages because, in most cases, the allopatric environments they occupy are not significantly more divergent than expected under a null model.

  3. Plant stem cell niches.

    Science.gov (United States)

    Stahl, Yvonne; Simon, Rüdiger

    2005-01-01

    Stem cells are required to support the indeterminate growth style of plants. Meristems are a plants stem cell niches that foster stem cell survival and the production of descendants destined for differentiation. In shoot meristems, stem cell fate is decided at the populational level. The size of the stem cell domain at the meristem tip depends on signals that are exchanged with cells of the organizing centre underneath. In root meristems, individual stem cells are controlled by direct interaction with cells of the quiescent centre that lie in the immediate neighbourhood. Analysis of the interactions and signaling processes in the stem cell niches has delivered some insights into the molecules that are involved and revealed that the two major niches for plant stem cells are more similar than anticipated.

  4. Microbial biosensors

    International Nuclear Information System (INIS)

    Le Yu; Chen, Wilfred; Mulchandani, Ashok

    2006-01-01

    A microbial biosensor is an analytical device that couples microorganisms with a transducer to enable rapid, accurate and sensitive detection of target analytes in fields as diverse as medicine, environmental monitoring, defense, food processing and safety. The earlier microbial biosensors used the respiratory and metabolic functions of the microorganisms to detect a substance that is either a substrate or an inhibitor of these processes. Recently, genetically engineered microorganisms based on fusing of the lux, gfp or lacZ gene reporters to an inducible gene promoter have been widely applied to assay toxicity and bioavailability. This paper reviews the recent trends in the development and application of microbial biosensors. Current advances and prospective future direction in developing microbial biosensor have also been discussed

  5. Bone Marrow Vascular Niche: Home for Hematopoietic Stem Cells

    Directory of Open Access Journals (Sweden)

    Ningning He

    2014-01-01

    Full Text Available Though discovered later than osteoblastic niche, vascular niche has been regarded as an alternative indispensable niche operating regulation on hematopoietic stem cells (HSCs. As significant progresses gained on this type niche, it is gradually clear that the main work of vascular niche is undertaking to support hematopoiesis. However, compared to what have been defined in the mechanisms through which the osteoblastic niche regulates hematopoiesis, we know less in vascular niche. In this review, based on research data hitherto we will focus on component foundation and various functions of vascular niche that guarantee the normal hematopoiesis process within bone marrow microenvironments. And the possible pathways raised by various research results through which this environment undergoes its function will be discussed as well.

  6. Niche-specific cognitive strategies

    DEFF Research Database (Denmark)

    Hulgard, K.; Ratcliffe, J. M.

    2014-01-01

    Related species with different diets are predicted to rely on different cognitive strategies: those best suited for locating available and appropriate foods. Here we tested two predictions of the niche-specific cognitive strategies hypothesis in bats, which suggests that predatory species should...... the niche-specific cognitive strategies hypothesis and suggest that for gleaning and clutter-resistant aerial hawking bats, learning to associate shape with food interferes with subsequent spatial memory learning....

  7. Functional traits, convergent evolution, and periodic tables of niches.

    Science.gov (United States)

    Winemiller, Kirk O; Fitzgerald, Daniel B; Bower, Luke M; Pianka, Eric R

    2015-08-01

    Ecology is often said to lack general theories sufficiently predictive for applications. Here, we examine the concept of a periodic table of niches and feasibility of niche classification schemes from functional trait and performance data. Niche differences and their influence on ecological patterns and processes could be revealed effectively by first performing data reduction/ordination analyses separately on matrices of trait and performance data compiled according to logical associations with five basic niche 'dimensions', or aspects: habitat, life history, trophic, defence and metabolic. Resultant patterns then are integrated to produce interpretable niche gradients, ordinations and classifications. Degree of scheme periodicity would depend on degrees of niche conservatism and convergence causing species clustering across multiple niche dimensions. We analysed a sample data set containing trait and performance data to contrast two approaches for producing niche schemes: species ordination within niche gradient space, and niche categorisation according to trait-value thresholds. Creation of niche schemes useful for advancing ecological knowledge and its applications will depend on research that produces functional trait and performance datasets directly related to niche dimensions along with criteria for data standardisation and quality. As larger databases are compiled, opportunities will emerge to explore new methods for data reduction, ordination and classification. © 2015 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

  8. Ecological niche of plant pathogens

    Directory of Open Access Journals (Sweden)

    Ecaterina Fodor

    2011-06-01

    Full Text Available Disease ecology is a new approach to the understanding of the spread and dynamics of pathogens in natural and man-made environments. Defining and describing the ecological niche of the pathogens is one of the major tasks for ecological theory, as well as for practitioners preoccupied with the control and forecasting of established and emerging diseases. Niche theory has been periodically revised, not including in an explicit way the pathogens. However, many progresses have been achieved in niche modeling of disease spread, but few attempts were made to construct a theoretical frame for the ecological niche of pathogens. The paper is a review of the knowledge accumulated during last decades in the niche theory of pathogens and proposes an ecological approach in research. It quest for new control methods in what concerns forest plant pathogens, with a special emphasis on fungi like organisms of the genus Phytophthora. Species of Phytophthora are the most successful plant pathogens of the moment, affecting forest and agricultural systems worldwide, many of them being invasive alien organisms in many ecosystems. The hyperspace of their ecological niche is defined by hosts, environment and human interference, as main axes. To select most important variables within the hyperspace, is important the understanding of the complex role of pathogens in the ecosystems as well as for control programs. Biotic relationships within ecosystem of host-pathogen couple are depicted by ecological network and specific metrics attached to this. The star shaped network is characterized by few high degree nodes, by short path lengths and relatively low connectivity, premises for a rapid disturbance spread. 

  9. Ecological niche of plant pathogens

    Directory of Open Access Journals (Sweden)

    Ecaterina Fodor

    2011-02-01

    Full Text Available Disease ecology is a new approach to the understanding of the spread and dynamics of pathogens in natural and man-made environments. Defining and describing the ecological niche of the pathogens is one of the major tasks for ecological theory, as well as for practitioners preoccupied with the control and forecasting of established and emerging diseases. Niche theory has been periodically revised, not including in an explicit way the pathogens. However, many progresses have been achieved in niche modeling of disease spread, but few attempts were made to construct a theoretical frame for the ecological niche of pathogens. The paper is a review of the knowledge accumulated during last decades in the niche theory of pathogens and proposes an ecological approach in research. It quest for new control methods in what concerns forest plant pathogens, with a special emphasis on fungi like organisms of the genus Phytophthora. Species of Phytophthora are the most successful plant pathogens of the moment, affecting forest and agricultural systems worldwide, many of them being invasive alien organisms in many ecosystems. The hyperspace of their ecological niche is defined by hosts, environment and human interference, as main axes. To select most important variables within the hyperspace, is important for the understanding of the complex role of pathogens in the ecosystems as well as for control programs. Biotic relationships within ecosystem of host-pathogen couple are depicted by ecological network and specific metrics attached to this. The star shaped network is characterized by few high degree nodes, by short path lengths and relatively low connectivity, premises for a rapid disturbance spread.

  10. CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline.

    Science.gov (United States)

    Agrawal, Sonia; Arze, Cesar; Adkins, Ricky S; Crabtree, Jonathan; Riley, David; Vangala, Mahesh; Galens, Kevin; Fraser, Claire M; Tettelin, Hervé; White, Owen; Angiuoli, Samuel V; Mahurkar, Anup; Fricke, W Florian

    2017-04-27

    The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuitive, automated, and cloud-enabled analysis pipeline for comparative microbial genomics. CloVR-Comparative runs on annotated complete or draft genome sequences that are uploaded by the user or selected via a taxonomic tree-based user interface and downloaded from NCBI. CloVR-Comparative runs reference-free multiple whole-genome alignments to determine unique, shared and core coding sequences (CDSs) and single nucleotide polymorphisms (SNPs). Output includes short summary reports and detailed text-based results files, graphical visualizations (phylogenetic trees, circular figures), and a database file linked to the Sybil comparative genome browser. Data up- and download, pipeline configuration and monitoring, and access to Sybil are managed through CloVR-Comparative web interface. CloVR-Comparative and Sybil are distributed as part of the CloVR virtual appliance, which runs on local computers or the Amazon EC2 cloud. Representative datasets (e.g. 40 draft and complete Escherichia coli genomes) are processed in genomics projects, while eliminating the need for on-site computational resources and expertise.

  11. A locomotor innovation enables water-land transition in a marine fish.

    Directory of Open Access Journals (Sweden)

    Shi-Tong Tonia Hsieh

    Full Text Available BACKGROUND: Morphological innovations that significantly enhance performance capacity may enable exploitation of new resources and invasion of new ecological niches. The invasion of land from the aquatic realm requires dramatic structural and physiological modifications to permit survival in a gravity-dominated, aerial environment. Most fishes are obligatorily aquatic, with amphibious fishes typically making slow-moving and short forays on to land. METHODOLOGY/PRINCIPAL FINDINGS: Here I describe the behaviors and movements of a little known marine fish that moves extraordinarily rapidly on land. I found that the Pacific leaping blenny, Alticus arnoldorum, employs a tail-twisting movement on land, previously unreported in fishes. Focal point behavioral observations of Alticus show that they have largely abandoned the marine realm, feed and reproduce on land, and even defend terrestrial territories. Comparisons of these blennies' terrestrial kinematic and kinetic (i.e., force measurements with those of less terrestrial sister genera show A. arnoldorum move with greater stability and locomotor control, and can move away more rapidly from impending threats. CONCLUSIONS/SIGNIFICANCE: My results demonstrate that axial tail twisting serves as a key innovation enabling invasion of a novel marine niche. This paper highlights the potential of using this system to address general evolutionary questions about water-land transitions and niche invasions.

  12. The niche construction perspective: a critical appraisal.

    Science.gov (United States)

    Scott-Phillips, Thomas C; Laland, Kevin N; Shuker, David M; Dickins, Thomas E; West, Stuart A

    2014-05-01

    Niche construction refers to the activities of organisms that bring about changes in their environments, many of which are evolutionarily and ecologically consequential. Advocates of niche construction theory (NCT) believe that standard evolutionary theory fails to recognize the full importance of niche construction, and consequently propose a novel view of evolution, in which niche construction and its legacy over time (ecological inheritance) are described as evolutionary processes, equivalent in importance to natural selection. Here, we subject NCT to critical evaluation, in the form of a collaboration between one prominent advocate of NCT, and a team of skeptics. We discuss whether niche construction is an evolutionary process, whether NCT obscures or clarifies how natural selection leads to organismal adaptation, and whether niche construction and natural selection are of equivalent explanatory importance. We also consider whether the literature that promotes NCT overstates the significance of niche construction, whether it is internally coherent, and whether it accurately portrays standard evolutionary theory. Our disagreements reflect a wider dispute within evolutionary theory over whether the neo-Darwinian synthesis is in need of reformulation, as well as different usages of some key terms (e.g., evolutionary process). © 2013 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

  13. c-Kit-mediated functional positioning of stem cells to their niches is essential for maintenance and regeneration of adult hematopoiesis.

    Directory of Open Access Journals (Sweden)

    Yuki Kimura

    Full Text Available The mechanism by which hematopoietic stem and progenitor cells (HSPCs through interaction with their niches maintain and reconstitute adult hematopoietic cells is unknown. To functionally and genetically track localization of HSPCs with their niches, we employed novel mutant loxPs, lox66 and lox71 and Cre-recombinase technology to conditionally delete c-Kit in adult mice, while simultaneously enabling GFP expression in the c-Kit-deficient cells. Conditional deletion of c-Kit resulted in hematopoietic failure and splenic atrophy both at steady state and after marrow ablation leading to the demise of the treated adult mice. Within the marrow, the c-Kit-expressing GFP(+ cells were positioned to Kit ligand (KL-expressing niche cells. This c-Kit-mediated cellular adhesion was essential for long-term maintenance and expansion of HSPCs. These results lay the foundation for delivering KL within specific niches to maintain and restore hematopoiesis.

  14. The niche party concept and its measurement.

    Science.gov (United States)

    Meyer, Thomas M; Miller, Bernhard

    2015-03-01

    The concept of the niche party has become increasingly popular in analyses of party competition. Yet, existing approaches vary in their definitions and their measurement approaches. We propose using a minimal definition that allows us to compare political parties in terms of their 'nicheness'. We argue that the conceptual core of the niche party concept is based on issue emphasis and that a niche party emphasizes policy areas neglected by its rivals. Based on this definition, we propose a continuous measure that allows for more fine-grained measurement of a party's 'nicheness' than the dominant, dichotomous approaches and thereby limits the risk of measurement error. Drawing on data collected by the Comparative Manifesto Project, we show that (1) our measure has high face validity and (2) exposes differences among parties that are not captured by alternative, static or dichotomous measures.

  15. Plant stem cell niches.

    Science.gov (United States)

    Aichinger, Ernst; Kornet, Noortje; Friedrich, Thomas; Laux, Thomas

    2012-01-01

    Multicellular organisms possess pluripotent stem cells to form new organs, replenish the daily loss of cells, or regenerate organs after injury. Stem cells are maintained in specific environments, the stem cell niches, that provide signals to block differentiation. In plants, stem cell niches are situated in the shoot, root, and vascular meristems-self-perpetuating units of organ formation. Plants' lifelong activity-which, as in the case of trees, can extend over more than a thousand years-requires that a robust regulatory network keep the balance between pluripotent stem cells and differentiating descendants. In this review, we focus on current models in plant stem cell research elaborated during the past two decades, mainly in the model plant Arabidopsis thaliana. We address the roles of mobile signals on transcriptional modules involved in balancing cell fates. In addition, we discuss shared features of and differences between the distinct stem cell niches of Arabidopsis.

  16. The evolution of climatic niches in squamate reptiles.

    Science.gov (United States)

    Pie, Marcio R; Campos, Leonardo L F; Meyer, Andreas L S; Duran, Andressa

    2017-07-12

    Despite the remarkable diversity found in squamate reptiles, most of their species tend to be found in warm/dry environments, suggesting that climatic requirements played a crucial role in their diversification, yet little is known about the evolution of their climatic niches. In this study, we integrate climatic information associated with the geographical distribution of 1882 squamate species and their phylogenetic relationships to investigate the tempo and mode of climatic niche evolution in squamates, both over time and among lineages. We found that changes in climatic niche dynamics were pronounced over their recent squamate evolutionary history, and we identified extensive evidence for rate heterogeneity in squamate climatic niche evolution. Most rate shifts involved accelerations, particularly over the past 50 Myr. Most squamates occupy similar regions of the climatic niche space, with only a few lineages diversifying into colder and humid climatic conditions. The changes from arid to mesic conditions in some regions of the globe may have provided opportunities for climatic niche evolution, although most lineages tended to remain near their ancestral niche. Variation in rates of climatic niche evolution seems common, particularly in response to the availability of new climatic conditions over evolutionary time. © 2017 The Author(s).

  17. The HysNiche trial: hysteroscopic resection of uterine caesarean scar defect (niche) in patients with abnormal bleeding, a randomised controlled trial.

    Science.gov (United States)

    Vervoort, A J M W; Van der Voet, L F; Witmer, M; Thurkow, A L; Radder, C M; van Kesteren, P J M; Quartero, H W P; Kuchenbecker, W K H; Bongers, M Y; Geomini, P M A J; de Vleeschouwer, L H M; van Hooff, M H A; van Vliet, H A A M; Veersema, S; Renes, W B; van Meurs, H S; Bosmans, J; Oude Rengerink, K; Brölmann, H A M; Mol, B W J; Huirne, J A F

    2015-11-12

    A caesarean section (CS) can cause a defect or disruption of the myometrium at the site of the uterine scar, called a niche. In recent years, an association between a niche and postmenstrual spotting after a CS has been demonstrated. Hysteroscopic resection of these niches is thought to reduce spotting and menstrual pain. However, there are no randomised trials assessing the effectiveness of a hysteroscopic niche resection. We planned a multicentre randomised trial comparing hysteroscopic niche resection to no intervention. We study women with postmenstrual spotting after a CS and a niche with a residual myometrium of at least 3 mm during sonohysterography. After informed consent is obtained, eligible women will be randomly allocated to hysteroscopic resection of the niche or expectant management for 6 months. The primary outcome is the number of days with postmenstrual spotting during one menstrual cycle 6 months after randomisation. Secondary outcomes are menstrual characteristics, menstruation related pain and experienced discomfort due to spotting or menstrual pain, quality of life, patient satisfaction, sexual function, urological symptoms, medical consultations, medication use, complications, lost productivity and medical costs. Measurements will be performed at baseline and at 3 and 6 months after randomisation. A cost-effectiveness analysis will be performed from a societal perspective at 6 months after randomisation. This trial will provide insight in the (cost)effectiveness of hysteroscopic resection of a niche versus expectant management in women who have postmenstrual spotting and a niche with sufficient residual myometrium to perform a hysteroscopic niche resection. Dutch Trial Register NTR3269 . Registered 1 February 2012. ZonMw Grant number 80-82305-97-12030.

  18. Local niche planning and its strategic implications for implementation of energy-efficient technology

    DEFF Research Database (Denmark)

    Quitzau, Maj-Britt; Hoffmann, Birgitte; Elle, Morten

    2012-01-01

    -management process for enabling transitions. The study outlines the proactive spatial planning of a Danish local authority in order to illustrate how the strategic work performed in this kind of local development project represents a special form of niche management that is able to create room for innovation...... such a gap between policy visions and their implementation in practice specific forms of strategic work is needed, according to new transformative ideas in spatial planning. The aim of this paper is to characterize the transformative capacities of this kind of strategic work at the spatial scale of the town...... in order to assess how such activities engage with sustainable transitions. The theoretical contribution of the paper is to compare strategic work performed in transformative forms of spatial planning with the strategic work intended in strategic niche management, which represent a change...

  19. A review of gastrointestinal microbiology with special emphasis on molecular microbial ecology approaches

    International Nuclear Information System (INIS)

    Mackie, R.I.; Cann, I.K.O.

    2005-01-01

    ecology in gut ecosystems involves investigation of the organisms present (abundance and diversity), their activity (usually determined in vitro, but in vivo activity or expression of activity is really required), and their relationship with each other and the host animal (synergistic and competitive interactions). This entails the study and measurement of many types of interactions, both beneficial and competitive. Traditionally, media for isolation of bacteria from natural environments are basically of two types: those that simulate the habitat in broad terns, i.e. habitat-simulating and non-selective media; and those designed to enumerate and isolate bacteria of a particular type or from a specific biochemical niche, i.e. niche-simulating or functional or nutritional group analysis. A third type, less important in the ecological sense, does not simulate the habitat, is often highly selective and is used to isolate specific bacterial groups. Specific nutritional types of bacteria may be isolated by the use of enrichment media. This type of medium, basically a refinement of the habitat-simulating medium, is widely used in environmental microbiology and has been applied with some success to the gut ecosystem. Although estimates of microbial number rely on culture techniques, microscopic examination is a most useful technique for evaluating the efficacy of other enumeration approaches. The combination of microscopy with specific phylogenetic stains or fluorescent antibodies enables bacteria to be specifically detected and enumerated in mixed populations. The introduction of genetic-based technologies, and in particular those relating to 16S rRNA typing, are rapidly replacing conventional detection and enumeration methods in studies of the mammalian intestinal tract. Although molecular techniques promise a fuller and more accurate description of the true diversity, structure and dynamics of complex microbial communities than the present culturing studies, each technique

  20. Modulating the stem cell niche for tissue regeneration

    Science.gov (United States)

    Lane, Steven W; Williams, David A; Watt, Fiona M

    2015-01-01

    The field of regenerative medicine holds considerable promise for treating diseases that are currently intractable. Although many researchers are adopting the strategy of cell transplantation for tissue repair, an alternative approach to therapy is to manipulate the stem cell microenvironment, or niche, to facilitate repair by endogenous stem cells. The niche is highly dynamic, with multiple opportunities for intervention. These include administration of small molecules, biologics or biomaterials that target specific aspects of the niche, such as cell-cell and cell–extracellular matrix interactions, to stimulate expansion or differentiation of stem cells, or to cause reversion of differentiated cells to stem cells. Nevertheless, there are several challenges in targeting the niche therapeutically, not least that of achieving specificity of delivery and responses. We envisage that successful treatments in regenerative medicine will involve different combinations of factors to target stem cells and niche cells, applied at different times to effect recovery according to the dynamics of stem cell–niche interactions. PMID:25093887

  1. [Mesenchymal stroma cells and their niche].

    Science.gov (United States)

    Schneider, R K

    2013-11-01

    Stem cells reside in a highly specialized, complex microenvironment that is known as the stem cell niche. The stem cell niche can be described as an anatomically defined space where the stem cell is localized and nourished and stem cell quiescence, proliferation and differentiation are maintained. Tissue engineering aims to imitate the stem cell niche to (I) induce a directed differentiation, (II) maintain the self-renewal capacity or (III) find a regulated balance between self-renewal and differentiation. Mesenchymal stem or stromal cells (MSC) can differentiate in three-dimensional collagen gels into functional osteoblasts when subjected to a phosphate-rich cultivation medium. Furthermore, they acquire a prosynthetic, matrix remodeling, contractile phenotype. Medial artery calcification in patients with chronic kidney disease also proceeds through intramembranous ossification resulting from osteoblast-induced calcification of the collagen extracellular matrix. Thus, the influence of uremic cultivation conditions as a pathophysiological stimulus on MSC and endothelial cells was analyzed with special regards to matrix remodeling, vascularization and calcification. The results showed that BMP-2/4 mediated MSC (mal)differentiation into osteoblasts with acquired matrix remodeling phenotype and loss of proangiogenic capacity. These studies have led to the conclusion that uremia has detrimental effects on the stem cell niche and promotes the continuous calcification by osteogenic (mal)differentiation. In summary, recent studies have shown the conducting and regulating effect of the stem cell niche under physiological conditions that can be applied and mimicked for tissue engineering applications. However, under pathological conditions the stem cell niche can have detrimental effects on stem cell function and can promote disease progression.

  2. Lipid Biomarkers for a Hypersaline Microbial Mat Community

    Science.gov (United States)

    Jahnke, Linda L.; Embaye, Tsege; Turk, Kendra A.

    2003-01-01

    The use of lipid biomarkers and their carbon isotopic compositions are valuable tools for establishing links to ancient microbial ecosystems. As witnessed by the stromatolite record, benthic microbial mats grew in shallow water lagoonal environments where microorganisms had virtually no competition apart from the harsh conditions of hypersalinity, desiccation and intense light. Today, the modern counterparts of these microbial ecosystems find appropriate niches in only a few places where extremes eliminate eukaryotic grazers. Answers to many outstanding questions about the evolution of microorganisms and their environments on early Earth are best answered through study of these extant analogs. Lipids associated with various groups of bacteria can be valuable biomarkers for identification of specific groups of microorganisms both in ancient organic-rich sedimentary rocks (geolipids) and contemporary microbial communities (membrane lipids). Use of compound specific isotope analysis adds additional refinement to the identification of biomarker source, so that it is possible to take advantage of the 3C-depletions associated with various functional groups of organisms (i.e. autotrophs, heterotrophs, methanotrophs, methanogens) responsible for the cycling of carbon within a microbial community. Our recent work has focused on a set of hypersaline evaporation ponds at Guerrero Negro, Baja California Sur, Mexico which support the abundant growth of Microcoleus-dominated microbial mats. Specific biomarkers for diatoms, cyanobacteria, archaea, green nonsulfur (GNS), sulfate reducing, and methanotrophic bacteria have been identified. Analyses of the ester-bound fatty acids indicate a highly diverse microbial community, dominated by photosynthetic organisms at the surface.

  3. Vascular and perivascular niches, but not the osteoblastic niche, are numerically restored following allogeneic hematopoietic stem cell transplantation in patients with aplastic anemia.

    Science.gov (United States)

    Wu, Liangliang; Mo, Wenjian; Zhang, Yuping; Zhou, Ming; Li, Yumiao; Zhou, Ruiqing; Xu, Shiling; Pan, Shiyi; Deng, Hui; Mao, Ping; Wang, Shunqing

    2017-07-01

    Bone marrow (BM) niches, including the osteoblastic, vascular, and perivascular niches, are numerically impaired in patients with aplastic anemia (AA). It remains unclear whether these niches are numerically restored in AA patients after allogenic hematopoietic stem cell transplantation (allo-HSCT). To investigate changes in BM niches, we monitored 52 patients with AA who had undergone allo-HSCT and performed immunohistochemical studies of BM niches using antibodies against CD34, CD146, and osteopontin. After allo-HSCT, patients with AA exhibited a remarkable increase in the number of cellular elements in the BM niches, including the vascular and perivascular cells. However, no significant differences in endosteal cells were detected. We explored the cause of this restoration by analyzing the origin of BM mesenchymal stem cells (BM-MSCs) and the expression of cytokines in BM plasma. STR-PCR revealed that the BM-MSCs were derived from the host, not the donor. In addition, significantly elevated levels of vascular endothelial growth factor (VEGF) were found after allo-HSCT. Our data indicates that vascular and perivascular niches are numerically restored, but the endosteal niche remains numerically impaired in patients with AA after allo-HSCT, and that levels of VEGF, but not donor-derived BM-MSCs, may correlate with the restoration of BM niches.

  4. Comparison of the microbial communities of hot springs waters and the microbial biofilms in the acidic geothermal area of Copahue (Neuquén, Argentina).

    Science.gov (United States)

    Urbieta, María Sofía; González-Toril, Elena; Bazán, Ángeles Aguilera; Giaveno, María Alejandra; Donati, Edgardo

    2015-03-01

    Copahue is a natural geothermal field (Neuquén province, Argentina) dominated by the Copahue volcano. As a consequence of the sustained volcanic activity, Copahue presents many acidic pools, hot springs and solfataras with different temperature and pH conditions that influence their microbial diversity. The occurrence of microbial biofilms was observed on the surrounding rocks and the borders of the ponds, where water movements and thermal activity are less intense. Microbial biofilms are particular ecological niches within geothermal environments; they present different geochemical conditions from that found in the water of the ponds and hot springs which is reflected in different microbial community structure. The aim of this study is to compare microbial community diversity in the water of ponds and hot springs and in microbial biofilms in the Copahue geothermal field, with particular emphasis on Cyanobacteria and other photosynthetic species that have not been detected before in Copahue. In this study, we report the presence of Cyanobacteria, Chloroflexi and chloroplasts of eukaryotes in the microbial biofilms not detected in the water of the ponds. On the other hand, acidophilic bacteria, the predominant species in the water of moderate temperature ponds, are almost absent in the microbial biofilms in spite of having in some cases similar temperature conditions. Species affiliated with Sulfolobales in the Archaea domain are the predominant microorganism in high temperature ponds and were also detected in the microbial biofilms.

  5. The HysNiche trial: hysteroscopic resection of uterine caesarean scar defect (niche) in patients with abnormal bleeding, a randomised controlled trial

    NARCIS (Netherlands)

    Vervoort, A. J. M. W.; van der Voet, L. F.; Witmer, M.; Thurkow, A. L.; Radder, C. M.; van Kesteren, P. J. M.; Quartero, H. W. P.; Kuchenbecker, W. K. H.; Bongers, M. Y.; Geomini, P. M. A. J.; de Vleeschouwer, L. H. M.; van Hooff, M. H. A.; van Vliet, H. A. A. M.; Veersema, S.; Renes, W. B.; van Meurs, H. S.; Bosmans, J.; Oude Rengerink, K.; Brölmann, H. A. M.; Mol, B. W. J.; Huirne, J. A. F.

    2015-01-01

    A caesarean section (CS) can cause a defect or disruption of the myometrium at the site of the uterine scar, called a niche. In recent years, an association between a niche and postmenstrual spotting after a CS has been demonstrated. Hysteroscopic resection of these niches is thought to reduce

  6. Sustainable energy transitions in emerging economies: The formation of a palm oil biomass waste-to-energy niche in Malaysia 1990–2011

    International Nuclear Information System (INIS)

    Hansen, Ulrich Elmer; Nygaard, Ivan

    2014-01-01

    The economic development in emerging economies in Southeast Asia has significantly increased the use of fossil fuel based energy. This has severe implications for global climate change, and against this background, scholars within the sustainable transition tradition have taken an interest in addressing how transitions towards more sustainable development pathways in this region may be achieved. This paper contributes to the abovementioned literature by examining the conducive and limiting factors for development and proliferation of a palm oil biomass waste-to-energy niche in Malaysia during the period 1990–2011. Rising oil prices, strong pressure on the palm oil industry from environmental groups, and a persisting palm oil biomass waste disposal problem in Malaysia appear to have been conducive to niche proliferation, and on top of this national renewable energy policies and large-scale donor programmes have specifically supported the utilisation of palm oil biomass waste for energy. However, in spite of this, the niche development process has only made slow progress. The paper identifies reluctant implementation of energy policy, rise in biomass resource prices, limited network formation and negative results at the niche level, as the main factors hindering niche development. - Highlights: • We examine crucial factors for developing a biomass-to-energy niche in Malaysia. • In spite of interventions for policy support the niche has only made slow progress. • Oil prices, NGO pressure, waste problems and policy support were the enabling factors. • First, reluctant implementation of energy policy was hindering niche development. • Later, low performance level of implemented plants was hindering niche development

  7. Microbial endocrinology: Why the intersection of microbiology and neurobiology matters to poultry health.

    Science.gov (United States)

    Villageliu, Daniel N; Lyte, Mark

    2017-08-01

    The union of microbiology and neurobiology has led to a revolution in the way we view the microbiome. Now recognized as important symbionts, the microorganisms which inhabit multiple niches in mammalian and avian (chicken) hosts, such as the intestinal tract and skin, serve and influence many important physiological functions. The realization that the gut microbiome serves as a kind of "microbial organ" has important implications for many areas of biology. In this paper advances in the field of microbial endocrinology which may hold relevance for the poultry industry are examined. © 2017 Poultry Science Association Inc.

  8. Diet and trophic niche of Lithobates catesbeianus (Amphibia: Anura

    Directory of Open Access Journals (Sweden)

    Peterson T. Leivas

    2012-10-01

    Full Text Available Lithobates catesbeianus (Shaw, 1802 is an invasive anuran introduced in Brazil that is associated with the displacement and the decline of populations of native species worldwide. There is evidence that biological invasions are facilitated by certain attributes of the invading species, for instance niche breath, and that invasive species have a broader ecological niche with respect to native ones. We designed a study to ascertain the temporal, ontogenetic, and sex differences in the niche dynamics of the American bullfrog. We sampled monthly from June 2008 to May 2009 in the state of Paraná, southern Brazil. For each individual, we gathered biometric and stomach content data. We then estimated the niche breath of the juveniles and adults, and compared it between the sexes. A total of 104 females and 77 males were sampled. Lithobates catesbeianus has a generalist diet, preying upon invertebrates and vertebrates. Even though the diet of the studied population varied seasonally, it did not differ between the sexes nor did it respond to biometric variables. Niche breadth was more restricted in the winter than in the autumn. The trophic niche of juveniles and adults did not overlap much when compared with the trophic niche overlap between males and females. Adult males and females had a considerable niche overlap, but females had a broader trophic niche than males in the winter and in the spring. These niche characteristics point to an opportunistic predation strategy that may have facilitated the process of invasion and establishment of this species in the study area.

  9. Niches for the Long-Term Maintenance of Tissue-Resident Memory T Cells

    Science.gov (United States)

    Takamura, Shiki

    2018-01-01

    Tissue-resident memory T cells (TRM cells) are a population of immune cells that reside in the lymphoid and non-lymphoid organs without recirculation through the blood. These important cells occupy and utilize unique anatomical and physiological niches that are distinct from those for other memory T cell populations, such as central memory T cells in the secondary lymphoid organs and effector memory T cells that circulate through the tissues. CD8+ TRM cells typically localize in the epithelial layers of barrier tissues where they are optimally positioned to act as sentinels to trigger antigen-specific protection against reinfection. CD4+ TRM cells typically localize below the epithelial layers, such as below the basement membrane, and cluster in lymphoid structures designed to optimize interactions with antigen-presenting cells upon reinfection. A key feature of TRM populations is their ability to be maintained in barrier tissues for prolonged periods of time. For example, skin CD8+ TRM cells displace epidermal niches originally occupied by γδ T cells, thereby enabling their stable persistence for years. It is also clear that the long-term maintenance of TRM cells in different microenvironments is dependent on multiple tissue-specific survival cues, although the specific details are poorly understood. However, not all TRM persist over the long term. Recently, we identified a new spatial niche for the maintenance of CD8+ TRM cells in the lung, which is created at the site of tissue regeneration after injury [termed repair-associated memory depots (RAMD)]. The short-lived nature of RAMD potentially explains the short lifespans of CD8+ TRM cells in this particular tissue. Clearly, a better understanding of the niche-dependent maintenance of TRM cells will be important for the development of vaccines designed to promote barrier immunity. In this review, we discuss recent advances in our understanding of the properties and nature of tissue-specific niches that

  10. Ecological and evolutionary consequences of niche construction for its agent.

    Science.gov (United States)

    Kylafis, Grigoris; Loreau, Michel

    2008-10-01

    Niche construction can generate ecological and evolutionary feedbacks that have been underinvestigated so far. We present an eco-evolutionary model that incorporates the process of niche construction to reveal its effects on the ecology and evolution of the niche-constructing agent. We consider a simple plant-soil nutrient ecosystem in which plants have the ability to increase the input of inorganic nutrient as an example of positive niche construction. On an ecological time scale, the model shows that niche construction allows the persistence of plants under infertile soil conditions that would otherwise lead to their extinction. This expansion of plants' niche, however, requires a high enough rate of niche construction and a high enough initial plant biomass to fuel the positive ecological feedback between plants and their soil environment. On an evolutionary time scale, we consider that the rates of niche construction and nutrient uptake coevolve in plants while a trade-off constrains their values. Different evolutionary outcomes are possible depending on the shape of the trade-off. We show that niche construction results in an evolutionary feedback between plants and their soil environment such that plants partially regulate soil nutrient content. The direct benefit accruing to plants, however, plays a crucial role in the evolutionary advantage of niche construction.

  11. Market niche analysis in the casino gaming industry.

    Science.gov (United States)

    Dandurand, L

    1990-03-01

    This article discusses the nature of market niche analysis in the casino gaming industry. It presents four approaches for conducting market niche analysis. An an example of one approach, the Las Vegas Visitor Profile Study is used to identify a premium niche in the Las Vegas Slot Target Market. A detailed examination of the premium niche profile provides a description of the typical premium slot player. The description of the typical premium player leads to hypotheses regarding needs (the unique preference set) of the premium player. An analysis of the unique preference set suggests an appropriate enhanced marketing program.

  12. Biotechnological Aspects of Microbial Extracellular Electron Transfer

    Science.gov (United States)

    Kato, Souichiro

    2015-01-01

    Extracellular electron transfer (EET) is a type of microbial respiration that enables electron transfer between microbial cells and extracellular solid materials, including naturally-occurring metal compounds and artificial electrodes. Microorganisms harboring EET abilities have received considerable attention for their various biotechnological applications, in addition to their contribution to global energy and material cycles. In this review, current knowledge on microbial EET and its application to diverse biotechnologies, including the bioremediation of toxic metals, recovery of useful metals, biocorrosion, and microbial electrochemical systems (microbial fuel cells and microbial electrosynthesis), were introduced. Two potential biotechnologies based on microbial EET, namely the electrochemical control of microbial metabolism and electrochemical stimulation of microbial symbiotic reactions (electric syntrophy), were also discussed. PMID:26004795

  13. THE GERMLINE STEM CELL NICHE UNIT IN MAMMALIAN TESTES

    Science.gov (United States)

    Oatley, Jon M.; Brinster, Ralph L.

    2014-01-01

    This review addresses current understanding of the germline stem cell niche unit in mammalian testes. Spermatogenesis is a classic model of tissue-specific stem cell function relying on self-renewal and differentiation of spermatogonial stem cells (SSCs). These fate decisions are influenced by a niche microenvironment composed of a growth factor milieu that is provided by several testis somatic support cell populations. Investigations over the last two decades have identified key determinants of the SSC niche including cytokines that regulate SSC functions and support cells providing these factors, adhesion molecules that influence SSC homing, and developmental heterogeneity of the niche during postnatal aging. Emerging evidence suggests that Sertoli cells are a key support cell population influencing the formation and function of niches by secreting soluble factors and possibly orchestrating contributions of other support cells. Investigations with mice have shown that niche influence on SSC proliferation differs during early postnatal development and adulthood. Moreover, there is mounting evidence of an age-related decline in niche function, which is likely influenced by systemic factors. Defining the attributes of stem cell niches is key to developing methods to utilize these cells for regenerative medicine. The SSC population and associated niche comprise a valuable model system for study that provides fundamental knowledge about the biology of tissue-specific stem cells and their capacity to sustain homeostasis of regenerating tissue lineages. While the stem cell is essential for maintenance of all self-renewing tissues and has received considerable attention, the role of niche cells is at least as important and may prove to be more receptive to modification in regenerative medicine. PMID:22535892

  14. Primer and interviews: The dynamic stem cell niche.

    Science.gov (United States)

    Kiefer, Julie C

    2011-03-01

    A stem cell niche is a microenvironment that supports self-renewal of a population of stem cells, and their production of differentiated cells. While the definition evokes images of a stem cell Shangri-La-where a serene stem cell pool nestles within a niche that shelters and sustains it-the reality is much more tumultuous. Niches are subject to an ever-changing maelstrom of environmental factors, the ravages of old age, and the sly tactics of disease. Presented here is a basic overview of the different ways in which stem cell niches respond to local and systemic environments, and their impact on stem cell behavior. The primer culminates with a discussion of the topic with stem cell and niche biologists D. Leanne Jones, Ph.D., and Tudorita Tumbar, Ph.D. Copyright © 2011 Wiley-Liss, Inc.

  15. The crosstalk between hematopoietic stem cells and their niches.

    Science.gov (United States)

    Durand, Charles; Charbord, Pierre; Jaffredo, Thierry

    2018-07-01

    Hematopoietic stem cells (HSCs) reside in specific microenvironments also called niches that regulate HSC functions. Understanding the molecular and cellular mechanisms involved in the crosstalk between HSCs and niche cells is a major issue in stem cell biology and regenerative medicine. The purpose of this review is to discuss recent advances in this field with particular emphasis on the transcriptional landscape of HSC niche cells and the roles of extracellular vesicles (EVs) in the dialog between HSCs and their microenvironments. The development of high-throughput technologies combined with computational methods has considerably improved our knowledge on the molecular identity of HSC niche cells. Accumulating evidence strongly suggest that the dialog between HSCs and their niches is bidirectional and that EVs play an important role in this process. These advances bring a unique conceptual and methodological framework for understanding the molecular complexity of the HSC niche and identifying novel HSC regulators. They are also promising for exploring the reciprocal influence of HSCs on niche cells and delivering specific molecules to HSCs in regenerative medicine.

  16. Time- and depth-wise trophic niche shifts in Antarctic benthos.

    Science.gov (United States)

    Calizza, Edoardo; Careddu, Giulio; Sporta Caputi, Simona; Rossi, Loreto; Costantini, Maria Letizia

    2018-01-01

    Climate change is expected to affect resource-consumer interactions underlying stability in polar food webs. Polar benthic organisms have adapted to the marked seasonality characterising their habitats by concentrating foraging and reproductive activity in summer months, when inputs from sympagic and pelagic producers increase. While this enables the persistence of biodiverse food webs, the mechanisms underlying changes in resource use and nutrient transfer are poorly understood. Thus, our understanding of how temporal and spatial variations in the supply of resources may affect food web structure and functioning is limited. By means of C and N isotopic analyses of two key Antarctic benthic consumers (Adamussium colbecki, Bivalvia, and Sterechinus neumayeri, Echinoidea) and Bayesian mixing models, we describe changes in trophic niche and nutrient transfer across trophic levels associated with the long- and short-term diet and body size of specimens sampled in midsummer in both shallow and deep waters. Samplings occurred soon after the sea-ice broke up at Tethys Bay, an area characterised by extreme seasonality in sea-ice coverage and productivity in the Ross Sea. In the long term, the trophic niche was broader and variation between specimens was greater, with intermediate-size specimens generally consuming a higher number of resources than small and large specimens. The coupling of energy channels in the food web was consequently more direct than in the short term. Sediment and benthic algae were more frequently consumed in the long term, before the sea-ice broke up, while consumers specialised on sympagic algae and plankton in the short term. Regardless of the time scale, sympagic algae were more frequently consumed in shallow waters, while plankton was more frequently consumed in deep waters. Our results suggest a strong temporal relationship between resource availability and the trophic niche of benthic consumers in Antarctica. Potential climate-driven changes

  17. Energy, ecology and the distribution of microbial life.

    Science.gov (United States)

    Macalady, Jennifer L; Hamilton, Trinity L; Grettenberger, Christen L; Jones, Daniel S; Tsao, Leah E; Burgos, William D

    2013-07-19

    Mechanisms that govern the coexistence of multiple biological species have been studied intensively by ecologists since the turn of the nineteenth century. Microbial ecologists in the meantime have faced many fundamental challenges, such as the lack of an ecologically coherent species definition, lack of adequate methods for evaluating population sizes and community composition in nature, and enormous taxonomic and functional diversity. The accessibility of powerful, culture-independent molecular microbiology methods offers an opportunity to close the gap between microbial science and the main stream of ecological theory, with the promise of new insights and tools needed to meet the grand challenges humans face as planetary engineers and galactic explorers. We focus specifically on resources related to energy metabolism because of their direct links to elemental cycling in the Earth's history, engineering applications and astrobiology. To what extent does the availability of energy resources structure microbial communities in nature? Our recent work on sulfur- and iron-oxidizing autotrophs suggests that apparently subtle variations in the concentration ratios of external electron donors and acceptors select for different microbial populations. We show that quantitative knowledge of microbial energy niches (population-specific patterns of energy resource use) can be used to predict variations in the abundance of specific taxa in microbial communities. Furthermore, we propose that resource ratio theory applied to micro-organisms will provide a useful framework for identifying how environmental communities are organized in space and time.

  18. Control of germline stem cell self-renewal and differentiation in the Drosophila ovary: concerted actions of niche signals and intrinsic factors.

    Science.gov (United States)

    Xie, Ting

    2013-01-01

    In the Drosophila ovary, germline stem cells (GSCs) physically interact with their niche composed of terminal filament cells, cap cells, and possibly GSC-contacting escort cells (ECs). A GSC divides to generate a self-renewing stem cell that remains in the niche and a differentiating daughter that moves away from the niche. The GSC niche provides a bone morphogenetic protein (BMP) signal that maintains GSC self-renewal by preventing stem cell differentiation via repression of the differentiation-promoting gene bag of marbles (bam). In addition, it expresses E-cadherin, which mediates cell adhesion for anchoring GSCs in the niche, enabling continuous self-renewal. GSCs themselves also express different classes of intrinsic factors, including signal transducers, transcription factors, chromatin remodeling factors, translation regulators, and miRNAs, which control self-renewal by strengthening interactions with the niche and repressing various differentiation pathways. Differentiated GSC daughters, known as cystoblasts (CBs), also express distinct classes of intrinsic factors to inhibit self-renewal and promote germ cell differentiation. Surprisingly, GSC progeny are also dependent on their surrounding ECs for proper differentiation at least partly by preventing BMP from diffusing to the differentiated germ cell zone and by repressing ectopic BMP expression. Therefore, both GSC self-renewal and CB differentiation are controlled by collaborative actions of extrinsic signals and intrinsic factors. Copyright © 2012 Wiley Periodicals, Inc.

  19. Astrocitary niches in human adult medulla oblongata.

    Science.gov (United States)

    Rusu, Mugurel Constantin; Dermengiu, Dan; Loreto, Carla; Motoc, Andrei Gheorghe Marius; Pop, Elena

    2013-04-01

    Astrocytes are considered as neuromodulators of the CNS. Whereas experimental studies on astrocitary functions are gaining importance, the anatomy of the astrocitary niches in the human CNS has been overlooked. The study was performed on the brainstem of 10 adult cadavers. We aimed to determine astrocitary niches in the human medulla oblongata using immunohistochemical labeling with vimentin and also CD34 immunostaining to accurately diagnose associated microvessels. Niches rich in astrocytes were identified as follows: (a) the superficial layer of astrocytes, ventral and ventrolateral, in the rostral medulla oblongata; (b) the median raphe; (c) medullary nuclei: arcuate nucleus, area postrema, nucleus of the solitary tract; (d) the subependymal zone (SEZ, caudal medulla) and subventricular zone (SVZ, rostral medulla). Astrocytes were scarce in the ventrolateral medulla, and mostly present within the pyramidal tract and the olivary nucleus. Apart from the SEZ and SVZ, the brainstem niches of astrocytes mostly overlap those regions known to perform roles as central respiratory chemoreceptors. The astrocytes of the SEZ and SVZ, which are known as stem cell niches, are related to an increased microvascular density. Copyright © 2012 Elsevier GmbH. All rights reserved.

  20. Glioblastoma niches: from the concept to the phenotypical reality.

    Science.gov (United States)

    Schiffer, Davide; Mellai, Marta; Bovio, Enrica; Bisogno, Ilaria; Casalone, Cristina; Annovazzi, Laura

    2018-05-08

    Recently, the concept of niches as sites of tumor progression, invasion, and angiogenesis in glioblastoma (GB) has been extensively debated. Niches, considered the sites in which glioblastoma stem cells (GSCs) reside, have been classified as perivascular, perinecrotic, and invasive. However, from a neuropathological point of view, it is not easy to establish when a tumor structure can be considered a niche. The relevant literature has been reviewed in the light of our recent experience on the subject. As for perinecrotic niches, the occurrence of GSCs around necrosis is interpreted as triggered by hypoxia through HIF-1α. Our alternative hypothesis is that, together with progenitors, they are the cell constituents of hyper-proliferative areas of GB, where perinecrotic niches have developed, and they would, therefore, represent the remnants of GSCs/progenitors spared by the developing necrosis. Perivascular structures originate from both transport vessels and exchange vessels, i.e., venules, arterioles, or the undefinable neo-formed small vessels, but only those in which a direct contact between GSCs/progenitors and endothelial cells occurs can be called niches. Both pericytes and microglia/macrophages play a role in niche function: Macrophages of blood origin invade GB only after the appearance of "mother vessels" with consequent blood-brain barrier disruption. Not all vessel/tumor cell structures can be considered niches, that is, crucial sites of tumor progression, invasion, and angiogenesis.

  1. Habitat niche breadth predicts invasiveness in solitary ascidians.

    Science.gov (United States)

    Granot, Itai; Shenkar, Noa; Belmaker, Jonathan

    2017-10-01

    A major focus of invasion biology is understanding the traits associated with introduction success. Most studies assess these traits in the invaded region, while only few compare nonindigenous species to the pool of potential invaders in their native region. We focused on the niche breadth hypothesis , commonly evoked but seldom tested, which states that generalist species are more likely to become introduced as they are capable of thriving under a wide set of conditions. Based on the massive introduction of tropical species into the Mediterranean via the Suez Canal (Lessepsian migration), we defined ascidians in the Red Sea as the pool of potential invaders. We constructed unique settlement plates, each representing six different niches, to assess ascidian niche breadth, and deployed them in similar habitats in the native and invaded regions. For each species found on plates, we evaluated its abundance, relative abundance across successional stages, and niche breadth, and then compared (1) species in the Red Sea known to have been introduced into the Mediterranean (Lessepsian species) and those not known from the Mediterranean (non-Lessepsian); and (2) nonindigenous and indigenous species in the Mediterranean. Lessepsian species identified on plates in the Red Sea demonstrated wider niche breadth than non-Lessepsian species, supporting the niche breadth hypothesis within the native region. No differences were found between Lessepsian and non-Lessepsian species in species abundance and successional stages. In the Mediterranean, nonindigenous species numerically dominated the settlement plates. This precluded robust comparisons of niche breadth between nonindigenous and indigenous species in the invaded region. In conclusion, using Red Sea ascidians as the pool of potential invaders, we found clear evidence supporting the niche breadth hypothesis in the native region. We suggest that such patterns may often be obscured when conducting trait-based studies in the

  2. Niche conservatism and the invasive potential of the wild boar.

    Science.gov (United States)

    Sales, Lilian Patrícia; Ribeiro, Bruno R; Hayward, Matt Warrington; Paglia, Adriano; Passamani, Marcelo; Loyola, Rafael

    2017-09-01

    Niche conservatism, i.e. the retention of a species' fundamental niche through evolutionary time, is cornerstone for biological invasion assessments. The fact that species tend to maintain their original climate niche allows predictive maps of invasion risk to anticipate potential invadable areas. Unravelling the mechanisms driving niche shifts can shed light on the management of invasive species. Here, we assessed niche shifts in one of the world's worst invasive species: the wild boar Sus scrofa. We also predicted potential invadable areas based on an ensemble of three ecological niche modelling methods, and evaluated the performance of models calibrated with native vs. pooled (native plus invaded) species records. By disentangling the drivers of change on the exotic wild boar population's niches, we found strong evidence for niche conservatism during biological invasion. Ecological niche models calibrated with both native and pooled range records predicted convergent areas. Also, observed niche shifts are mostly explained by niche unfilling, i.e. there are unoccupied areas in the exotic range where climate is analogous to the native range. Niche unfilling is expected as result of recent colonization and ongoing dispersal, and was potentially stronger for the Neotropics, where a recent wave of introductions for pig-farming and game-hunting has led to high wild boar population growth rates. The invasive potential of wild boar in the Neotropics is probably higher than in other regions, which has profound management implications if we are to prevent their invasion into species-rich areas, such as Amazonia, coupled with expansion of African swine fever and possibly great economic losses. Although the originally Eurasian-wide distribution suggests a pre-adaptation to a wide array of climates, the wild boar world-wide invasion does not exhibit evidence of niche evolution. The invasive potential of the wild boar therefore probably lies on the reproductive, dietary and

  3. Ecological niches of open ocean phytoplankton taxa

    DEFF Research Database (Denmark)

    Brun, Philipp Georg; Vogt, Meike; Payne, Mark

    2015-01-01

    We characterize the realized ecological niches of 133 phytoplankton taxa in the open ocean based on observations from the MAREDAT initiative and a statistical species distribution model (MaxEnt). The models find that the physical conditions (mixed layer depth, temperature, light) govern large...... conditions in the open ocean. Our estimates of the realized niches roughly match the predictions of Reynolds' C-S-R model for the global ocean, namely that taxa classified as nutrient stress tolerant have niches at lower nutrient and higher irradiance conditions than light stress tolerant taxa. Yet...

  4. Stem cell autotomy and niche interaction in different systems.

    Science.gov (United States)

    Dorn, David C; Dorn, August

    2015-07-26

    The best known cases of cell autotomy are the formation of erythrocytes and thrombocytes (platelets) from progenitor cells that reside in special niches. Recently, autotomy of stem cells and its enigmatic interaction with the niche has been reported from male germline stem cells (GSCs) in several insect species. First described in lepidopterans, the silkmoth, followed by the gipsy moth and consecutively in hemipterans, foremost the milkweed bug. In both, moths and the milkweed bug, GSCs form finger-like projections toward the niche, the apical cells (homologs of the hub cells in Drosophila). Whereas in the milkweed bug the projection terminals remain at the surface of the niche cells, in the gipsy moth they protrude deeply into the singular niche cell. In both cases, the projections undergo serial retrograde fragmentation with progressing signs of autophagy. In the gipsy moth, the autotomized vesicles are phagocytized and digested by the niche cell. In the milkweed bug the autotomized vesicles accumulate at the niche surface and disintegrate. Autotomy and sprouting of new projections appears to occur continuously. The significance of the GSC-niche interactions, however, remains enigmatic. Our concept on the signaling relationship between stem cell-niche in general and GSC and niche (hub cells and cyst stem cells) in particular has been greatly shaped by Drosophila melanogaster. In comparing the interactions of GSCs with their niche in Drosophila with those in species exhibiting GSC autotomy it is obvious that additional or alternative modes of stem cell-niche communication exist. Thus, essential signaling pathways, including niche-stem cell adhesion (E-cadherin) and the direction of asymmetrical GSC division - as they were found in Drosophila - can hardly be translated into the systems where GSC autotomy was reported. It is shown here that the serial autotomy of GSC projections shows remarkable similarities with Wallerian axonal destruction, developmental axon

  5. Stem cell autotomy and niche interaction in different systems

    Science.gov (United States)

    Dorn, David C; Dorn, August

    2015-01-01

    The best known cases of cell autotomy are the formation of erythrocytes and thrombocytes (platelets) from progenitor cells that reside in special niches. Recently, autotomy of stem cells and its enigmatic interaction with the niche has been reported from male germline stem cells (GSCs) in several insect species. First described in lepidopterans, the silkmoth, followed by the gipsy moth and consecutively in hemipterans, foremost the milkweed bug. In both, moths and the milkweed bug, GSCs form finger-like projections toward the niche, the apical cells (homologs of the hub cells in Drosophila). Whereas in the milkweed bug the projection terminals remain at the surface of the niche cells, in the gipsy moth they protrude deeply into the singular niche cell. In both cases, the projections undergo serial retrograde fragmentation with progressing signs of autophagy. In the gipsy moth, the autotomized vesicles are phagocytized and digested by the niche cell. In the milkweed bug the autotomized vesicles accumulate at the niche surface and disintegrate. Autotomy and sprouting of new projections appears to occur continuously. The significance of the GSC-niche interactions, however, remains enigmatic. Our concept on the signaling relationship between stem cell-niche in general and GSC and niche (hub cells and cyst stem cells) in particular has been greatly shaped by Drosophila melanogaster. In comparing the interactions of GSCs with their niche in Drosophila with those in species exhibiting GSC autotomy it is obvious that additional or alternative modes of stem cell-niche communication exist. Thus, essential signaling pathways, including niche-stem cell adhesion (E-cadherin) and the direction of asymmetrical GSC division - as they were found in Drosophila - can hardly be translated into the systems where GSC autotomy was reported. It is shown here that the serial autotomy of GSC projections shows remarkable similarities with Wallerian axonal destruction, developmental axon

  6. Ten Niche Strategies To Commercialize New High-Tech Products

    NARCIS (Netherlands)

    Ortt, J.R.; Langley, D.J.; Pals, N.

    2013-01-01

    There are serious gaps in the scientific literature relating to niche strategies as a means for commercializing new high-tech products. In particular, there is no clarity about what types of niche strategies can be distinguished, or how a niche strategy can be selected to suit a certain ituation. In

  7. Niche conservatism in Gynandropaa frogs on the southeastern Qinghai-Tibetan Plateau.

    Science.gov (United States)

    Hu, Junhua; Broennimann, Olivier; Guisan, Antoine; Wang, Bin; Huang, Yan; Jiang, Jianping

    2016-09-07

    The role of ecological niche in lineage diversification has been the subject of long-standing interest of ecologists and evolutionary biologists. Gynandropaa frogs diversified into three independent clades endemic to the southeastern Qinghai-Tibetan Plateau. Here, we address the question whether these clades kept the same niche after separation, and what it tells us about possible diversification processes. We applied predictions in geographical (G)-space and tests of niche conservatism in environmental (E)-space. Niche models in G-space indicate separate regions with high suitability for the different clades, with some potential areas of sympatry. While the pair of central and eastern clades displayed the largest niche overlap for most variables, and strict niche equivalency was rejected for all clade-pairs, we found no strong evidence for niche divergence, but rather the signature of niche conservatism compared to null models in E-space. These results suggest a common ancestral ecological niche, and as such give good support to divergence through allopatric speciation, but alternative explanations are also possible. Our findings illustrate how testing for niche conservatism in lineage diversification can provide insights into underlying speciation processes, and how this information may guide further research and conservation practices, as illustrated here for amphibians on the Qinghai-Tibetan Plateau.

  8. Microbial ecology of Thailand tsunami and non-tsunami affected terrestrials.

    Science.gov (United States)

    Somboonna, Naraporn; Wilantho, Alisa; Jankaew, Kruawun; Assawamakin, Anunchai; Sangsrakru, Duangjai; Tangphatsornruang, Sithichoke; Tongsima, Sissades

    2014-01-01

    The effects of tsunamis on microbial ecologies have been ill-defined, especially in Phang Nga province, Thailand. This ecosystem was catastrophically impacted by the 2004 Indian Ocean tsunami as well as the 600 year-old tsunami in Phra Thong island, Phang Nga province. No study has been conducted to elucidate their effects on microbial ecology. This study represents the first to elucidate their effects on microbial ecology. We utilized metagenomics with 16S and 18S rDNA-barcoded pyrosequencing to obtain prokaryotic and eukaryotic profiles for this terrestrial site, tsunami affected (S1), as well as a parallel unaffected terrestrial site, non-tsunami affected (S2). S1 demonstrated unique microbial community patterns than S2. The dendrogram constructed using the prokaryotic profiles supported the unique S1 microbial communities. S1 contained more proportions of archaea and bacteria domains, specifically species belonging to Bacteroidetes became more frequent, in replacing of the other typical floras like Proteobacteria, Acidobacteria and Basidiomycota. Pathogenic microbes, including Acinetobacter haemolyticus, Flavobacterium spp. and Photobacterium spp., were also found frequently in S1. Furthermore, different metabolic potentials highlighted this microbial community change could impact the functional ecology of the site. Moreover, the habitat prediction based on percent of species indicators for marine, brackish, freshwater and terrestrial niches pointed the S1 to largely comprise marine habitat indicating-species.

  9. Deciphering Diversity Indices for a Better Understanding of Microbial Communities.

    Science.gov (United States)

    Kim, Bo-Ra; Shin, Jiwon; Guevarra, Robin; Lee, Jun Hyung; Kim, Doo Wan; Seol, Kuk-Hwan; Lee, Ju-Hoon; Kim, Hyeun Bum; Isaacson, Richard

    2017-12-28

    The past decades have been a golden era during which great tasks were accomplished in the field of microbiology, including food microbiology. In the past, culture-dependent methods have been the primary choice to investigate bacterial diversity. However, using cultureindependent high-throughput sequencing of 16S rRNA genes has greatly facilitated studies exploring the microbial compositions and dynamics associated with health and diseases. These culture-independent DNA-based studies generate large-scale data sets that describe the microbial composition of a certain niche. Consequently, understanding microbial diversity becomes of greater importance when investigating the composition, function, and dynamics of the microbiota associated with health and diseases. Even though there is no general agreement on which diversity index is the best to use, diversity indices have been used to compare the diversity among samples and between treatments with controls. Tools such as the Shannon- Weaver index and Simpson index can be used to describe population diversity in samples. The purpose of this review is to explain the principles of diversity indices, such as Shannon- Weaver and Simpson, to aid general microbiologists in better understanding bacterial communities. In this review, important questions concerning microbial diversity are addressed. Information from this review should facilitate evidence-based strategies to explore microbial communities.

  10. Microbial biodiversity of Sardinian oleic ecosystems.

    Science.gov (United States)

    Santona, Mario; Sanna, Maria Lina; Multineddu, Chiara; Fancello, Francesco; de la Fuente, Sara Audije; Dettori, Sandro; Zara, Severino

    2018-04-01

    The olives are rich in microorganisms that, during the extraction process may persist in the oils and can influence their physicochemical and sensory characteristics. In this work, and for the first time, we isolated and identified microbial species, yeast and bacteria, present during the production process in four Sardinian (Italy) oleic ecosystems. Among these varieties, we found that Nera di Gonnos was associated to the highest microbial biodiversity, which was followed by Bosana, Nocellara del Belice and Semidana. Among the different microbial species isolated, some are specific of olive ecological niches, such as Cryptococcus spp and Serratia spp; and others to olive oils such as Candida spp and Saccharomyces. Some other species identified in this work were not found before in oleic ecosystems. The enzymatic analyses of yeast and bacteria showed that they have good β-glucosidase activity and yeast also showed good β-glucanase activity. The majority of bacteria presented lipolytic and catalase activities while in yeast were species-specific. Interestingly, yeast and bacteria isolates presented a high resistance to bile acid, and about 65% of the yeast were able to resist at pH 2.5 for 2 h. Finally, bacteria showed no biofilm activity compared to yeast. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Exosomes as novel regulators of adult neurogenic niches

    Directory of Open Access Journals (Sweden)

    Luis Federico Batiz

    2016-01-01

    Full Text Available Adult neurogenesis has been convincingly demonstrated in two regions of the mammalian brain: the sub-granular zone (SGZ of the dentate gyrus (DG in the hippocampus, and the sub-ventricular zone (SVZ of the lateral ventricles. SGZ newborn neurons are destined to the granular cell layer of the DG, while new neurons from the SVZ neurons migrate rostrally into the olfactory bulb. The process of adult neurogenesis persists throughout life and is supported by a pool of neural stem cells (NSCs, which reside in a unique and specialized microenvironment known as neurogenic niche. Neurogenic niches are structured by a complex organization of different cell types, including the NSC-neuron lineage, glial cells and vascular cells. Thus, cell-to-cell communication plays a key role in the dynamic modulation of homeostasis and plasticity of the adult neurogenic process. Specific cell-cell contacts and extracellular signals originated locally provide the necessary support and regulate the balance between self-renewal and differentiation of NSCs. Furthermore, extracellular signals originated at distant locations, including other brain regions or systemic organs, may reach the niche through the cerebrospinal fluid or the vasculature and influence its nature. The role of several secreted molecules, such as cytokines, growth factors, neurotransmitters, and hormones, in the biology of adult NSCs, has been systematically addressed. Interestingly, in addition to these well-recognized signals, a novel type of intercellular messengers has been identified recently: the extracellular vesicles (EVs. EVs, and particularly exosomes, are implicated in the transfer of mRNAs, microRNAs (miRNAs, proteins and lipids between cells and thus are able to modify the function of recipient cells. Exosomes appear to play a significant role in different stem cell niches such as the mesenchymal stem cell niche, cancer stem cell niche and pre-metastatic niche; however, their roles in adult

  12. Niche construction, sources of selection and trait coevolution.

    Science.gov (United States)

    Laland, Kevin; Odling-Smee, John; Endler, John

    2017-10-06

    Organisms modify and choose components of their local environments. This 'niche construction' can alter ecological processes, modify natural selection and contribute to inheritance through ecological legacies. Here, we propose that niche construction initiates and modifies the selection directly affecting the constructor, and on other species, in an orderly, directed and sustained manner. By dependably generating specific environmental states, niche construction co-directs adaptive evolution by imposing a consistent statistical bias on selection. We illustrate how niche construction can generate this evolutionary bias by comparing it with artificial selection. We suggest that it occupies the middle ground between artificial and natural selection. We show how the perspective leads to testable predictions related to: (i) reduced variance in measures of responses to natural selection in the wild; (ii) multiple trait coevolution, including the evolution of sequences of traits and patterns of parallel evolution; and (iii) a positive association between niche construction and biodiversity. More generally, we submit that evolutionary biology would benefit from greater attention to the diverse properties of all sources of selection.

  13. Ecological niche transferability using invasive species as a case study.

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    Miguel Fernández

    Full Text Available Species distribution modeling is widely applied to predict invasive species distributions and species range shifts under climate change. Accurate predictions depend upon meeting the assumption that ecological niches are conserved, i.e., spatially or temporally transferable. Here we present a multi-taxon comparative analysis of niche conservatism using biological invasion events well documented in natural history museum collections. Our goal is to assess spatial transferability of the climatic niche of a range of noxious terrestrial invasive species using two complementary approaches. First we compare species' native versus invasive ranges in environmental space using two distinct methods, Principal Components Analysis and Mahalanobis distance. Second we compare species' native versus invaded ranges in geographic space as estimated using the species distribution modeling technique Maxent and the comparative index Hellinger's I. We find that species exhibit a range of responses, from almost complete transferability, in which the invaded niches completely overlap with the native niches, to a complete dissociation between native and invaded ranges. Intermediate responses included expansion of dimension attributable to either temperature or precipitation derived variables, as well as niche expansion in multiple dimensions. We conclude that the ecological niche in the native range is generally a poor predictor of invaded range and, by analogy, the ecological niche may be a poor predictor of range shifts under climate change. We suggest that assessing dimensions of niche transferability prior to standard species distribution modeling may improve the understanding of species' dynamics in the invaded range.

  14. Target Article with Commentaries: Developmental Niche Construction

    Science.gov (United States)

    Flynn, Emma G.; Laland, Kevin N.; Kendal, Rachel L.; Kendal, Jeremy R.

    2013-01-01

    Niche construction is the modification of components of the environment through an organism's activities. Humans modify their environments mainly through ontogenetic and cultural processes, and it is this reliance on learning, plasticity and culture that lends human niche construction a special potency. In this paper we aim to facilitate…

  15. Selective laser melting-enabled electrospinning: Introducing complexity within electrospun membranes.

    Science.gov (United States)

    Paterson, Thomas E; Beal, Selina N; Santocildes-Romero, Martin E; Sidambe, Alfred T; Hatton, Paul V; Asencio, Ilida Ortega

    2017-06-01

    Additive manufacturing technologies enable the creation of very precise and well-defined structures that can mimic hierarchical features of natural tissues. In this article, we describe the development of a manufacturing technology platform to produce innovative biodegradable membranes that are enhanced with controlled microenvironments produced via a combination of selective laser melting techniques and conventional electrospinning. This work underpins the manufacture of a new generation of biomaterial devices that have significant potential for use as both basic research tools and components of therapeutic implants. The membranes were successfully manufactured and a total of three microenvironment designs (niches) were chosen for thorough characterisation. Scanning electron microscopy analysis demonstrated differences in fibre diameters within different areas of the niche structures as well as differences in fibre density. We also showed the potential of using the microfabricated membranes for supporting mesenchymal stromal cell culture and proliferation. We demonstrated that mesenchymal stromal cells grow and populate the membranes penetrating within the niche-like structures. These findings demonstrate the creation of a very versatile tool that can be used in a variety of tissue regeneration applications including bone healing.

  16. Enhancement of metal bioremediation by use of microbial surfactants

    International Nuclear Information System (INIS)

    Singh, Pooja; Cameotra, Swaranjit Singh

    2004-01-01

    Metal pollution all around the globe, especially in the mining and plating areas of the world, has been found to have grave consequences. An excellent option for enhanced metal contaminated site bioremediation is the use of microbial products viz. microbial surfactants and extracellular polymers which would increase the efficiency of metal reducing/sequestering organisms for field bioremediation. Important here is the advantage of such compounds at metal and organic compound co-contaminated site since microorganisms have long been found to produce surface-active compounds when grown on hydrocarbons. Other options capable of proving efficient enhancers include exploiting the chemotactic potential and biofilm forming ability of the relevant microorganisms. Chemotaxis towards environmental pollutants has excellent potential to enhance the biodegradation of many contaminants and biofilm offers them a better survival niche even in the presence of high levels of toxic compounds

  17. Beware batch culture: Seasonality and niche construction predicted to favor bacterial adaptive diversification.

    Directory of Open Access Journals (Sweden)

    Charles Rocabert

    2017-03-01

    Full Text Available Metabolic cross-feeding interactions between microbial strains are common in nature, and emerge during evolution experiments in the laboratory, even in homogeneous environments providing a single carbon source. In sympatry, when the environment is well-mixed, the reasons why emerging cross-feeding interactions may sometimes become stable and lead to monophyletic genotypic clusters occupying specific niches, named ecotypes, remain unclear. As an alternative to evolution experiments in the laboratory, we developed Evo2Sim, a multi-scale model of in silico experimental evolution, equipped with the whole tool case of experimental setups, competition assays, phylogenetic analysis, and, most importantly, allowing for evolvable ecological interactions. Digital organisms with an evolvable genome structure encoding an evolvable metabolic network evolved for tens of thousands of generations in environments mimicking the dynamics of real controlled environments, including chemostat or batch culture providing a single limiting resource. We show here that the evolution of stable cross-feeding interactions requires seasonal batch conditions. In this case, adaptive diversification events result in two stably co-existing ecotypes, with one feeding on the primary resource and the other on by-products. We show that the regularity of serial transfers is essential for the maintenance of the polymorphism, as it allows for at least two stable seasons and thus two temporal niches. A first season is externally generated by the transfer into fresh medium, while a second one is internally generated by niche construction as the provided nutrient is replaced by secreted by-products derived from bacterial growth. In chemostat conditions, even if cross-feeding interactions emerge, they are not stable on the long-term because fitter mutants eventually invade the whole population. We also show that the long-term evolution of the two stable ecotypes leads to character

  18. Chironomidae larvae (Diptera) of Neotropical floodplain: overlap niche in different habitats.

    Science.gov (United States)

    Butakka, C M M; Ragonha, F H; Takeda, A M

    2014-05-01

    The niche overlap between trophic groups of Chironomidae larvae in different habitats was observed between trophic groups and between different environments in Neotropical floodplain. For the evaluation we used the index of niche overlap (CXY) and analysis of trophic networks, both from the types and amount of food items identified in the larval alimentary canal. In all environments, the larvae fed on mainly organic matter such as plants fragments and algae, but there were many omnivore larvae. Species that have high values of food items occurred in diverse environments as generalists with great overlap niche and those with a low amount of food items with less overlap niche were classified as specialists. The largest number of trophic niche overlap was observed among collector-gatherers in connected floodplain lakes. The lower values of index niche overlap were predators. The similarity in the diet of different taxa in the same niche does not necessarily imply competition between them, but coexistence when the food resource is not scarce in the environment even in partially overlapping niches.

  19. A Novel Method for Analyzing Microbially Affiliated Volatile Organic Compounds in Soil Environments

    Science.gov (United States)

    Ruhs, C. V.; McNeal, K. S.

    2010-12-01

    A concerted, international effort by citizens, governments, industries and educational systems is necessary to address the myriad environmental issues that face us today. The authors of this paper concentrate on soil environments and, specifically, the methods currently used to characterize them. The ability to efficiently and effectively monitor and characterize various soils is desired, allows for the study, supervision, and protection of natural and cultivated ecosystems, and may assist stakeholders in meeting governmentally-imposed environmental standards. This research addresses soil characterization by a comparison of four methods that emphasize a combination of microbial community and metabolic measures: BIOLOG, fatty acid methyl-ester analysis (FAME), descriptive physical and chemical analysis (moisture content, pH, carbon content, nutrient content, and grain size), and the novel soil-microbe volatile organic compound analysis (SMVOC) presented in this work. In order to achieve the method comparison, soils were collected from three climatic regions (Bahamas, Michigan, and Mississippi), with three samples taken from niche ecosystems found at each climatic region (a total of nine sites). Of interest to the authors is whether or not an investigation of microbial communities and the volatile organic compounds (VOCs) produced by microbial communities from nine separate soil ecosystems provides useful information about soil dynamics. In essence, is analysis of soil-derived VOCs using gas chromatography-mass spectrometry (GC-MS) an effective method for characterizing microbial communities and their metabolic activity of soils rapidly and accurately compared with the other three traditional characterization methods? Preliminary results suggest that VOCs in each of these locales differ with changes in soil types, soil moisture, and bacterial community. Each niche site shows distinct patterns in both VOCs and BIOLOG readings. Results will be presented to show the

  20. Evolution of climatic niche specialization: a phylogenetic analysis in amphibians.

    Science.gov (United States)

    Bonetti, Maria Fernanda; Wiens, John J

    2014-11-22

    The evolution of climatic niche specialization has important implications for many topics in ecology, evolution and conservation. The climatic niche reflects the set of temperature and precipitation conditions where a species can occur. Thus, specialization to a limited set of climatic conditions can be important for understanding patterns of biogeography, species richness, community structure, allopatric speciation, spread of invasive species and responses to climate change. Nevertheless, the factors that determine climatic niche width (level of specialization) remain poorly explored. Here, we test whether species that occur in more extreme climates are more highly specialized for those conditions, and whether there are trade-offs between niche widths on different climatic niche axes (e.g. do species that tolerate a broad range of temperatures tolerate only a limited range of precipitation regimes?). We test these hypotheses in amphibians, using phylogenetic comparative methods and global-scale datasets, including 2712 species with both climatic and phylogenetic data. Our results do not support either hypothesis. Rather than finding narrower niches in more extreme environments, niches tend to be narrower on one end of a climatic gradient but wider on the other. We also find that temperature and precipitation niche breadths are positively related, rather than showing trade-offs. Finally, our results suggest that most amphibian species occur in relatively warm and dry environments and have relatively narrow climatic niche widths on both of these axes. Thus, they may be especially imperilled by anthropogenic climate change. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  1. Engineering the hematopoietic stem cell niche: Frontiers in biomaterial science

    Science.gov (United States)

    Choi, Ji Sun; Mahadik, Bhushan P.; Harley, Brendan A. C.

    2016-01-01

    Hematopoietic stem cells (HSCs) play a crucial role in the generation of the body’s blood and immune cells. This process takes place primarily in the bone marrow in specialized ‘niche’ microenvironments, which provide signals responsible for maintaining a balance between HSC quiescence, self-renewal, and lineage specification required for life-long hematopoiesis. While our understanding of these signaling mechanisms continues to improve, our ability to engineer them in vitro for the expansion of clinically relevant HSC populations is still lacking. In this review, we focus on development of biomaterials-based culture platforms for in vitro study of interactions between HSCs and their local microenvironment. The tools and techniques used for both examining HSC-niche interactions as well as applying these findings towards controlled HSC expansion or directed differentiation in 2D and 3D platforms are discussed. These novel techniques hold the potential to push the existing boundaries of HSC cultures towards high-throughput, real-time, and single-cell level biomimetic approaches that enable a more nuanced understanding of HSC regulation and function. Their application in conjunction with innovative biomaterial platforms can pave the way for engineering artificial bone marrow niches for clinical applications as well as elucidating the pathology of blood-related cancers and disorders. PMID:26356030

  2. Microbial Cell Dynamics Lab (MCDL)

    Data.gov (United States)

    Federal Laboratory Consortium — The Microbial Cell Dynamics Laboratory at PNNL enables scientists to study the molecular details of microbes under relevant environmental conditions. The MCDL seeks...

  3. Microbial interactions: ecology in a molecular perspective.

    Science.gov (United States)

    Braga, Raíssa Mesquita; Dourado, Manuella Nóbrega; Araújo, Welington Luiz

    2016-12-01

    The microorganism-microorganism or microorganism-host interactions are the key strategy to colonize and establish in a variety of different environments. These interactions involve all ecological aspects, including physiochemical changes, metabolite exchange, metabolite conversion, signaling, chemotaxis and genetic exchange resulting in genotype selection. In addition, the establishment in the environment depends on the species diversity, since high functional redundancy in the microbial community increases the competitive ability of the community, decreasing the possibility of an invader to establish in this environment. Therefore, these associations are the result of a co-evolution process that leads to the adaptation and specialization, allowing the occupation of different niches, by reducing biotic and abiotic stress or exchanging growth factors and signaling. Microbial interactions occur by the transference of molecular and genetic information, and many mechanisms can be involved in this exchange, such as secondary metabolites, siderophores, quorum sensing system, biofilm formation, and cellular transduction signaling, among others. The ultimate unit of interaction is the gene expression of each organism in response to an environmental (biotic or abiotic) stimulus, which is responsible for the production of molecules involved in these interactions. Therefore, in the present review, we focused on some molecular mechanisms involved in the microbial interaction, not only in microbial-host interaction, which has been exploited by other reviews, but also in the molecular strategy used by different microorganisms in the environment that can modulate the establishment and structuration of the microbial community. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

  4. Base-Catalyzed Depolymerization of Solid Lignin-Rich Streams Enables Microbial Conversion

    DEFF Research Database (Denmark)

    Rodriguez, Alberto; Salvachúa, Davinia; Katahira, Rui

    2017-01-01

    hydroxycinnamic acids. BCD liquors were tested for microbial growth using seven aromatic-catabolizing bacteria and two yeasts. Three organisms (Pseudomonas putida KT2440, Rhodotorula mucilaginosa, and Corynebacterium glutamicum) tolerate high BCD liquor concentrations (up to 90% v/v) and rapidly consume the main...

  5. Time- and depth-wise trophic niche shifts in Antarctic benthos.

    Directory of Open Access Journals (Sweden)

    Edoardo Calizza

    Full Text Available Climate change is expected to affect resource-consumer interactions underlying stability in polar food webs. Polar benthic organisms have adapted to the marked seasonality characterising their habitats by concentrating foraging and reproductive activity in summer months, when inputs from sympagic and pelagic producers increase. While this enables the persistence of biodiverse food webs, the mechanisms underlying changes in resource use and nutrient transfer are poorly understood. Thus, our understanding of how temporal and spatial variations in the supply of resources may affect food web structure and functioning is limited. By means of C and N isotopic analyses of two key Antarctic benthic consumers (Adamussium colbecki, Bivalvia, and Sterechinus neumayeri, Echinoidea and Bayesian mixing models, we describe changes in trophic niche and nutrient transfer across trophic levels associated with the long- and short-term diet and body size of specimens sampled in midsummer in both shallow and deep waters. Samplings occurred soon after the sea-ice broke up at Tethys Bay, an area characterised by extreme seasonality in sea-ice coverage and productivity in the Ross Sea. In the long term, the trophic niche was broader and variation between specimens was greater, with intermediate-size specimens generally consuming a higher number of resources than small and large specimens. The coupling of energy channels in the food web was consequently more direct than in the short term. Sediment and benthic algae were more frequently consumed in the long term, before the sea-ice broke up, while consumers specialised on sympagic algae and plankton in the short term. Regardless of the time scale, sympagic algae were more frequently consumed in shallow waters, while plankton was more frequently consumed in deep waters. Our results suggest a strong temporal relationship between resource availability and the trophic niche of benthic consumers in Antarctica. Potential

  6. High definition for systems biology of microbial communities: metagenomics gets genome-centric and strain-resolved.

    Science.gov (United States)

    Turaev, Dmitrij; Rattei, Thomas

    2016-06-01

    The systems biology of microbial communities, organismal communities inhabiting all ecological niches on earth, has in recent years been strongly facilitated by the rapid development of experimental, sequencing and data analysis methods. Novel experimental approaches and binning methods in metagenomics render the semi-automatic reconstructions of near-complete genomes of uncultivable bacteria possible, while advances in high-resolution amplicon analysis allow for efficient and less biased taxonomic community characterization. This will also facilitate predictive modeling approaches, hitherto limited by the low resolution of metagenomic data. In this review, we pinpoint the most promising current developments in metagenomics. They facilitate microbial systems biology towards a systemic understanding of mechanisms in microbial communities with scopes of application in many areas of our daily life. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. Socs36E Controls Niche Competition by Repressing MAPK Signaling in the Drosophila Testis.

    Directory of Open Access Journals (Sweden)

    Marc Amoyel

    2016-01-01

    Full Text Available The Drosophila testis is a well-established system for studying stem cell self-renewal and competition. In this tissue, the niche supports two stem cell populations, germ line stem cells (GSCs, which give rise to sperm, and somatic stem cells called cyst stem cells (CySCs, which support GSCs and their descendants. It has been established that CySCs compete with each other and with GSCs for niche access, and mutations have been identified that confer increased competitiveness to CySCs, resulting in the mutant stem cell and its descendants outcompeting wild type resident stem cells. Socs36E, which encodes a negative feedback inhibitor of the JAK/STAT pathway, was the first identified regulator of niche competition. The competitive behavior of Socs36E mutant CySCs was attributed to increased JAK/STAT signaling. Here we show that competitive behavior of Socs36E mutant CySCs is due in large part to unbridled Mitogen-Activated Protein Kinase (MAPK signaling. In Socs36E mutant clones, MAPK activity is elevated. Furthermore, we find that clonal upregulation of MAPK in CySCs leads to their outcompetition of wild type CySCs and of GSCs, recapitulating the Socs36E mutant phenotype. Indeed, when MAPK activity is removed from Socs36E mutant clones, they lose their competitiveness but maintain self-renewal, presumably due to increased JAK/STAT signaling in these cells. Consistently, loss of JAK/STAT activity in Socs36E mutant clones severely impairs their self-renewal. Thus, our results enable the genetic separation of two essential processes that occur in stem cells. While some niche signals specify the intrinsic property of self-renewal, which is absolutely required in all stem cells for niche residence, additional signals control the ability of stem cells to compete with their neighbors. Socs36E is node through which these processes are linked, demonstrating that negative feedback inhibition integrates multiple aspects of stem cell behavior.

  8. Niche construction drives social dependence in hermit crabs.

    Science.gov (United States)

    Laidre, Mark E

    2012-10-23

    Organisms can receive not only a genetic inheritance from their ancestors but also an ecological inheritance, involving modifications their ancestors made to the environment through niche construction. Ecological inheritances may persist as a legacy, potentially generating selection pressures that favor sociality. Yet, most proposed cases of sociality being impacted by an ecological inheritance come from organisms that live among close kin and were highly social before their niche construction began. Here, I show that in terrestrial hermit crabs (Coenobita compressus)--organisms that do not live with kin and reside alone, each in its own shell--niche-construction drives social dependence, such that individuals can only survive in remodeled shells handed down from conspecifics. These results suggest that niche construction can be an important initiator of evolutionary pressures to socialize, even among unrelated and otherwise asocial organisms. Copyright © 2012 Elsevier Ltd. All rights reserved.

  9. Stem cell dynamics in the hair follicle niche

    Science.gov (United States)

    Rompolas, Panteleimon; Greco, Valentina

    2014-01-01

    Hair follicles are skin appendages of the mammalian skin that have the ability to periodically and stereotypically regenerate in order to continuously produce new hair over our lifetime. The ability of the hair follicle to regenerate is due to the presence of stem cells that along with other cell populations and non-cellular components, including molecular signals and extracellular material, make up a niche microenvironment. Mounting evidence suggests that the niche is critical for regulating stem cell behavior and thus the process of regeneration. Here we review the literature concerning past and current studies that have utilized mouse genetic models, combined with other approaches to dissect the molecular and cellular composition of the hair follicle niche. We also discuss our current understanding of how stem cells operate within the niche during the process of tissue regeneration and the factors that regulate their behavior. PMID:24361866

  10. Niche specificity of ammonia-oxidizing archaeal and bacterial communities in a freshwater wetland receiving municipal wastewater in Daqing, Northeast China.

    Science.gov (United States)

    Lee, Kwok-Ho; Wang, Yong-Feng; Li, Hui; Gu, Ji-Dong

    2014-12-01

    Ecophysiological differences between ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) enable them to adapt to different niches in complex freshwater wetland ecosystems. The community characters of AOA and AOB in the different niches in a freshwater wetland receiving municipal wastewater, as well as the physicochemical parameters of sediment/soil samples, were investigated in this study. AOA community structures varied and separated from each other among four different niches. Wetland vegetation including aquatic macrophytes and terrestrial plants affected the AOA community composition but less for AOB, whereas sediment depths might contribute to the AOB community shift. The diversity of AOA communities was higher than that of AOB across all four niches. Archaeal and bacterial amoA genes (encoding for the alpha-subunit of ammonia monooxygenases) were most diverse in the dry-land niche, indicating O2 availability might favor ammonia oxidation. The majority of AOA amoA sequences belonged to the Soil/sediment Cluster B in the freshwater wetland ecosystems, while the dominant AOB amoA sequences were affiliated with Nitrosospira-like cluster. In the Nitrosospira-like cluster, AOB amoA gene sequences affiliated with the uncultured ammonia-oxidizing beta-proteobacteria constituted the largest portion (99%). Moreover, independent methods for phylogenetic tree analysis supported high parsimony bootstrap values. As a consequence, it is proposed that Nitrosospira-like amoA gene sequences recovered in this study represent a potentially novel cluster, grouping with the sequences from Gulf of Mexico deposited in the public databases.

  11. Synergistic selection between ecological niche and mate preference primes diversification.

    Science.gov (United States)

    Boughman, Janette W; Svanbäck, Richard

    2017-01-01

    The ecological niche and mate preferences have independently been shown to be important for the process of speciation. Here, we articulate a novel mechanism by which ecological niche use and mate preference can be linked to promote speciation. The degree to which individual niches are narrow and clustered affects the strength of divergent natural selection and population splitting. Similarly, the degree to which individual mate preferences are narrow and clustered affects the strength of divergent sexual selection and assortative mating between diverging forms. This novel perspective is inspired by the literature on ecological niches; it also explores mate preferences and how they may contribute to speciation. Unlike much comparative work, we do not search for evolutionary patterns using proxies for adaptation and sexual selection, but rather we elucidate how ideas from niche theory relate to mate preference, and how this relationship can foster speciation. Recognizing that individual and population niches are conceptually and ecologically linked to individual and population mate preference functions will significantly increase our understanding of rapid evolutionary diversification in nature. It has potential to help solve the difficult challenge of testing the role of sexual selection in the speciation process. We also identify ecological factors that are likely to affect individual niche and individual mate preference in synergistic ways and as a consequence to promote speciation. The ecological niche an individual occupies can directly affect its mate preference. Clusters of individuals with narrow, differentiated niches are likely to have narrow, differentiated mate preference functions. Our approach integrates ecological and sexual selection research to further our understanding of diversification processes. Such integration may be necessary for progress because these processes seem inextricably linked in the natural world. © 2016 The Author(s). Evolution

  12. Contrasting microbial community assembly hypotheses: a reconciling tale from the Río Tinto.

    Science.gov (United States)

    Palacios, Carmen; Zettler, Erik; Amils, Ricardo; Amaral-Zettler, Linda

    2008-01-01

    The Río Tinto (RT) is distinguished from other acid mine drainage systems by its natural and ancient origins. Microbial life from all three domains flourishes in this ecosystem, but bacteria dominate metabolic processes that perpetuate environmental extremes. While the patchy geochemistry of the RT likely influences the dynamics of bacterial populations, demonstrating which environmental variables shape microbial diversity and unveiling the mechanisms underlying observed patterns, remain major challenges in microbial ecology whose answers rely upon detailed assessments of community structures coupled with fine-scale measurements of physico-chemical parameters. By using high-throughput environmental tag sequencing we achieved saturation of richness estimators for the first time in the RT. We found that environmental factors dictate the distribution of the most abundant taxa in this system, but stochastic niche differentiation processes, such as mutation and dispersal, also contribute to observed diversity patterns. We predict that studies providing clues to the evolutionary and ecological processes underlying microbial distributions will reconcile the ongoing debate between the Baas Becking vs. Hubbell community assembly hypotheses.

  13. Contrasting microbial community assembly hypotheses: a reconciling tale from the Río Tinto.

    Directory of Open Access Journals (Sweden)

    Carmen Palacios

    Full Text Available The Río Tinto (RT is distinguished from other acid mine drainage systems by its natural and ancient origins. Microbial life from all three domains flourishes in this ecosystem, but bacteria dominate metabolic processes that perpetuate environmental extremes. While the patchy geochemistry of the RT likely influences the dynamics of bacterial populations, demonstrating which environmental variables shape microbial diversity and unveiling the mechanisms underlying observed patterns, remain major challenges in microbial ecology whose answers rely upon detailed assessments of community structures coupled with fine-scale measurements of physico-chemical parameters.By using high-throughput environmental tag sequencing we achieved saturation of richness estimators for the first time in the RT. We found that environmental factors dictate the distribution of the most abundant taxa in this system, but stochastic niche differentiation processes, such as mutation and dispersal, also contribute to observed diversity patterns.We predict that studies providing clues to the evolutionary and ecological processes underlying microbial distributions will reconcile the ongoing debate between the Baas Becking vs. Hubbell community assembly hypotheses.

  14. Sediment Microbial Communities Influenced by Cool Hydrothermal Fluid Migration

    Directory of Open Access Journals (Sweden)

    Laura A. Zinke

    2018-06-01

    Full Text Available Cool hydrothermal systems (CHSs are prevalent across the seafloor and discharge fluid volumes that rival oceanic input from rivers, yet the microbial ecology of these systems are poorly constrained. The Dorado Outcrop on the ridge flank of the Cocos Plate in the northeastern tropical Pacific Ocean is the first confirmed CHS, discharging minimally altered <15°C fluid from the shallow lithosphere through diffuse venting and seepage. In this paper, we characterize the resident sediment microbial communities influenced by cool hydrothermal advection, which is evident from nitrate and oxygen concentrations. 16S rRNA gene sequencing revealed that Thaumarchaea, Proteobacteria, and Planctomycetes were the most abundant phyla in all sediments across the system regardless of influence from seepage. Members of the Thaumarchaeota (Marine Group I, Alphaproteobacteria (Rhodospirillales, Nitrospirae, Nitrospina, Acidobacteria, and Gemmatimonadetes were enriched in the sediments influenced by CHS advection. Of the various geochemical parameters investigated, nitrate concentrations correlated best with microbial community structure, indicating structuring based on seepage of nitrate-rich fluids. A comparison of microbial communities from hydrothermal sediments, seafloor basalts, and local seawater at Dorado Outcrop showed differences that highlight the distinct niche space in CHS. Sediment microbial communities from Dorado Outcrop differ from those at previously characterized, warmer CHS sediment, but are similar to deep-sea sediment habitats with surficial ferromanganese nodules, such as the Clarion Clipperton Zone. We conclude that cool hydrothermal venting at seafloor outcrops can alter the local sedimentary oxidation–reduction pathways, which in turn influences the microbial communities within the fluid discharge affected sediment.

  15. Reproductive Interference and Niche Partitioning in Aphidophagous Insects

    Directory of Open Access Journals (Sweden)

    Suzuki Noriyuki

    2016-01-01

    Full Text Available The range and quality of prey species differ greatly among closely related species of predators. However, the factors responsible for this diversified niche utilization are unclear. This is because the predation and resource competition do not always prevent species coexistence. In this paper, we present evidence in support of reproductive interference as a driver of niche partitioning, focusing on aphidophagous insect. Firstly, we present closely related generalist and specialist species pairs in aphidophagous lacewings to compare the reproductive interference hypothesis with two other hypotheses that have been proposed to explain niche partitioning in lacewings and sympatric speciation through host race formation and sexual selection. Secondly, we present a case study that shows how reproductive interference can drive niche partitioning in sibling ladybird species. Thirdly, we show that many ladybird genera include species inhabiting the same region but having different food and habitat preferences, raising the possibility that reproductive interference might occur in these groups. Finally, we show that intraguild predation cannot always explain the niche partitioning in aphidophagous insects including hoverflies and parasitoids. On the basis of the evidence presented, we urge that future studies investigating predator communities should take account of the role of reproductive interference.

  16. Are species' responses to global change predicted by past niche evolution?

    Science.gov (United States)

    Lavergne, Sébastien; Evans, Margaret E. K.; Burfield, Ian J.; Jiguet, Frederic; Thuiller, Wilfried

    2013-01-01

    Predicting how and when adaptive evolution might rescue species from global change, and integrating this process into tools of biodiversity forecasting, has now become an urgent task. Here, we explored whether recent population trends of species can be explained by their past rate of niche evolution, which can be inferred from increasingly available phylogenetic and niche data. We examined the assemblage of 409 European bird species for which estimates of demographic trends between 1970 and 2000 are available, along with a species-level phylogeny and data on climatic, habitat and trophic niches. We found that species' proneness to demographic decline is associated with slow evolution of the habitat niche in the past, in addition to certain current-day life-history and ecological traits. A similar result was found at a higher taxonomic level, where families prone to decline have had a history of slower evolution of climatic and habitat niches. Our results support the view that niche conservatism can prevent some species from coping with environmental change. Thus, linking patterns of past niche evolution and contemporary species dynamics for large species samples may provide insights into how niche evolution may rescue certain lineages in the face of global change. PMID:23209172

  17. Haematopoietic stem cell niches: new insights inspire new questions

    Science.gov (United States)

    Ugarte, Fernando; Forsberg, E Camilla

    2013-01-01

    Haematopoietic stem cell (HSC) niches provide an environment essential for life-long HSC function. Intense investigation of HSC niches both feed off and drive technology development to increase our capability to assay functionally defined cells with high resolution. A major driving force behind the desire to understand the basic biology of HSC niches is the clear implications for clinical therapies. Here, with particular emphasis on cell type-specific deletion of SCL and CXCL12, we focus on unresolved issues on HSC niches, framed around some very recent advances and novel discoveries on the extrinsic regulation of HSC maintenance. We also provide ideas for possible paths forward, some of which are clearly within reach while others will require both novel tools and vision. PMID:24022369

  18. Reactor performances and microbial communities of biogas reactors: effects of inoculum sources.

    Science.gov (United States)

    Han, Sheng; Liu, Yafeng; Zhang, Shicheng; Luo, Gang

    2016-01-01

    Anaerobic digestion is a very complex process that is mediated by various microorganisms, and the understanding of the microbial community assembly and its corresponding function is critical in order to better control the anaerobic process. The present study investigated the effect of different inocula on the microbial community assembly in biogas reactors treating cellulose with various inocula, and three parallel biogas reactors with the same inoculum were also operated in order to reveal the reproducibility of both microbial communities and functions of the biogas reactors. The results showed that the biogas production, volatile fatty acid (VFA) concentrations, and pH were different for the biogas reactors with different inocula, and different steady-state microbial community patterns were also obtained in different biogas reactors as reflected by Bray-Curtis similarity matrices and taxonomic classification. It indicated that inoculum played an important role in shaping the microbial communities of biogas reactor in the present study, and the microbial community assembly in biogas reactor did not follow the niche-based ecology theory. Furthermore, it was found that the microbial communities and reactor performances of parallel biogas reactors with the same inoculum were different, which could be explained by the neutral-based ecology theory and stochastic factors should played important roles in the microbial community assembly in the biogas reactors. The Bray-Curtis similarity matrices analysis suggested that inoculum affected more on the microbial community assembly compared to stochastic factors, since the samples with different inocula had lower similarity (10-20 %) compared to the samples from the parallel biogas reactors (30 %).

  19. A hypothesis-testing framework for studies investigating ontogenetic niche shifts using stable isotope ratios.

    Directory of Open Access Journals (Sweden)

    Caroline M Hammerschlag-Peyer

    Full Text Available Ontogenetic niche shifts occur across diverse taxonomic groups, and can have critical implications for population dynamics, community structure, and ecosystem function. In this study, we provide a hypothesis-testing framework combining univariate and multivariate analyses to examine ontogenetic niche shifts using stable isotope ratios. This framework is based on three distinct ontogenetic niche shift scenarios, i.e., (1 no niche shift, (2 niche expansion/reduction, and (3 discrete niche shift between size classes. We developed criteria for identifying each scenario, as based on three important resource use characteristics, i.e., niche width, niche position, and niche overlap. We provide an empirical example for each ontogenetic niche shift scenario, illustrating differences in resource use characteristics among different organisms. The present framework provides a foundation for future studies on ontogenetic niche shifts, and also can be applied to examine resource variability among other population sub-groupings (e.g., by sex or phenotype.

  20. Niche evolution and diversification in a Neotropical radiation of birds (Aves: Furnariidae).

    Science.gov (United States)

    Seeholzer, Glenn F; Claramunt, Santiago; Brumfield, Robb T

    2017-03-01

    Rapid diversification may be caused by ecological adaptive radiation via niche divergence. In this model, speciation is coupled with niche divergence and lineage diversification is predicted to be correlated with rates of niche evolution. Studies of the role of niche evolution in diversification have generally focused on ecomorphological diversification but climatic-niche evolution may also be important. We tested these alternatives using a phylogeny of 298 species of ovenbirds (Aves: Furnariidae). We found that within Furnariidae, variation in species richness and diversification rates of subclades were best predicted by rate of climatic-niche evolution than ecomorphological evolution. Although both are clearly important, univariate regression and multivariate model averaging more consistently supported the climatic-niche as the best predictor of lineage diversification. Our study adds to the growing body of evidence, suggesting that climatic-niche divergence may be an important driver of rapid diversification in addition to ecomorphological evolution. However, this pattern may depend on the phylogenetic scale at which rate heterogeneity is examined. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  1. Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene

    DEFF Research Database (Denmark)

    Bowman, Jeff S.; Rasmussen, Simon; Blom, Nikolaj

    2011-01-01

    community in MYI at two sites near the geographic North Pole using parallel tag sequencing of the 16S rRNA gene. Although the composition of the MYI microbial community has been characterized by previous studies, microbial community structure has not been. Although richness was lower in MYI than....... In addition, several low-abundance clades not previously reported in sea ice were present, including the phylum TM7 and the classes Spartobacteria and Opitutae. Members of Coraliomargarita, a recently described genus of the class Opitutae, were present in sufficient numbers to suggest niche occupation within...

  2. Trophic specialization influences the rate of environmental niche evolution in damselfishes (Pomacentridae).

    Science.gov (United States)

    Litsios, Glenn; Pellissier, Loïc; Forest, Félix; Lexer, Christian; Pearman, Peter B; Zimmermann, Niklaus E; Salamin, Nicolas

    2012-09-22

    The rate of environmental niche evolution describes the capability of species to explore the available environmental space and is known to vary among species owing to lineage-specific factors. Trophic specialization is a main force driving species evolution and is responsible for classical examples of adaptive radiations in fishes. We investigate the effect of trophic specialization on the rate of environmental niche evolution in the damselfish, Pomacentridae, which is an important family of tropical reef fishes. First, phylogenetic niche conservatism is not detected in the family using a standard test of phylogenetic signal, and we demonstrate that the environmental niches of damselfishes that differ in trophic specialization are not equivalent while they still overlap at their mean values. Second, we estimate the relative rates of niche evolution on the phylogenetic tree and show the heterogeneity among rates of environmental niche evolution of the three trophic groups. We suggest that behavioural characteristics related to trophic specialization can constrain the evolution of the environmental niche and lead to conserved niches in specialist lineages. Our results show the extent of influence of several traits on the evolution of the environmental niche and shed new light on the evolution of damselfishes, which is a key lineage in current efforts to conserve biodiversity in coral reefs.

  3. Probabilistic and spatially variable niches inferred from demography

    Science.gov (United States)

    Jeffrey M. Diez; Itamar Giladi; Robert Warren; H. Ronald. Pulliam

    2014-01-01

    Summary 1. Mismatches between species distributions and habitat suitability are predicted by niche theory and have important implications for forecasting how species may respond to environmental changes. Quantifying these mismatches is challenging, however, due to the high dimensionality of species niches and the large spatial and temporal variability in population...

  4. Niche conservatism of Eulophia alta, a trans-Atlantic orchid species

    Directory of Open Access Journals (Sweden)

    Marta Kolanowska

    2014-03-01

    Full Text Available The genus Eulophia embraces over 230 species distributed through the tropical and subtropical Africa, Asia, Australia and the Americas. In Neotropics it is represented by a sole species – E. alta. The aim of the presented study was to evaluate the difference between ecological niches occupied by American and African populations of this species based on the ecological niche modeling. The similarity between the glacial and present niches occupied by E. alta was calculated and the factors limiting the species occurrence were identified. Areas of seasonal tropical forest, tropical savanna and woodland served as refugia for the studied species during last glacial maximum and they were more widespread in Neotropics than in Africa. No significant niche shift after last glacial maximum was observed. The distribution of E. alta in its whole range is restricted mainly by temperature seasonality. The differences in the niches occupied by African and Neotropical populations of E. alta suggest preglacial disjunction of the species range and independent adaptation of both groups. Despite the significant range disjunction of E. alta the species is characterized by relatively high degree of niche conservatism.

  5. Niche Marketing Potentials for Farm Entrepreneurs in Nigeria https ...

    African Journals Online (AJOL)

    User

    . Niche marketing involves targetting a product or service to a small but specific well ... Table 1: Examples of possible niche markets for entrepreneurs in Nigeria. Farm Business .... Concepts, Principles and Decisions, 2nd Edition. Afritowers ...

  6. In a niche of time: do specialty hospitals outperform general services hospitals?

    Science.gov (United States)

    Poole, LeJon; Davis, Jullet A; Gunby, Norris W

    2013-01-01

    Niche hospitals represent a growing segment in the health care industry. Niche facilities are primarily engaged in the treatment of cardiac or orthopedic conditions. The effectiveness of this strategy is of interest because niche hospitals focus on only the most profitable services. The purpose of this research was to assess the financial effectiveness of the niche strategy. We theorize that firm and market-level factors concomitantly with the strategy of the hospital-niche versus traditional-are associated with financial performance. This research used 2 data sources, the 2003 Medicare Cost Report and the 2003 Area Resource File. The sample was limited to only for-profit, urban, nongovernmental hospitals (n = 995). The data were analyzed using hierarchical least squares regression. Financial performance was operationalized using the hospital's return on assets. The principal finding of this project is that niche hospitals had significantly higher performance than traditional facilities. From the organizational perspective, the niche strategy leads to better financial performance. From a societal perspective, the niche strategy provides increased focus and efficiencies through repetition. Despite the limited focus of this strategy, patients who can access these providers may experience better outcomes than patients in more traditional hospitals.

  7. Spontaneous Cognition and Epistemic Agency in the Cognitive Niche

    Science.gov (United States)

    Fabry, Regina E.

    2018-01-01

    According to Thomas Metzinger, many human cognitive processes in the waking state are spontaneous and are deprived of the experience of epistemic agency. He considers mind wandering as a paradigm example of our recurring loss of epistemic agency. I will enrich this view by extending the scope of the concept of epistemic agency to include cases of depressive rumination and creative cognition, which are additional types of spontaneous cognition. Like mind wandering, they are characterized by unique phenomenal and functional properties that give rise to varying degrees of epistemic agency. The main claim of this paper will be that the experience of being an epistemic agent within a certain time frame is a relational phenomenon that emerges from the organism’s capacity to interact with its cognitive niche. To explore this relation, I develop a new framework that integrates phenomenological considerations on epistemic agency with a functional account of the reciprocal coupling of the embodied organism with its cognitive niche. This account rests upon dynamical accounts of strong embodied and embedded cognition and recent work on cognitive niche construction. Importantly, epistemic agency and organism-niche coupling are gradual phenomena ranging from weak to strong realizations. The emerging framework will be employed to analyze mind wandering, depressive rumination, and creative cognition as well as their commonalities and differences. Mind wandering and depressive rumination are cases of weak epistemic agency and organism-niche coupling. However, there are also important phenomenological, functional, and neuronal differences. In contrast, creative cognition is a case of strong epistemic agency and organism-niche coupling. By providing a phenomenological and functional analysis of these distinct types of spontaneous cognition, we can gain a better understanding of the importance of organism-niche interaction for the realization of epistemic agency.

  8. Climatic niche conservatism and the evolutionary dynamics in species range boundaries

    DEFF Research Database (Denmark)

    Olalla-Tárraga1, Miguel Á.; McInnes, Linsey; Bini, Luis M.

    2011-01-01

    Aim Comparative evidence for phylogenetic niche conservatism – the tendency for lineages to retain their ancestral niches over long time scales – has so far been mixed, depending on spatial and taxonomic scale. We quantify and compare conservatism in the climatic factors defining range boundaries...... conservatism, as expected from their greater physiological sensitivity and lower dispersal abilities. Location Global; continental land masses excluding Antarctica. Methods We used nearly complete global distributional databases to estimate the climatic niche conservatism in extant continental mammals...... and amphibians. We characterized the climatic niche of each species by using a suite of variables and separately investigate conservatism in each variable using both taxonomic and phylogenetic approaches. Finally, we explored the spatial, taxonomic and phylogenetic patterns in recent climatic niche evolution...

  9. Development of a laboratory niche Web site.

    Science.gov (United States)

    Dimenstein, Izak B; Dimenstein, Simon I

    2013-10-01

    This technical note presents the development of a methodological laboratory niche Web site. The "Grossing Technology in Surgical Pathology" (www.grossing-technology.com) Web site is used as an example. Although common steps in creation of most Web sites are followed, there are particular requirements for structuring the template's menu on methodological laboratory Web sites. The "nested doll principle," in which one object is placed inside another, most adequately describes the methodological approach to laboratory Web site design. Fragmentation in presenting the Web site's material highlights the discrete parts of the laboratory procedure. An optimally minimal triad of components can be recommended for the creation of a laboratory niche Web site: a main set of media, a blog, and an ancillary component (host, contact, and links). The inclusion of a blog makes the Web site a dynamic forum for professional communication. By forming links and portals, cloud computing opens opportunities for connecting a niche Web site with other Web sites and professional organizations. As an additional source of information exchange, methodological laboratory niche Web sites are destined to parallel both traditional and new forms, such as books, journals, seminars, webinars, and internal educational materials. Copyright © 2013 Elsevier Inc. All rights reserved.

  10. Widespread correlations between climatic niche evolution and species diversification in birds.

    Science.gov (United States)

    Cooney, Christopher R; Seddon, Nathalie; Tobias, Joseph A

    2016-07-01

    The adaptability of species' climatic niches can influence the dynamics of colonization and gene flow across climatic gradients, potentially increasing the likelihood of speciation or reducing extinction in the face of environmental change. However, previous comparative studies have tested these ideas using geographically, taxonomically and ecologically restricted samples, yielding mixed results, and thus the processes linking climatic niche evolution with diversification remain poorly understood. Focusing on birds, the largest and most widespread class of terrestrial vertebrates, we test whether variation in species diversification among clades is correlated with rates of climatic niche evolution and the extent to which these patterns are modified by underlying gradients in biogeography and species' ecology. We quantified climatic niches, latitudinal distribution and ecological traits for 7657 (˜75%) bird species based on geographical range polygons and then used Bayesian phylogenetic analyses to test whether niche evolution was related to species richness and rates of diversification across genus- and family-level clades. We found that the rate of climatic niche evolution has a positive linear relationship with both species richness and diversification rate at two different taxonomic levels (genus and family). Furthermore, this positive association between labile climatic niches and diversification was detected regardless of variation in clade latitude or key ecological traits. Our findings suggest either that rapid adaptation to unoccupied areas of climatic niche space promotes avian diversification, or that diversification promotes adaptation. Either way, we propose that climatic niche evolution is a fundamental process regulating the link between climate and biodiversity at global scales, irrespective of the geographical and ecological context of speciation and extinction. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.

  11. Geographical parthenogenesis: General purpose genotypes and frozen niche variation

    DEFF Research Database (Denmark)

    Vrijenhoek, Robert C.; Parker, Dave

    2009-01-01

    hypotheses concerning the evolution of niche breadth in asexual species - the "general-purpose genotype" (GPG) and "frozen niche-variation" (FNV) models. The two models are often portrayed as mutually exclusive, respectively viewing clonal lineages as generalists versus specialists. Nonetheless...

  12. A family business: stem cell progeny join the niche to regulate homeostasis.

    Science.gov (United States)

    Hsu, Ya-Chieh; Fuchs, Elaine

    2012-01-23

    Stem cell niches, the discrete microenvironments in which the stem cells reside, play a dominant part in regulating stem cell activity and behaviours. Recent studies suggest that committed stem cell progeny become indispensable components of the niche in a wide range of stem cell systems. These unexpected niche inhabitants provide versatile feedback signals to their stem cell parents. Together with other heterologous cell types that constitute the niche, they contribute to the dynamics of the microenvironment. As progeny are often located in close proximity to stem cell niches, similar feedback regulations may be the underlying principles shared by different stem cell systems.

  13. Analysis of 16S rRNA and mxaF genes revealing insights into Methylobacterium niche-specific plant association

    Science.gov (United States)

    Dourado, Manuella Nóbrega; Andreote, Fernando Dini; Dini-Andreote, Francisco; Conti, Raphael; Araújo, Janete Magali; Araújo, Welington Luiz

    2012-01-01

    The genus Methylobacterium comprises pink-pigmented facultative methylotrophic (PPFM) bacteria, known to be an important plant-associated bacterial group. Species of this group, described as plant-nodulating, have the dual capacity of producing cytokinin and enzymes, such as pectinase and cellulase, involved in systemic resistance induction and nitrogen fixation under specific plant environmental conditions. The aim hereby was to evaluate the phylogenetic distribution of Methylobacterium spp. isolates from different host plants. Thus, a comparative analysis between sequences from structural (16S rRNA) and functional mxaF (which codifies for a subunit of the enzyme methanol dehydrogenase) ubiquitous genes, was undertaken. Notably, some Methylobacterium spp. isolates are generalists through colonizing more than one host plant, whereas others are exclusively found in certain specific plant-species. Congruency between phylogeny and specific host inhabitance was higher in the mxaF gene than in the 16S rRNA, a possible indication of function-based selection in this niche. Therefore, in a first stage, plant colonization by Methylobacterium spp. could represent generalist behavior, possibly related to microbial competition and adaptation to a plant environment. Otherwise, niche-specific colonization is apparently impelled by the host plant. PMID:22481887

  14. Analysis of 16S rRNA and mxaF genes reveling insights into Methylobacterium niche-specific plant association

    Directory of Open Access Journals (Sweden)

    Manuella Nóbrega Dourado

    2012-01-01

    Full Text Available The genus Methylobacterium comprises pink-pigmented facultative methylotrophic (PPFM bacteria, known to be an important plant-associated bacterial group. Species of this group, described as plant-nodulating, have the dual capacity of producing cytokinin and enzymes, such as pectinase and cellulase, involved in systemic resistance induction and nitrogen fixation under specific plant environmental conditions. The aim hereby was to evaluate the phylogenetic distribution of Methylobacterium spp. isolates from different host plants. Thus, a comparative analysis between sequences from structural (16S rRNA and functional mxaF (which codifies for a subunit of the enzyme methanol dehydrogenase ubiquitous genes, was undertaken. Notably, some Methylobacterium spp. isolates are generalists through colonizing more than one host plant, whereas others are exclusively found in certain specific plant-species. Congruency between phylogeny and specific host inhabitance was higher in the mxaF gene than in the 16S rRNA, a possible indication of function-based selection in this niche. Therefore, in a first stage, plant colonization by Methylobacterium spp. could represent generalist behavior, possibly related to microbial competition and adaptation to a plant environment. Otherwise, niche-specific colonization is apparently impelled by the host plant.

  15. Analysis of 16S rRNA and mxaF genes revealing insights into Methylobacterium niche-specific plant association.

    Science.gov (United States)

    Dourado, Manuella Nóbrega; Andreote, Fernando Dini; Dini-Andreote, Francisco; Conti, Raphael; Araújo, Janete Magali; Araújo, Welington Luiz

    2012-01-01

    The genus Methylobacterium comprises pink-pigmented facultative methylotrophic (PPFM) bacteria, known to be an important plant-associated bacterial group. Species of this group, described as plant-nodulating, have the dual capacity of producing cytokinin and enzymes, such as pectinase and cellulase, involved in systemic resistance induction and nitrogen fixation under specific plant environmental conditions. The aim hereby was to evaluate the phylogenetic distribution of Methylobacterium spp. isolates from different host plants. Thus, a comparative analysis between sequences from structural (16S rRNA) and functional mxaF (which codifies for a subunit of the enzyme methanol dehydrogenase) ubiquitous genes, was undertaken. Notably, some Methylobacterium spp. isolates are generalists through colonizing more than one host plant, whereas others are exclusively found in certain specific plant-species. Congruency between phylogeny and specific host inhabitance was higher in the mxaF gene than in the 16S rRNA, a possible indication of function-based selection in this niche. Therefore, in a first stage, plant colonization by Methylobacterium spp. could represent generalist behavior, possibly related to microbial competition and adaptation to a plant environment. Otherwise, niche-specific colonization is apparently impelled by the host plant.

  16. A niche marketing guide for lamb cooperatives

    OpenAIRE

    Kazmierczak, Tamra Kirkpatrick; Bell, James B.

    1995-01-01

    The two types of niche markets targeted by lamb marketing cooperatives are described in this guide. The first type includes specialty middlemen outlets that cooperatives used to market lamb to specialized niches within the traditional meat marketing system of retail food stores, restaurants, food service outlets, and specialty distributors. The second type includes those outlets that cooperatives used to market lamb directly to the consumer, such as freezer markets, farmers' markets, mobile m...

  17. Compatible ecological niche signals between biological and archaeological datasets for late-surviving Neandertals.

    Science.gov (United States)

    Bible, Rachael C; Peterson, A Townsend

    2018-04-17

    To assess ecological niche similarity for biological and archaeological samples representing late-surviving Neandertals in Europe to evaluate the validity of combining these two types of data in ecological niche modeling analyses. Tests of niche conservatism were used to assess niche similarity and niche identity of samples of morphologically diagnostic Neandertal remains and Middle Paleolithic (MP) archaeological sites dating to the time period leading up to Neandertal extinction. Paleoenvironmental reconstructions for the Pre-H4 (43.3-40.2 ky cal BP) were used as environmental space analyses. Null hypotheses of niche similarity and identity of the two types of samples could not be rejected. As primary and secondary evidence of Neandertal occurrence during the Pre-H4 show high levels of niche similarity and identity, combining the two types of occurrence data to create larger samples for niche analyses is justified without the concern that different environmental signals could complicate future research. © 2018 Wiley Periodicals, Inc.

  18. Insights from ecological niche modeling on the taxonomic distinction and niche differentiation between the black-spotted and red-spotted tokay geckoes (Gekko gecko).

    Science.gov (United States)

    Zhang, Yueyun; Chen, Chongtao; Li, Li; Zhao, Chengjian; Chen, Weicai; Huang, Yong

    2014-09-01

    The black-spotted tokay and the red-spotted tokay are morphologically distinct and have largely allopatric distributions. The black-spotted tokay is characterized by a small body size and dark skin with sundry spots, while the red-spotted tokay has a relatively large body size and red spots. Based on morphological, karyotypic, genetic, and distribution differences, recent studies suggested their species status; however, their classifications remain controversial, and additional data such as ecological niches are necessary to establish firm hypotheses regarding their taxonomic status. We reconstructed their ecological niches models using climatic and geographic data. We then performed niche similarity tests (niche identity and background tests) and point-based analyses to explore whether ecological differentiation has occurred, and whether such differences are sufficient to explain the maintenance of their separate segments of environmental ranges. We found that both niche models of the black- and the red-spotted tokay had a good fit and a robust performance, as indicated by the high area under the curve (AUC) values ("black" = 0.982, SD = ± 0.002, "red" = 0.966 ± 0.02). Significant ecological differentiation across the entire geographic range was found, indicating that the involvement of ecological differentiation is important for species differentiation. Divergence along the environmental axes is highly associated with climatic conditions, with isothermality being important for the "black" form, while temperature seasonality, precipitation of warmest quarter, and annual temperature range together being important for the "red" form. These factors are likely important factors in niche differentiation between the two forms, which result in morphological replacement. Overall, beside morphological and genetic differentiation information, our results contribute to additional insights into taxonomic distinction and niche differentiation between the black- and the red

  19. Behavioural manipulation of insect hosts by Baculoviridae as a process of niche construction.

    Science.gov (United States)

    Hamblin, Steven; Tanaka, Mark M

    2013-08-16

    Niche construction has received increasing attention in recent years as a vital force in evolution and examples of niche construction have been identified in a wide variety of taxa, but viruses are conspicuously absent. In this study we explore how niche construction can lead to viruses engineering their hosts (including behavioural manipulation) with feedback on selective pressures for viral transmission and virulence. To illustrate this concept we focus on Baculoviridae, a family of invertebrate viruses that have evolved to modify the feeding behaviour of their lepidopteran hosts and liquefy their cadavers as part of the course of infection. We present a mathematical model showing how niche construction leads to feedback from the behavioural manipulation to the liquefaction of the host, linking the evolution of both of these traits, and show how this association arises from the action of niche construction. Model results show that niche construction is plausible in this system and delineates the conditions under which niche construction will occur. Niche construction in this system is also shown to be sensitive to parameter values that reflect ecological forces. Our model demonstrates that niche construction can be a potent force in viral evolution and can lead to the acquisition and maintenance of the behavioural manipulation and liquefaction traits in Baculoviridae via the niche constructing effects on the host. These results show the potential for niche construction theory to provide new insights into viral evolution.

  20. Seasonality in ocean microbial communities.

    Science.gov (United States)

    Giovannoni, Stephen J; Vergin, Kevin L

    2012-02-10

    Ocean warming occurs every year in seasonal cycles that can help us to understand long-term responses of plankton to climate change. Rhythmic seasonal patterns of microbial community turnover are revealed when high-resolution measurements of microbial plankton diversity are applied to samples collected in lengthy time series. Seasonal cycles in microbial plankton are complex, but the expansion of fixed ocean stations monitoring long-term change and the development of automated instrumentation are providing the time-series data needed to understand how these cycles vary across broad geographical scales. By accumulating data and using predictive modeling, we gain insights into changes that will occur as the ocean surface continues to warm and as the extent and duration of ocean stratification increase. These developments will enable marine scientists to predict changes in geochemical cycles mediated by microbial communities and to gauge their broader impacts.

  1. Global niche of marine anaerobic metabolisms expanded by particle microenvironments

    Science.gov (United States)

    Bianchi, Daniele; Weber, Thomas S.; Kiko, Rainer; Deutsch, Curtis

    2018-04-01

    In ocean waters, anaerobic microbial respiration should be confined to the anoxic waters found in coastal regions and tropical oxygen minimum zones, where it is energetically favourable. However, recent molecular and geochemical evidence has pointed to a much broader distribution of denitrifying and sulfate-reducing microbes. Anaerobic metabolisms are thought to thrive in microenvironments that develop inside sinking organic aggregates, but the global distribution and geochemical significance of these microenvironments is poorly understood. Here, we develop a new size-resolved particle model to predict anaerobic respiration from aggregate properties and seawater chemistry. Constrained by observations of the size spectrum of sinking particles, the model predicts that denitrification and sulfate reduction can be sustained throughout vast, hypoxic expanses of the ocean, and could explain the trace metal enrichment observed in particles due to sulfide precipitation. Globally, the expansion of the anaerobic niche due to particle microenvironments doubles the rate of water column denitrification compared with estimates based on anoxic zones alone, and changes the sensitivity of the marine nitrogen cycle to deoxygenation in a warming climate.

  2. Niche evolution and adaptive radiation: Testing the order of trait divergence

    Science.gov (United States)

    Ackerly, D.D.; Schwilk, D.W.; Webb, C.O.

    2006-01-01

    In the course of an adaptive radiation, the evolution of niche parameters is of particular interest for understanding modes of speciation and the consequences for coexistence of related species within communities. We pose a general question: In the course of an evolutionary radiation, do traits related to within-community niche differences (?? niche) evolve before or after differentiation of macrohabitat affinity or climatic tolerances (?? niche)? Here we introduce a new test to address this question, based on a modification of the method of independent contrasts. The divergence order test (DOT) is based on the average age of the nodes on a tree, weighted by the absolute magnitude of the contrast at each node for a particular trait. The comparison of these weighted averages reveals whether large divergences for one trait have occurred earlier or later in the course of diversification, relative to a second trait; significance is determined by bootstrapping from maximum-likelihood ancestral state reconstructions. The method is applied to the evolution of Ceanothus, a woody plant group in California, in which co-occurring species exhibit significant differences in a key leaf trait (specific leaf area) associated with contrasting physiological and life history strategies. Co-occurring species differ more for this trait than expected under a null model of community assembly. This ?? niche difference evolved early in the divergence of two major subclades within Ceanothus, whereas climatic distributions (?? niche traits) diversified later within each of the subclades. However, rapid evolution of climate parameters makes inferences of early divergence events highly uncertain, and differentiation of the ?? niche might have taken place throughout the evolution of the group, without leaving a clear phylogenetic signal. Similar patterns observed in several plant and animal groups suggest that early divergence of ?? niche traits might be a common feature of niche evolution in

  3. Microhabitat and Climatic Niche Change Explain Patterns of Diversification among Frog Families.

    Science.gov (United States)

    Moen, Daniel S; Wiens, John J

    2017-07-01

    A major goal of ecology and evolutionary biology is to explain patterns of species richness among clades. Differences in rates of net diversification (speciation minus extinction over time) may often explain these patterns, but the factors that drive variation in diversification rates remain uncertain. Three important candidates are climatic niche position (e.g., whether clades are primarily temperate or tropical), rates of climatic niche change among species within clades, and microhabitat (e.g., aquatic, terrestrial, arboreal). The first two factors have been tested separately in several studies, but the relative importance of all three is largely unknown. Here we explore the correlates of diversification among families of frogs, which collectively represent ∼88% of amphibian species. We assemble and analyze data on phylogeny, climate, and microhabitat for thousands of species. We find that the best-fitting phylogenetic multiple regression model includes all three types of variables: microhabitat, rates of climatic niche change, and climatic niche position. This model explains 67% of the variation in diversification rates among frog families, with arboreal microhabitat explaining ∼31%, niche rates ∼25%, and climatic niche position ∼11%. Surprisingly, we show that microhabitat can have a much stronger influence on diversification than climatic niche position or rates of climatic niche change.

  4. Hadal biosphere: insight into the microbial ecosystem in the deepest ocean on Earth.

    Science.gov (United States)

    Nunoura, Takuro; Takaki, Yoshihiro; Hirai, Miho; Shimamura, Shigeru; Makabe, Akiko; Koide, Osamu; Kikuchi, Tohru; Miyazaki, Junichi; Koba, Keisuke; Yoshida, Naohiro; Sunamura, Michinari; Takai, Ken

    2015-03-17

    Hadal oceans at water depths below 6,000 m are the least-explored aquatic biosphere. The Challenger Deep, located in the western equatorial Pacific, with a water depth of ∼11 km, is the deepest ocean on Earth. Microbial communities associated with waters from the sea surface to the trench bottom (0∼10,257 m) in the Challenger Deep were analyzed, and unprecedented trench microbial communities were identified in the hadal waters (6,000∼10,257 m) that were distinct from the abyssal microbial communities. The potentially chemolithotrophic populations were less abundant in the hadal water than those in the upper abyssal waters. The emerging members of chemolithotrophic nitrifiers in the hadal water that likely adapt to the higher flux of electron donors were also different from those in the abyssal waters that adapt to the lower flux of electron donors. Species-level niche separation in most of the dominant taxa was also found between the hadal and abyssal microbial communities. Considering the geomorphology and the isolated hydrotopographical nature of the Mariana Trench, we hypothesized that the distinct hadal microbial ecosystem was driven by the endogenous recycling of organic matter in the hadal waters associated with the trench geomorphology.

  5. The making of an immigrant niche.

    Science.gov (United States)

    Waldinger, R

    1994-01-01

    "This article speaks to the conceptual and methodological issues in research on the making of an immigrant niche through a case study of immigrant professionals in New York City government." The author argues that "the growth of this immigrant niche resulted from changes in the relative supply of native workers and in the structure of employment, which opened the bureaucracy to immigrants and reduced native/immigrant competition. These shifts opened hiring portals; given the advantages of network hiring for workers and managers, and an immigrant propensity for government employment, network recruitment led to a rapid buildup in immigrant ranks." excerpt

  6. Design and construction of synthetic microbial consortia in China

    Directory of Open Access Journals (Sweden)

    Ming-Zhu Ding

    2016-12-01

    Full Text Available The rapid development of synthetic biology enables the design, construction and optimization of synthetic microbial consortia to achieve specific functions. In China, the “973” project-“Design and Construction of Microbial Consortia” was funded by the National Basic Research Program of China in January 2014. It was proposed to address the fundamental challenges in engineering natural microbial consortia and reconstructing microbial consortia to meet industrial demands. In this review, we will introduce this “973” project, including the significance of microbial consortia, the fundamental scientific issues, the recent research progresses, and some case studies about synthetic microbial consortia in the past two and a half years.

  7. Stem cell niche-specific Ebf3 maintains the bone marrow cavity.

    Science.gov (United States)

    Seike, Masanari; Omatsu, Yoshiki; Watanabe, Hitomi; Kondoh, Gen; Nagasawa, Takashi

    2018-03-01

    Bone marrow is the tissue filling the space between bone surfaces. Hematopoietic stem cells (HSCs) are maintained by special microenvironments known as niches within bone marrow cavities. Mesenchymal cells, termed CXC chemokine ligand 12 (CXCL12)-abundant reticular (CAR) cells or leptin receptor-positive (LepR + ) cells, are a major cellular component of HSC niches that gives rise to osteoblasts in bone marrow. However, it remains unclear how osteogenesis is prevented in most CAR/LepR + cells to maintain HSC niches and marrow cavities. Here, using lineage tracing, we found that the transcription factor early B-cell factor 3 (Ebf3) is preferentially expressed in CAR/LepR + cells and that Ebf3-expressing cells are self-renewing mesenchymal stem cells in adult marrow. When Ebf3 is deleted in CAR/LepR + cells, HSC niche function is severely impaired, and bone marrow is osteosclerotic with increased bone in aged mice. In mice lacking Ebf1 and Ebf3 , CAR/LepR + cells exhibiting a normal morphology are abundantly present, but their niche function is markedly impaired with depleted HSCs in infant marrow. Subsequently, the mutants become progressively more osteosclerotic, leading to the complete occlusion of marrow cavities in early adulthood. CAR/LepR + cells differentiate into bone-producing cells with reduced HSC niche factor expression in the absence of Ebf1/Ebf3 Thus, HSC cellular niches express Ebf3 that is required to create HSC niches, to inhibit their osteoblast differentiation, and to maintain spaces for HSCs. © 2018 Seike et al.; Published by Cold Spring Harbor Laboratory Press.

  8. Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments

    DEFF Research Database (Denmark)

    Klatt, Christian G.; Inskeep, William P.; Herrgard, Markus

    2013-01-01

    Six phototrophic microbial mat communities from different geothermal springs (YNP) were studied using metagenome sequencing and geochemical analyses. The primary goals of this work were to determine differences in community composition of high-temperature phototrophic mats distributed across...... the Yellowstone geothermal ecosystem, and to identify metabolic attributes of predominant organisms present in these communities that may correlate with environmental attributes important in niche differentiation. Random shotgun metagenome sequences from six phototrophic communities (average 53Mbp/site) were...

  9. Neural Crossroads in the Hematopoietic Stem Cell Niche.

    Science.gov (United States)

    Agarwala, Sobhika; Tamplin, Owen J

    2018-05-29

    The hematopoietic stem cell (HSC) niche supports steady-state hematopoiesis and responds to changing needs during stress and disease. The nervous system is an important regulator of the niche, and its influence is established early in development when stem cells are specified. Most research has focused on direct innervation of the niche, however recent findings show there are different modes of neural control, including globally by the central nervous system (CNS) and hormone release, locally by neural crest-derived mesenchymal stem cells, and intrinsically by hematopoietic cells that express neural receptors and neurotransmitters. Dysregulation between neural and hematopoietic systems can contribute to disease, however new therapeutic opportunities may be found among neuroregulator drugs repurposed to support hematopoiesis. Copyright © 2018 Elsevier Ltd. All rights reserved.

  10. Fibrocytes and the tissue niche in lung repair

    Directory of Open Access Journals (Sweden)

    Bjermer Leif

    2011-06-01

    Full Text Available Abstract Human fibrocytes are bone marrow-derived mesenchymal progenitor cells that express a variety of markers related to leukocytes, hematopoietic stem cells and a diverse set of fibroblast phenotypes. Fibrocytes can be recruited from the circulation to the tissue where they further can differentiate and proliferate into various mesenchymal cell types depending on the tissue niche. This local tissue niche is important because it modulates the fibrocytes and coordinates their role in tissue behaviour and repair. However, plasticity of a niche may be co-opted in chronic airway diseases such as asthma, idiopathic pulmonary fibrosis and obliterative bronchiolitis. This review will therefore focus on a possible role of fibrocytes in pathological tissue repair processes in those diseases.

  11. Niche dimensions in fishes: an integrative view.

    Science.gov (United States)

    Pörtner, H O; Schulte, P M; Wood, C M; Schiemer, F

    2010-01-01

    Current shifts in ecosystem composition and function emphasize the need for an understanding of the links between environmental factors and organism fitness and tolerance. The examples discussed here illustrate how recent progress in the field of comparative physiology may provide a better mechanistic understanding of the ecological concepts of the fundamental and realized niches and thus provide insights into the impacts of anthropogenic disturbance. Here we argue that, as a link between physiological and ecological indicators of organismal performance, the mechanisms shaping aerobic scope and passive tolerance set the dimensions of an animal's niche, here defined as its capacity to survive, grow, behave, and interact with other species. We demonstrate how comparative studies of cod or killifish populations in a latitudinal cline have unraveled mitochondrial mechanisms involved in establishing a species' niche, performance, and energy budget. Riverine fish exemplify how the performance windows of various developmental stages follow the dynamic regimes of both seasonal temperatures and river hydrodynamics, as synergistic challenges. Finally, studies of species in extreme environments, such as the tilapia of Lake Magadi, illustrate how on evolutionary timescales functional and morphological shifts can occur, associated with new specializations. We conclude that research on the processes and time course of adaptations suitable to overcome current niche limits is urgently needed to assess the resilience of species and ecosystems to human impact, including the challenges of global climate change.

  12. Microbial ecology to manage processes in environmental biotechnology.

    Science.gov (United States)

    Rittmann, Bruce E

    2006-06-01

    Microbial ecology and environmental biotechnology are inherently tied to each other. The concepts and tools of microbial ecology are the basis for managing processes in environmental biotechnology; and these processes provide interesting ecosystems to advance the concepts and tools of microbial ecology. Revolutionary advancements in molecular tools to understand the structure and function of microbial communities are bolstering the power of microbial ecology. A push from advances in modern materials along with a pull from a societal need to become more sustainable is enabling environmental biotechnology to create novel processes. How do these two fields work together? Five principles illuminate the way: (i) aim for big benefits; (ii) develop and apply more powerful tools to understand microbial communities; (iii) follow the electrons; (iv) retain slow-growing biomass; and (v) integrate, integrate, integrate.

  13. Interactions between structural and chemical biomimetism in synthetic stem cell niches

    International Nuclear Information System (INIS)

    Nava, Michele M; Raimondi, Manuela T; Credi, Caterina; De Marco, Carmela; Turri, Stefano; Cerullo, Giulio; Osellame, Roberto

    2015-01-01

    Advancements in understanding stem cell functions and differentiation are of key importance for the clinical success of stem-cell-based therapies. 3D structural niches fabricated by two-photon polymerization are a powerful platform for controlling stem cell growth and differentiation. In this paper, we investigate the possibility of further controlling stem cell fate by tuning the mechanical properties of such niches through coating with thin layers of biomimetic hyaluronan-based and gelatin-based hydrogels. We first assess the biocompatibility of chemical coatings and then study the interactions between structural and chemical biomimetism on the response of MSCs in terms of proliferation and differentiation. We observed a clear effect of the hydrogel coating on otherwise identical 3D scaffolds. In particular, in gelatin-coated niches we observed a stronger metabolic activity and commitment toward the osteo-chondral lineage with respect to hyaluronan-coated niches. Conversely, a reduction in the homing effect was observed in all the coated niches, especially in gelatin-coated niches. This study demonstrates the feasibility of controlling independently different mechanical cues, in bioengineered stem cell niches, i.e. the 3D scaffold geometry and the surface stiffness. This will allow, on the one hand, understanding their specific role in stem cell proliferation and differentiation and, on the other hand, finely tuning their synergistic effect. (paper)

  14. Biofilm formation and microbial community analysis of the simulated river bioreactor for contaminated source water remediation.

    Science.gov (United States)

    Xu, Xiang-Yang; Feng, Li-Juan; Zhu, Liang; Xu, Jing; Ding, Wei; Qi, Han-Ying

    2012-06-01

    The start-up pattern of biofilm remediation system affects the biofilm characteristics and operating performances. The objective of this study was to evaluate the performances of the contaminated source water remediation systems with different start-up patterns in view of the pollutants removal performances and microbial community succession. The operating performances of four lab-scale simulated river biofilm reactors were examined which employed different start-up methods (natural enrichment and artificial enhancement via discharging sediment with influent velocity gradient increase) and different bio-fillers (Elastic filler and AquaMats® ecobase). At the same time, the microbial communities of the bioreactors in different phases were analyzed by polymerase chain reaction, denaturing gradient gel electrophoresis, and sequencing. The pollutants removal performances became stable in the four reactors after 2 months' operation, with ammonia nitrogen and permanganate index (COD(Mn)) removal efficiencies of 84.41-94.21% and 69.66-76.60%, respectively. The biomass of mature biofilm was higher in the bioreactors by artificial enhancement than that by natural enrichment. Microbial community analysis indicated that elastic filler could enrich mature biofilm faster than AquaMats®. The heterotrophic bacteria diversity of biofilm decreased by artificial enhancement, which favored the ammonia-oxidizing bacteria (AOB) developing on the bio-fillers. Furthermore, Nitrosomonas- and Nitrosospira-like AOB coexisted in the biofilm, and Pseudomonas sp., Sphaerotilus sp., Janthinobacterium sp., Corynebacterium aurimucosum were dominant in the oligotrophic niche. Artificial enhancement via the combination of sediment discharging and influent velocity gradient increasing could enhance the biofilm formation and autotrophic AOB enrichment in oligotrophic niche.

  15. Phylogenetic signals in the climatic niches of the world's amphibians

    DEFF Research Database (Denmark)

    Hof, Christian; Rahbek, Carsten; Araújo, Miguel B.

    2010-01-01

    amphibian orders and across biogeographical regions. To our knowledge, this is the first study providing a comprehensive analysis of the phylogenetic signal in species climatic niches for an entire clade across the world. Even though our results do not provide a strong test of the niche conservatism......The question of whether closely related species share similar ecological requirements has attracted increasing attention, because of its importance for understanding global diversity gradients and the impacts of climate change on species distributions. In fact, the assumption that related species...... are also ecologically similar has often been made, although the prevalence of such a phylogenetic signal in ecological niches remains heavily debated. Here, we provide a global analysis of phylogenetic niche relatedness for the world's amphibians. In particular, we assess which proportion of the variance...

  16. Framework for analyzing ecological trait-based models in multidimensional niche spaces

    Science.gov (United States)

    Biancalani, Tommaso; DeVille, Lee; Goldenfeld, Nigel

    2015-05-01

    We develop a theoretical framework for analyzing ecological models with a multidimensional niche space. Our approach relies on the fact that ecological niches are described by sequences of symbols, which allows us to include multiple phenotypic traits. Ecological drivers, such as competitive exclusion, are modeled by introducing the Hamming distance between two sequences. We show that a suitable transform diagonalizes the community interaction matrix of these models, making it possible to predict the conditions for niche differentiation and, close to the instability onset, the asymptotically long time population distributions of niches. We exemplify our method using the Lotka-Volterra equations with an exponential competition kernel.

  17. Developing and using artificial soils to analyze soil microbial processes

    Science.gov (United States)

    Gao, X.; Cheng, H. Y.; Boynton, L.; Masiello, C. A.; Silberg, J. J.

    2017-12-01

    Microbial diversity and function in soils are governed by soil characteristics such as mineral composition, particles size and aggregations, soil organic matter (SOM), and availability of nutrients and H2O. The spatial and temporal heterogeneity of soils creates a range of niches (hotspots) differing in the availability of O2, H2O, and nutrients, which shapes microbial activities at scales ranging from nanometer to landscape. Synthetic biologists often examine microbial response trigged by their environment conditions in nutrient-rich aqueous media using single strain microbes. While these studies provided useful insight in the role of soil microbes in important soil biogeochemical processes (e.g., C cycling, N cycling, etc.), the results obtained from the over-simplified model systems are often not applicable natural soil systems. On the contrary, soil microbiologists examine microbial processes in natural soils using longer incubation time. However, due to its physical, chemical and biological complexity of natural soils, it is often difficult to examine soil characteristics independently and understand how each characteristic influences soil microbial activities and their corresponding soil functioning. Therefore, it is necessary to bridge the gap and develop a model matrix to exclude unpredictable influences from the environment while still reliably mimicking real environmental conditions. The objective of this study is to design a range of ecologically-relevant artificial soils with varying texture (particle size distribution), structure, mineralogy, SOM content, and nutrient heterogeneity. We thoroughly characterize the artificial soils for pH, active surface area and surface morphology, cation exchange capacity (CEC), and water retention curve. We demonstrate the effectiveness of the artificial soils as useful matrix for microbial processes, such as microbial growth and horizontal gene transfer (HGT), using the gas-reporting biosensors recently developed in

  18. Geochemical and physical drivers of microbial community structure in hot spring ecosystems

    Science.gov (United States)

    Havig, J. R.; Hamilton, T. L.; Boyd, E. S.; Meyer-Dombard, D. R.; Shock, E.

    2012-12-01

    Microbial communities in natural systems are typically characterized using samples collected from a single time point, thereby neglecting the temporal dynamics that characterize natural systems. The composition of these communities obtained from single point samples is then related to the geochemistry and physical parameters of the environment. Since most microbial life is adapted to a relatively narrow ecological niche (multiplicity of physical and chemical parameters that characterize a local habitat), these assessments provide only modest insight into the controls on community composition. Temporal variation in temperature or geochemical composition would be expected to add another dimension to the complexity of niche space available to support microbial diversity, with systems that experience greater variation supporting a greater biodiversity until a point where the variability is too extreme. . Hot springs often exhibit significant temporal variation, both in physical as well as chemical characteristics. This is a result of subsurface processes including boiling, phase separation, and differential mixing of liquid and vapor phase constituents. These characteristics of geothermal systems, which vary significantly over short periods of time, provide ideal natural laboratories for investigating how i) the extent of microbial community biodiversity and ii) the composition of those communities are shaped by temporal fluctuations in geochemistry. Geochemical and molecular samples were collected from 17 temporally variable hot springs across Yellowstone National Park, Wyoming. Temperature measurements using data-logging thermocouples, allowing accurate determination of temperature maximums, minimums, and ranges for each collection site, were collected in parallel, along with multiple geochemical characterizations as conditions varied. There were significant variations in temperature maxima (54.5 to 90.5°C), minima (12.5 to 82.5°C), and range (3.5 to 77.5°C) for

  19. Permissiveness of soil microbial communities towards broad host range plasmids

    DEFF Research Database (Denmark)

    Klümper, Uli

    . Plasmids are implicated in the rapid spread of antibiotic resistance and the emergence of multi-resistant pathogenic bacteria, making it crucial to be able to quantify, understand, and, ideally, control plasmid transfer in mixed microbial communities. The fate of plasmids in microbial communities...... of microbial communities may be directly interconnected through transfer of BHR plasmids at a so far unrecognized level. The developed method furthermore enabled me to explore how agronomic practices may affect gene transfer in soil microbial communities. I compared bacterial communities extracted from plots...

  20. Niche entrepreneurs in urban systems integration : On the role of individuals in niche formation

    NARCIS (Netherlands)

    Pesch, U.; Vernay, A.L.; van Bueren, E.M.; Pandis Iveroth, S

    2017-01-01

    In many sustainable urban innovation projects, the efforts, endurance and enthusiasm of individuals at key positions are considered a crucial factor for success. This article studies the role of individual agency in sociotechnical niches by using Kingdon’s agenda-setting model. Although strategic

  1. Language and other artifacts: socio-cultural dynamics of niche construction.

    Science.gov (United States)

    Sinha, Chris

    2015-01-01

    Niche construction theory is a relatively new approach in evolutionary biology that seeks to integrate an ecological dimension into the Darwinian theory of evolution by natural selection. It is regarded by many evolutionary biologists as providing a significant revision of the Neo-Darwinian modern synthesis that unified Darwin's theory of natural and sexual selection with 20th century population genetics. Niche construction theory has been invoked as a processual mediator of social cognitive evolution and of the emergence and evolution of language. I argue that language itself can be considered as a biocultural niche and evolutionary artifact. I provide both a general analysis of the cognitive and semiotic status of artifacts, and a formal analysis of language as a social and semiotic institution, based upon a distinction between the fundamental semiotic relations of "counting as" and "standing for." I explore the consequences for theories of language and language learning of viewing language as a biocultural niche. I suggest that not only do niches mediate organism-organism interactions, but also that organisms mediate niche-niche interactions in ways that affect evolutionary processes, with the evolution of human infancy and childhood as a key example. I argue that language as a social and semiotic system is not only grounded in embodied engagements with the material and social-interactional world, but also grounds a sub-class of artifacts of particular significance in the cultural history of human cognition. Symbolic cognitive artifacts materially and semiotically mediate human cognition, and are not merely informational repositories, but co-agentively constitutive of culturally and historically emergent cognitive domains. I provide examples of the constitutive cognitive role of symbolic cognitive artifacts drawn from my research with my colleagues on cultural and linguistic conceptualizations of time, and their cultural variability. I conclude by reflecting on

  2. Phylogenetic niche conservatism and the evolutionary basis of ecological speciation.

    Science.gov (United States)

    Pyron, R Alexander; Costa, Gabriel C; Patten, Michael A; Burbrink, Frank T

    2015-11-01

    Phylogenetic niche conservatism (PNC) typically refers to the tendency of closely related species to be more similar to each other in terms of niche than they are to more distant relatives. This has been implicated as a potential driving force in speciation and other species-richness patterns, such as latitudinal gradients. However, PNC has not been very well defined in most previous studies. Is it a pattern or a process? What are the underlying endogenous (e.g. genetic) and exogenous (e.g. ecological) factors that cause niches to be conserved? What degree of similarity is necessary to qualify as PNC? Is it possible for the evolutionary processes causing niches to be conserved to also result in niche divergence in different habitats? Here, we revisit these questions, codifying a theoretical and operational definition of PNC as a mechanistic evolutionary process resulting from several factors. We frame this both from a macroevolutionary and population-genetic perspective. We discuss how different axes of physical (e.g. geographic) and environmental (e.g. climatic) heterogeneity interact with the fundamental process of PNC to produce different outcomes of ecological speciation. We also review tests for PNC, and suggest ways that these could be improved or better utilized in future studies. Ultimately, PNC as a process has a well-defined mechanistic basis in organisms, and future studies investigating ecological speciation would be well served to consider this, and frame hypothesis testing in terms of the processes and expected patterns described herein. The process of PNC may lead to patterns where niches are conserved (more similar than expected), constrained (divergent within a limited subset of available niches), or divergent (less similar than expected), based on degree of phylogenetic relatedness between species. © 2014 Cambridge Philosophical Society.

  3. Language and other artifacts: socio-cultural dynamics of niche construction.

    Directory of Open Access Journals (Sweden)

    Chris eSinha

    2015-10-01

    Full Text Available Niche construction theory is a relatively new approach in evolutionary biology that seeks to integrate an ecological dimension into the Darwinian theory of evolution by natural selection. It is regarded by many evolutionary biologists as providing a significant revision of the Neo-Darwinian modern synthesis that unified Darwin’s theory of natural and sexual selection with 20th century population genetics. Niche construction theory has been invoked as a processual mediator of social cognitive evolution and of the emergence and evolution of language. I argue that language itself can be considered as a biocultural niche and evolutionary artifact. I provide both a general analysis of the cognitive and semiotic status of artifacts, and a formal analysis of language as a social and semiotic institution, based upon a distinction between the fundamental semiotic relations of counting as and standing for. I explore the consequences for theories of language and language learning of viewing language as a biocultural niche. I suggest that not only do niches mediate organism-organism interactions, but also that organisms mediate niche-niche interactions in ways that affect evolutionary processes, with the evolution of human infancy and childhood as a key example. I argue that language as a social and semiotic system is not only grounded in embodied engagements with the material and social-interactional world, but also grounds a sub-class of artifacts of particular significance in the cultural history of human cognition. Symbolic cognitive artifacts materially and semiotically mediate human cognition, and are not merely informational repositories, but co-agentively constitutive of culturally and historically emergent cognitive domains. I provide examples of the constitutive cognitive role of symbolic cognitive artifacts drawn from my research with my colleagues on cultural and linguistic conceptualizations of time, and their cultural variability. I conclude

  4. 2010 MICROBIAL STRESS RESPONSE GORDON RESEARCH CONFERENCE, JULY 18-23, 2010

    Energy Technology Data Exchange (ETDEWEB)

    Sarah Ades

    2011-07-23

    The 2010 Gordon Research Conference on Microbial Stress Responses provides an open and exciting forum for the exchange of scientific discoveries on the remarkable mechanisms used by microbes to survive in nearly every niche on the planet. Understanding these stress responses is critical for our ability to control microbial survival, whether in the context of biotechnology, ecology, or pathogenesis. From its inception in 1994, this conference has traditionally employed a very broad definition of stress in microbial systems. Sessions will cover the major steps of stress responses from signal sensing to transcriptional regulation to the effectors that mediate responses. A wide range of stresses will be represented. Some examples include (but are not limited to) oxidative stress, protein quality control, antibiotic-induced stress and survival, envelope stress, DNA damage, and nutritional stress. The 2010 meeting will also focus on the role of stress responses in microbial communities, applied and environmental microbiology, and microbial development. This conference brings together researchers from both the biological and physical sciences investigating stress responses in medically- and environmentally relevant microbes, as well as model organisms, using cutting-edge techniques. Computational, systems-level, and biophysical approaches to exploring stress responsive circuits will be integrated throughout the sessions alongside the more traditional molecular, physiological, and genetic approaches. The broad range of excellent speakers and topics, together with the intimate and pleasant setting at Mount Holyoke College, provide a fertile ground for the exchange of new ideas and approaches.

  5. Advances and Limitations of Disease Biogeography Using Ecological Niche Modeling.

    Science.gov (United States)

    Escobar, Luis E; Craft, Meggan E

    2016-01-01

    Mapping disease transmission risk is crucial in public and animal health for evidence based decision-making. Ecology and epidemiology are highly related disciplines that may contribute to improvements in mapping disease, which can be used to answer health related questions. Ecological niche modeling is increasingly used for understanding the biogeography of diseases in plants, animals, and humans. However, epidemiological applications of niche modeling approaches for disease mapping can fail to generate robust study designs, producing incomplete or incorrect inferences. This manuscript is an overview of the history and conceptual bases behind ecological niche modeling, specifically as applied to epidemiology and public health; it does not pretend to be an exhaustive and detailed description of ecological niche modeling literature and methods. Instead, this review includes selected state-of-the-science approaches and tools, providing a short guide to designing studies incorporating information on the type and quality of the input data (i.e., occurrences and environmental variables), identification and justification of the extent of the study area, and encourages users to explore and test diverse algorithms for more informed conclusions. We provide a friendly introduction to the field of disease biogeography presenting an updated guide for researchers looking to use ecological niche modeling for disease mapping. We anticipate that ecological niche modeling will soon be a critical tool for epidemiologists aiming to map disease transmission risk, forecast disease distribution under climate change scenarios, and identify landscape factors triggering outbreaks.

  6. A practical guideline for examining a uterine niche using ultrasonography in non-pregnant women

    DEFF Research Database (Denmark)

    Jordans, I P M; de Leeuw, R; Stegwee, S I

    2018-01-01

    OBJECTIVES: To generate a uniform, internationally recognized guideline for detailed uterine niche evaluation by ultrasonography in non-pregnant women using a modified Delphi method amongst international experts. METHODS: Fifteen international gynecological experts were recruited...... definitions, relevance, method of measurement and tips for visualization of the niche. All experts agreed on the proposed guideline for niche evaluation in non-pregnant women as presented in this paper. CONCLUSION: Consensus between niche experts was achieved on all items regarding ultrasonographic niche...

  7. Correlated evolution of thermal niches and functional physiology in tropical freshwater fishes.

    Science.gov (United States)

    Culumber, Zachary W; Tobler, Michael

    2018-05-01

    The role of ecology in phenotypic and species diversification is widely documented. Nonetheless, numerous nonadaptive processes can shape realized niches and phenotypic variation in natural populations, complicating inferences about adaptive evolution at macroevolutionary scales. We tested for evolved differences in thermal tolerances and their association with the realized thermal niche (including metrics describing diurnal and seasonal patterns of temperature extremes and variability) across a genus of tropical freshwater fishes reared in a standardized environment. There was limited evolution along the thermal niche axis associated with variation in maximum temperature and in upper thermal limits. In contrast, there was considerable diversification along the first major axis of the thermal niche associated with minimum temperatures and in lower thermal limits. Across our adaptive landscape analyses, 70% of species exhibited evidence of divergence in thermal niches. Most importantly, the first two major axes of thermal niche variation were significantly correlated with variation in lower thermal limits. Our results indicate adaptation to divergent thermal niches and adaptive evolution of related functional traits, and highlight the importance of divergence in lower thermal limits for the evolution of tropical biodiversity. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

  8. Ontogenetic niche shifts and evolutionary branching in size-structured populations

    NARCIS (Netherlands)

    Claessen, D.; Dieckmann, U.

    2002-01-01

    There are many examples of size-structured populations where individuals sequentially exploit several niches in the course of their life history. Efficient exploitation of such ontogenetic niches generally requires specific morphological adaptations. Here, we study the evolutionary implications of

  9. Mammalian niche conservation through deep time.

    Directory of Open Access Journals (Sweden)

    Larisa R G DeSantis

    Full Text Available Climate change alters species distributions, causing plants and animals to move north or to higher elevations with current warming. Bioclimatic models predict species distributions based on extant realized niches and assume niche conservation. Here, we evaluate if proxies for niches (i.e., range areas are conserved at the family level through deep time, from the Eocene to the Pleistocene. We analyze the occurrence of all mammalian families in the continental USA, calculating range area, percent range area occupied, range area rank, and range polygon centroids during each epoch. Percent range area occupied significantly increases from the Oligocene to the Miocene and again from the Pliocene to the Pleistocene; however, mammalian families maintain statistical concordance between rank orders across time. Families with greater taxonomic diversity occupy a greater percent of available range area during each epoch and net changes in taxonomic diversity are significantly positively related to changes in percent range area occupied from the Eocene to the Pleistocene. Furthermore, gains and losses in generic and species diversity are remarkably consistent with ~2.3 species gained per generic increase. Centroids demonstrate southeastern shifts from the Eocene through the Pleistocene that may correspond to major environmental events and/or climate changes during the Cenozoic. These results demonstrate range conservation at the family level and support the idea that niche conservation at higher taxonomic levels operates over deep time and may be controlled by life history traits. Furthermore, families containing megafauna and/or terminal Pleistocene extinction victims do not incur significantly greater declines in range area rank than families containing only smaller taxa and/or only survivors, from the Pliocene to Pleistocene. Collectively, these data evince the resilience of families to climate and/or environmental change in deep time, the absence of

  10. Biogeographic ranges do not support niche theory in radiating Canary Island plant clades

    DEFF Research Database (Denmark)

    Steinbauer, Manuel; Field, Richard; Fernández-Palacios, José María

    2016-01-01

    in allopatry. Main conclusions: The expectations from niche conservatism were frequently not met; instead our results suggest considerable climatic niche lability. All significant differences in climatic niche differentiation were opposite to the predictions from competitive displacement. These forces may...

  11. Ecological distribution and population physiology defined by proteomics in a natural microbial community

    Science.gov (United States)

    Mueller, Ryan S.; Denef, Vincent J.; Kalnejais, Linda H.; Suttle, K. Blake; Thomas, Brian C.; Wilmes, Paul; Smith, Richard L.; Nordstrom, D. Kirk; McCleskey, R. Blaine; Shah, Menesh B.; VerBekmoes, Nathan C.; Hettich, Robert L.; Banfield, Jillian F.

    2010-01-01

    An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems. We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism's metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ.

  12. Overlap and partitioning of the ecological and isotopic niches

    Science.gov (United States)

    Elizabeth A. Flaherty; Merav Ben-David

    2010-01-01

    Recently, it was proposed that stable isotope patterns can be used to quantify the width of the ecological niche of animals. However, the potential effects of habitat use on isotopic patterns of consumers have not been fully explored and consequently isotopic patterns may yield deceptive estimates of niche width. Here, we simulated four different scenarios of a...

  13. Human niche, human behaviour, human nature.

    Science.gov (United States)

    Fuentes, Agustin

    2017-10-06

    The concept of a 'human nature' or 'human natures' retains a central role in theorizing about the human experience. In Homo sapiens it is clear that we have a suite of capacities generated via our evolutionary past, and present, and a flexible capacity to create and sustain particular kinds of cultures and to be shaped by them. Regardless of whether we label these capacities 'human natures' or not, humans occupy a distinctive niche and an evolutionary approach to examining it is critical. At present we are faced with a few different narratives as to exactly what such an evolutionary approach entails. There is a need for a robust and dynamic theoretical toolkit in order to develop a richer, and more nuanced, understanding of the cognitively sophisticated genus Homo and the diverse sorts of niches humans constructed and occupied across the Pleistocene, Holocene, and into the Anthropocene. Here I review current evolutionary approaches to 'human nature', arguing that we benefit from re-framing our investigations via the concept of the human niche and in the context of the extended evolutionary synthesis (EES). While not a replacement of standard evolutionary approaches, this is an expansion and enhancement of our toolkit. I offer brief examples from human evolution in support of these assertions.

  14. Environmental niche conservatism explains the accumulation of species richness in Mediterranean-hotspot plant genera.

    Science.gov (United States)

    Skeels, Alexander; Cardillo, Marcel

    2017-03-01

    The causes of exceptionally high plant diversity in Mediterranean-climate biodiversity hotspots are not fully understood. We asked whether a mechanism similar to the tropical niche conservatism hypothesis could explain the diversity of four large genera (Protea, Moraea, Banksia, and Hakea) with distributions within and adjacent to the Greater Cape Floristic Region (South Africa) or the Southwest Floristic Region (Australia). Using phylogenetic and spatial data we estimated the environmental niche of each species, and reconstructed the mode and dynamics of niche evolution, and the geographic history, of each genus. For three genera, there were strong positive relationships between the diversity of clades within a region and their inferred length of occupation of that region. Within genera, there was evidence for strong evolutionary constraint on niche axes associated with climatic seasonality and aridity, with different niche optima for hotspot and nonhotspot clades. Evolutionary transitions away from hotspots were associated with increases in niche breadth and elevated rates of niche evolution. Our results point to a process of "hotspot niche conservatism" whereby the accumulation of plant diversity in Mediterranean-type ecosystems results from longer time for speciation, with dispersal away from hotspots limited by narrow and phylogenetically conserved environmental niches. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  15. Not all renal stem cell niches are the same: anatomy of an evolution

    Directory of Open Access Journals (Sweden)

    Clara Gerosa

    2016-08-01

    Full Text Available The renal stem cell niche represents the most important structure of the developing kidney, responsible for nephrogenesis. Recently, some Authors have reported, at ultrastructural level, a previously unknown complexity of the architecture of renal stem cell niche in experimental models. This study was aimed at studying, at histological level, the anatomy of renal stem cell niches in the human fetal kidney. To this end, ten fetal kidneys, whose gestational ages ranged from 11 up to 24 weeks, were studied. H&E-stained sections were observed at high power. The study of the anatomy of renal stem cell niches in the human kidney revealed a previously unreported complexity: some niches appeared as a roundish arrangement of mesenchymal cells; others showed the initial phases of induction by ureteric buds; in other niches the process of mesenchymal epithelial transition was more evident; finally, in other stem cell niches the first signs of nephron origin were detectable. These findings suggest the existence of niches with different anatomy in the same kidney, indicating different stages of evolution even in adjacent niches. All stem cell niches were in strict contact with the capsular cells, suggesting a major role of the renal capsule in nephrogenesis. Finally, our study confirms the existence of a strict contact between the bud tip cells and the surrounding mesenchyme in the human developing kidney, giving a morphological support to the theory of intercellular channels allowing the passage of transcription factors from the epithelial to the mesenchymal stem/progenitors cells.Proceedings of the 2nd International Course on Perinatal Pathology (part of the 11th International Workshop on Neonatology · October 26th-31st, 2015 · Cagliari (Italy · October 31st, 2015 · Stem cells: present and future Guest Editors: Gavino Faa, Vassilios Fanos, Antonio Giordano

  16. Bentonite. Geotechnical barrier and source for microbial life

    International Nuclear Information System (INIS)

    Matschiavelli, Nicole; Kluge, Sindy; Cherkouk, Andrea; Steglich, Jennifer

    2017-01-01

    Due to their properties, namely a high swelling capacity and a low hydraulic conductivity, Bentonites fulfil as geotechnical barrier a sealing and buffering function in the nuclear waste repository. Depending on the mineral composition Bentonites contain many suitable electron-donors and -acceptors, enabling potential microbial life. For the potential repository of highly radioactive waste the microbial mediated transformation of Bentonite could influence its properties as a barrier material. Microcosms were set up containing Bentonite and anaerobic synthetic Opalinus-clay-pore water solution under an N_2/CO_2-atmosphere to elucidate the microbial potential within selected Bentonites. Substrates like acetate and lactate were supplemented to stimulate potential microbial activity. First results show that bentonites represent a source for microbial life, demonstrated by the consumption of lactate and the formation of pyruvate. Furthermore, microbial iron-reduction was determined, which plays a crucial role in Betonite-transformation.

  17. Bentonite. Geotechnical barrier and source for microbial life

    Energy Technology Data Exchange (ETDEWEB)

    Matschiavelli, Nicole; Kluge, Sindy; Cherkouk, Andrea [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). HZDR Young Investigator Group; Steglich, Jennifer

    2017-06-01

    Due to their properties, namely a high swelling capacity and a low hydraulic conductivity, Bentonites fulfil as geotechnical barrier a sealing and buffering function in the nuclear waste repository. Depending on the mineral composition Bentonites contain many suitable electron-donors and -acceptors, enabling potential microbial life. For the potential repository of highly radioactive waste the microbial mediated transformation of Bentonite could influence its properties as a barrier material. Microcosms were set up containing Bentonite and anaerobic synthetic Opalinus-clay-pore water solution under an N{sub 2}/CO{sub 2}-atmosphere to elucidate the microbial potential within selected Bentonites. Substrates like acetate and lactate were supplemented to stimulate potential microbial activity. First results show that bentonites represent a source for microbial life, demonstrated by the consumption of lactate and the formation of pyruvate. Furthermore, microbial iron-reduction was determined, which plays a crucial role in Betonite-transformation.

  18. Range bagging: a new method for ecological niche modelling from presence-only data.

    Science.gov (United States)

    Drake, John M

    2015-06-06

    The ecological niche is the set of environments in which a population of a species can persist without introduction of individuals from other locations. A good mathematical or computational representation of the niche is a prerequisite to addressing many questions in ecology, biogeography, evolutionary biology and conservation. A particularly challenging question for ecological niche modelling is the problem of presence-only modelling. That is, can an ecological niche be identified from records drawn only from the set of niche environments without records from non-niche environments for comparison? Here, I introduce a new method for ecological niche modelling from presence-only data called range bagging. Range bagging draws on the concept of a species' environmental range, but was inspired by the empirical performance of ensemble learning algorithms in other areas of ecological research. This paper extends the concept of environmental range to multiple dimensions and shows that range bagging is computationally feasible even when the number of environmental dimensions is large. The target of the range bagging base learner is an environmental tolerance of the species in a projection of its niche and is therefore an ecologically interpretable property of a species' biological requirements. The computational complexity of range bagging is linear in the number of examples, which compares favourably with the main alternative, Qhull. In conclusion, range bagging appears to be a reasonable choice for niche modelling in applications in which a presence-only method is desired and may provide a solution to problems in other disciplines where one-class classification is required, such as outlier detection and concept learning.

  19. The life sulfuric: microbial ecology of sulfur cycling in marine sediments.

    Science.gov (United States)

    Wasmund, Kenneth; Mußmann, Marc; Loy, Alexander

    2017-08-01

    Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

  20. Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents.

    Science.gov (United States)

    Anderson, Rika E; Sogin, Mitchell L; Baross, John A

    2015-01-01

    Environmental gradients generate countless ecological niches in deep-sea hydrothermal vent systems, which foster diverse microbial communities. The majority of distinct microbial lineages in these communities occur in very low abundance. However, the ecological role and distribution of rare and abundant lineages, particularly in deep, hot subsurface environments, remain unclear. Here, we use 16S rRNA tag sequencing to describe biogeographic patterning and microbial community structure of both rare and abundant archaea and bacteria in hydrothermal vent systems. We show that while rare archaeal lineages and almost all bacterial lineages displayed geographically restricted community structuring patterns, the abundant lineages of archaeal communities displayed a much more cosmopolitan distribution. Finally, analysis of one high-volume, high-temperature fluid sample representative of the deep hot biosphere described a unique microbial community that differed from microbial populations in diffuse flow fluid or sulfide samples, yet the rare thermophilic archaeal groups showed similarities to those that occur in sulfides. These results suggest that while most archaeal and bacterial lineages in vents are rare and display a highly regional distribution, a small percentage of lineages, particularly within the archaeal domain, are successful at widespread dispersal and colonization. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  1. Biodiversity influences plant productivity through niche-efficiency.

    Science.gov (United States)

    Liang, Jingjing; Zhou, Mo; Tobin, Patrick C; McGuire, A David; Reich, Peter B

    2015-05-05

    The loss of biodiversity is threatening ecosystem productivity and services worldwide, spurring efforts to quantify its effects on the functioning of natural ecosystems. Previous research has focused on the positive role of biodiversity on resource acquisition (i.e., niche complementarity), but a lack of study on resource utilization efficiency, a link between resource and productivity, has rendered it difficult to quantify the biodiversity-ecosystem functioning relationship. Here we demonstrate that biodiversity loss reduces plant productivity, other things held constant, through theory, empirical evidence, and simulations under gradually relaxed assumptions. We developed a theoretical model named niche-efficiency to integrate niche complementarity and a heretofore-ignored mechanism of diminishing marginal productivity in quantifying the effects of biodiversity loss on plant productivity. Based on niche-efficiency, we created a relative productivity metric and a productivity impact index (PII) to assist in biological conservation and resource management. Relative productivity provides a standardized measure of the influence of biodiversity on individual productivity, and PII is a functionally based taxonomic index to assess individual species' inherent value in maintaining current ecosystem productivity. Empirical evidence from the Alaska boreal forest suggests that every 1% reduction in overall plant diversity could render an average of 0.23% decline in individual tree productivity. Out of the 283 plant species of the region, we found that large woody plants generally have greater PII values than other species. This theoretical model would facilitate the integration of biological conservation in the international campaign against several pressing global issues involving energy use, climate change, and poverty.

  2. The human and murine hematopoietic stem cell niches: are they comparable?

    Science.gov (United States)

    van Pel, Melissa; Fibbe, Willem E; Schepers, Koen

    2016-04-01

    Hematopoietic stem cells (HSCs) reside in specific niches that provide various instructive cues that regulate HSC self-renewal and their development into all mature cells of the peripheral blood. Progress in this research field has largely been guided by mouse studies. However, parallel studies with human subjects, tissues, and cells, in combination with xenotransplantation experiments in immunodeficient mice, have contributed to our increased understanding of the human HSC niche. Here, we summarize our current knowledge of the various specialized subsets of both stromal and hematopoietic cells that support HSCs through cell-cell interactions and secreted factors, and the many parallels between the murine and human HSC niches. Furthermore, we discuss recent technological advances that are likely to improve our understanding of the human HSC niche, a better understanding of which may allow further identification of unique molecular and cellular pathways in the HSC niche. This information may help to further improve the outcome of HSC transplantation and refine the treatment of hematopoietic diseases. © 2015 New York Academy of Sciences.

  3. Macrophytes shape trophic niche variation among generalist fishes.

    Directory of Open Access Journals (Sweden)

    Ivana Vejříková

    Full Text Available Generalist species commonly have a fundamental role in ecosystems as they can integrate spatially distinct habitats and food-web compartments, as well as control the composition, abundance and behavior of organisms at different trophic levels. Generalist populations typically consist of specialized individuals, but the potential for and hence degree of individual niche variation can be largely determined by habitat complexity. We compared individual niche variation within three generalist fishes between two comparable lakes in the Czech Republic differing in macrophyte cover, i.e. macrophyte-rich Milada and macrophyte-poor Most. We tested the hypothesis that large individual niche variation among generalist fishes is facilitated by the presence of macrophytes, which provides niches and predation shelter for fish and their prey items. Based on results from stable nitrogen (δ15N and carbon (δ13C isotopic mixing models, perch (Perca fluviatilis L. and rudd (Scardinius erythrophthalmus (L. showed larger individual variation (i.e., variance in trophic position in Milada as compared to Most, whereas no significant between-lake differences were observed for roach (Rutilus rutilus (L.. Contrary to our hypothesis, all the three species showed significantly lower individual variation in the relative reliance on littoral food resources in Milada than in Most. Rudd relied significantly more whereas perch and roach relied less on littoral food resources in Milada than in Most, likely due to prevalent herbivory by rudd and prevalent zooplanktivory by perch and roach in the macrophyte-rich Milada as compared to macrophyte-poor Most. Our study demonstrates how the succession of macrophyte vegetation, via its effects on the physical and biological complexity of the littoral zone and on the availability of small prey fish and zooplankton, can strongly influence individual niche variation among generalist fishes with different ontogenetic trajectories, and hence

  4. Macrophytes shape trophic niche variation among generalist fishes

    Science.gov (United States)

    Vejřík, Lukáš; Šmejkal, Marek; Čech, Martin; Sajdlová, Zuzana; Frouzová, Jaroslava; Kiljunen, Mikko; Peterka, Jiří

    2017-01-01

    Generalist species commonly have a fundamental role in ecosystems as they can integrate spatially distinct habitats and food-web compartments, as well as control the composition, abundance and behavior of organisms at different trophic levels. Generalist populations typically consist of specialized individuals, but the potential for and hence degree of individual niche variation can be largely determined by habitat complexity. We compared individual niche variation within three generalist fishes between two comparable lakes in the Czech Republic differing in macrophyte cover, i.e. macrophyte-rich Milada and macrophyte-poor Most. We tested the hypothesis that large individual niche variation among generalist fishes is facilitated by the presence of macrophytes, which provides niches and predation shelter for fish and their prey items. Based on results from stable nitrogen (δ15N) and carbon (δ13C) isotopic mixing models, perch (Perca fluviatilis L.) and rudd (Scardinius erythrophthalmus (L.)) showed larger individual variation (i.e., variance) in trophic position in Milada as compared to Most, whereas no significant between-lake differences were observed for roach (Rutilus rutilus (L.)). Contrary to our hypothesis, all the three species showed significantly lower individual variation in the relative reliance on littoral food resources in Milada than in Most. Rudd relied significantly more whereas perch and roach relied less on littoral food resources in Milada than in Most, likely due to prevalent herbivory by rudd and prevalent zooplanktivory by perch and roach in the macrophyte-rich Milada as compared to macrophyte-poor Most. Our study demonstrates how the succession of macrophyte vegetation, via its effects on the physical and biological complexity of the littoral zone and on the availability of small prey fish and zooplankton, can strongly influence individual niche variation among generalist fishes with different ontogenetic trajectories, and hence the overall

  5. A practioner's view on Strategic Niche Management

    International Nuclear Information System (INIS)

    Mourik, R.; Raven, R.P.J.M.

    2006-11-01

    Strategic Niche Management (SNM) is a tool to support the societal introduction of radical sustainable innovations. However, it has been mainly used in retrospective to analyse historical case studies. This report discusses SNM from a practioner's perspective with the main aim to articulate questions that should be addressed for translating SNM from an ex-post to an ex-ante tool. The main conclusion is that an SNM tool should focus on the level of 'niches' rather than single projects, i.e. SNM should aim to support (program) managers who aim at orchestrating the interaction between multiple experiments

  6. Temporal and Spatial Distribution of the Microbial Community of Winogradsky Columns.

    Directory of Open Access Journals (Sweden)

    David J Esteban

    Full Text Available Winogradsky columns are model microbial ecosystems prepared by adding pond sediment to a clear cylinder with additional supplements and incubated with light. Environmental gradients develop within the column creating diverse niches that allow enrichment of specific bacteria. The enrichment culture can be used to study soil and sediment microbial community structure and function. In this study we used a 16S rRNA gene survey to characterize the microbial community dynamics during Winogradsky column development to determine the rate and extent of change from the source sediment community. Over a period of 60 days, the microbial community changed from the founding pond sediment population: Cyanobacteria, Chloroflexi, Nitrospirae, and Planctomycetes increased in relative abundance over time, while most Proteobacteria decreased in relative abundance. A unique, light-dependent surface biofilm community formed by 60 days that was less diverse and dominated by a few highly abundant bacteria. 67-72% of the surface community was comprised of highly enriched taxa that were rare in the source pond sediment, including the Cyanobacteria Anabaena, a member of the Gemmatimonadetes phylum, and a member of the Chloroflexi class Anaerolinea. This indicates that rare taxa can become abundant under appropriate environmental conditions and supports the hypothesis that rare taxa serve as a microbial seed bank. We also present preliminary findings that suggest that bacteriophages may be active in the Winogradsky community. The dynamics of certain taxa, most notably the Cyanobacteria, showed a bloom-and-decline pattern, consistent with bacteriophage predation as predicted in the kill-the-winner hypothesis. Time-lapse photography also supported the possibility of bacteriophage activity, revealing a pattern of colony clearance similar to formation of viral plaques. The Winogradsky column, a technique developed early in the history of microbial ecology to enrich soil

  7. Metabolic commensalism and competition in a two-species microbial consortium

    DEFF Research Database (Denmark)

    Christensen, Bjarke Bak; Haagensen, Janus Anders Juul; Heydorn, Arne

    2002-01-01

    We analyzed metabolic interactions and the importance of specific structural relationships in a benzyl alcohol-degrading microbial consortium comprising two species, Pseudomonas putida strain R1 and Acinetobacter strain C6, both of which are able to utilize benzyl alcohol as their sole carbon...... alcohol, which apparently gives Acinetobacter strain C6 a growth advantage, probably because it converts benzyl alcohol to benzoate with a higher yield per time unit than P. putida R1. In biofilms, however, the organisms establish structured, surface-attached consortia, in which heterogeneous ecological...... niches develop, and under these conditions competition for the primary carbon source is not the only determinant of biomass and population structure....

  8. The molecular dimension of microbial species: 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated ecotypes in the Mushroom Spring microbial mat

    Directory of Open Access Journals (Sweden)

    Millie T. Olsen

    2015-06-01

    Full Text Available Genomes were obtained for three closely related strains of Synechococcus that are representative of putative ecotypes that predominate at different depths in the 1 mm-thick, upper-green layer in the 60°C mat of Mushroom Spring, Yellowstone National Park, and exhibit different light adaptation and acclimation responses. The genomes were compared to the published genome of a previously obtained, closely related strain from a neighboring spring, and differences in both gene content and orthologous gene alleles between high-light-adapted and low-light-adapted strains were identified. Evidence of genetic differences that relate to adaptation to light intensity and/or quality, CO2 uptake, nitrogen metabolism, organic carbon metabolism, and uptake of other nutrients were found between strains of the different putative ecotypes. In situ diel transcription patterns of genes, including genes unique to either low-light-adapted or high-light-adapted strains and different alleles of an orthologous photosystem gene, revealed that expression is fine-tuned to the different light environments experienced by ecotypes prevalent at various depths in the mat. This study suggests that strains of closely related putative ecotypes have different genomic adaptations that enable them to inhabit distinct ecological niches while living in close proximity within a microbial community.

  9. Microbial diversity arising from thermodynamic constraints

    Science.gov (United States)

    Großkopf, Tobias; Soyer, Orkun S

    2016-01-01

    The microbial world displays an immense taxonomic diversity. This diversity is manifested also in a multitude of metabolic pathways that can utilise different substrates and produce different products. Here, we propose that these observations directly link to thermodynamic constraints that inherently arise from the metabolic basis of microbial growth. We show that thermodynamic constraints can enable coexistence of microbes that utilise the same substrate but produce different end products. We find that this thermodynamics-driven emergence of diversity is most relevant for metabolic conversions with low free energy as seen for example under anaerobic conditions, where population dynamics is governed by thermodynamic effects rather than kinetic factors such as substrate uptake rates. These findings provide a general understanding of the microbial diversity based on the first principles of thermodynamics. As such they provide a thermodynamics-based framework for explaining the observed microbial diversity in different natural and synthetic environments. PMID:27035705

  10. Microbial diversity arising from thermodynamic constraints.

    Science.gov (United States)

    Großkopf, Tobias; Soyer, Orkun S

    2016-11-01

    The microbial world displays an immense taxonomic diversity. This diversity is manifested also in a multitude of metabolic pathways that can utilise different substrates and produce different products. Here, we propose that these observations directly link to thermodynamic constraints that inherently arise from the metabolic basis of microbial growth. We show that thermodynamic constraints can enable coexistence of microbes that utilise the same substrate but produce different end products. We find that this thermodynamics-driven emergence of diversity is most relevant for metabolic conversions with low free energy as seen for example under anaerobic conditions, where population dynamics is governed by thermodynamic effects rather than kinetic factors such as substrate uptake rates. These findings provide a general understanding of the microbial diversity based on the first principles of thermodynamics. As such they provide a thermodynamics-based framework for explaining the observed microbial diversity in different natural and synthetic environments.

  11. Language and other artifacts: socio-cultural dynamics of niche construction

    Science.gov (United States)

    Sinha, Chris

    2015-01-01

    Niche construction theory is a relatively new approach in evolutionary biology that seeks to integrate an ecological dimension into the Darwinian theory of evolution by natural selection. It is regarded by many evolutionary biologists as providing a significant revision of the Neo-Darwinian modern synthesis that unified Darwin’s theory of natural and sexual selection with 20th century population genetics. Niche construction theory has been invoked as a processual mediator of social cognitive evolution and of the emergence and evolution of language. I argue that language itself can be considered as a biocultural niche and evolutionary artifact. I provide both a general analysis of the cognitive and semiotic status of artifacts, and a formal analysis of language as a social and semiotic institution, based upon a distinction between the fundamental semiotic relations of “counting as” and “standing for.” I explore the consequences for theories of language and language learning of viewing language as a biocultural niche. I suggest that not only do niches mediate organism-organism interactions, but also that organisms mediate niche-niche interactions in ways that affect evolutionary processes, with the evolution of human infancy and childhood as a key example. I argue that language as a social and semiotic system is not only grounded in embodied engagements with the material and social-interactional world, but also grounds a sub-class of artifacts of particular significance in the cultural history of human cognition. Symbolic cognitive artifacts materially and semiotically mediate human cognition, and are not merely informational repositories, but co-agentively constitutive of culturally and historically emergent cognitive domains. I provide examples of the constitutive cognitive role of symbolic cognitive artifacts drawn from my research with my colleagues on cultural and linguistic conceptualizations of time, and their cultural variability. I conclude by

  12. Thermal barriers constrain microbial elevational range size via climate variability.

    Science.gov (United States)

    Wang, Jianjun; Soininen, Janne

    2017-08-01

    Range size is invariably limited and understanding range size variation is an important objective in ecology. However, microbial range size across geographical gradients remains understudied, especially on mountainsides. Here, the patterns of range size of stream microbes (i.e., bacteria and diatoms) and macroorganisms (i.e., macroinvertebrates) along elevational gradients in Asia and Europe were examined. In bacteria, elevational range size showed non-significant phylogenetic signals. In all taxa, there was a positive relationship between niche breadth and species elevational range size, driven by local environmental and climatic variables. No taxa followed the elevational Rapoport's rule. Climate variability explained the most variation in microbial mean elevational range size, whereas local environmental variables were more important for macroinvertebrates. Seasonal and annual climate variation showed negative effects, while daily climate variation had positive effects on community mean elevational range size for all taxa. The negative correlation between range size and species richness suggests that understanding the drivers of range is key for revealing the processes underlying diversity. The results advance the understanding of microbial species thermal barriers by revealing the importance of seasonal and diurnal climate variation, and highlight that aquatic and terrestrial biota may differ in their response to short- and long-term climate variability. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  13. Seasonal and spatial patterns of microbial diversity along a trophic gradient in the interconnected lakes of the Osterseen Lake District, Bavaria

    Science.gov (United States)

    Zwirglmaier, Katrin; Keiz, Katharina; Engel, Marion; Geist, Juergen; Raeder, Uta

    2015-01-01

    The Osterseen Lake District in Bavaria consists of 19 small interconnected lakes that exhibit a pronounced trophic gradient from eutrophic to oligotrophic. It therefore presents a unique model system to address ecological questions regarding niche adaptation and Baas Becking's long standing hypothesis of “everything is everywhere, but the environment selects.” Here, we present the first assessment of the microbial diversity in these lakes. We sampled the lakes in August and December and used 454 pyrosequencing of 16S rRNA amplicons to analyze the microbial diversity. The diversity patterns between lakes and seasons were compared and the bacterial community composition was correlated with key chemical and physical parameters. Distinct patterns of bacterial diversity only emerged at the level of individual OTUs (operational taxonomic units), but not at the level of the major bacterial phyla. This emphasizes the high functional and physiological diversity among bacterial species within a phylum and calls for analysis of biodiversity at the level of OTUs in order to understand fine-scale biogeography. We were able to identify a number of cosmopolitan OTUs as well as specialist OTUs that were restricted to certain lakes or seasons, suggesting adaptation to specific ecological niches. PMID:26579082

  14. Stem Cell Plasticity and Niche Dynamics in Cancer Progression.

    Science.gov (United States)

    Picco, Noemi; Gatenby, Robert A; Anderson, Alexander R A

    2017-03-01

    Cancer stem cells (CSCs) have been hypothesized to initiate and drive tumor growth and recurrence due to their self-renewal ability. If correct, this hypothesis implies that successful therapy must focus primarily on eradication of this CSC fraction. However, recent evidence suggests stemness is niche dependent and may represent one of many phenotypic states that can be accessed by many cancer genotypes when presented with specific environmental cues. A better understanding of the relationship of stemness to niche-related phenotypic plasticity could lead to alternative treatment strategies. Here, we investigate the role of environmental context in the expression of stem-like cell properties through in-silico simulation of ductal carcinoma. We develop a two-dimensional hybrid discrete-continuum cellular automata model to describe the single-cell scale dynamics of multicellular tissue formation. Through a suite of simulations, we investigate interactions between a phenotypically heterogeneous cancer cell population and a dynamic environment. We generate homeostatic ductal structures that consist of a mixture of stem and differentiated cells governed by both intracellular and environmental dynamics. We demonstrate that a wide spectrum of tumor-like histologies can result from these structures by varying microenvironmental parameters. Niche driven phenotypic plasticity offers a simple first-principle explanation for the diverse ductal structures observed in histological sections from breast cancer. Conventional models of carcinogenesis largely focus on mutational events. We demonstrate that variations in the environmental niche can produce intraductal cancers independent of genetic changes in the resident cells. Therapies targeting the microenvironmental niche may offer an alternative cancer prevention strategy.

  15. Micropillar arrays enabling single microbial cell encapsulation in hydrogels.

    Science.gov (United States)

    Park, Kyun Joo; Lee, Kyoung G; Seok, Seunghwan; Choi, Bong Gill; Lee, Moon-Keun; Park, Tae Jung; Park, Jung Youn; Kim, Do Hyun; Lee, Seok Jae

    2014-06-07

    Single microbial cell encapsulation in hydrogels is an important task to find valuable biological resources for human welfare. The conventional microfluidic designs are mainly targeted only for highly dispersed spherical bioparticles. Advanced structures should be taken into consideration for handling such aggregated and non-spherical microorganisms. Here, to address the challenge, we propose a new type of cylindrical-shaped micropillar array in a microfluidic device for enhancing the dispersion of cell clusters and the isolation of individual cells into individual micro-hydrogels for potential practical applications. The incorporated micropillars act as a sieve for the breaking of Escherichia coli (E. coli) clusters into single cells in a polymer mixture. Furthermore, the combination of hydrodynamic forces and a flow-focusing technique will improve the probability of encapsulation of a single cell into each hydrogel with a broad range of cell concentrations. This proposed strategy and device would be a useful platform for genetically modified microorganisms for practical applications.

  16. Competition in a technological niche: the cars of the future

    NARCIS (Netherlands)

    Bakker, S.; Lente, H. van; Engels, R.

    2012-01-01

    The notion of ‘niche’has proved to be useful to account for the emergence of radical innovations. Most studies, however, deal with the development of single emerging technologies. In this paper we address the competition between multiple niche technologies.Within the niche of the ‘car of the future’

  17. Testing the niche variation hypothesis with a measure of body condition

    Science.gov (United States)

    Individual variation and fitness are cornerstones of evolution by natural selection. The niche variation hypothesis (NVH) posits that when interspecific competition is relaxed, intraspecific competition should drive niche expansion by selection favoring use of novel resources. Po...

  18. Evidence of niche shift and invasion potential of Lithobates catesbeianus in the habitat of Mexican endemic frogs.

    Directory of Open Access Journals (Sweden)

    Jorge Luis Becerra López

    Full Text Available Invasive alien species are one of most severe threats to biodiversity and natural resources. These biological invasions have been studied from the niche conservatism and niche shifts perspective. Niche differentiation may result from changes in fundamental niche or realized niche or both; in biological invasions, niche differences between native and non-native ranges can appear through niche expansion, niche unfilling and niche stability. The American bullfrog Lithobates catesbeianus is an invasive species that can have negative impacts on native amphibian populations. This research examines the climate niche shifts of this frog, its potential range of expansion in Mexico and the risk of invasion by bullfrog in the habitats of 82 frog species endemic to Mexico, that based on their climatic niche similarity were divided in four ecological groups. The results indicate that species in two ecological groups were the most vulnerable to invasion by bullfrog. However, the climate niche shifts of L. catesbeianus may allow it to adapt to new environmental conditions, so species from the two remaining groups cannot be dismissed as not vulnerable. This information is valuable for decision making in prioritizing areas for conservation of Mexican endemic frogs.

  19. Biogeochemical and Ecomorphological Niche Segregation of Mediterranean Woody Species along a Local Gradient

    Directory of Open Access Journals (Sweden)

    Enrique G. de la Riva

    2017-07-01

    Full Text Available According with niche theory the species are specialized in different ecological niches, being able to coexist as result of a differential use of resources. In this context, the biogeochemical niche hypothesis proposes that species have an optimal elemental composition which results from the link between the chemical and morphological traits for the optimum plant functioning. Thus, and attending to the limiting similarity concept, different elemental composition and plant structure among co-occurring species may reduce competition, promoting different functional niches. Different functional habits associated with leaf life-span or growth forms are associated with different strategies for resource uptake, which could promote niche partitioning. In the present study, based on the biogeochemical niche concept and the use of resources in different proportions, we have focused on leaf traits (morphological and chemical associated with resource uptake, and explored the niche partitioning among functional habits: leaf life-span (deciduous, evergreen, and semideciduous and growth (tree, shrub, and arborescent-shrub. To this end, we have quantified the hypervolume of the leaf functional trait space (both structure and chemical composition in a sample of 45 Mediterranean woody species from Sierra Morena Mountains (Spain growing along a local soil resource gradient. Our results show consistent variation in functional space for woody communities distributed along the environmental gradient. Thus, communities dominated by deciduous trees with faster growth and a predominant acquisitive strategy were characteristic of bottom forests and showed highest leaf biogeochemical space. While semideciduous shrubs and evergreen (arborescent, trees species, characterized by a conservative strategy, dominated ridge forests and showed smaller functional space. In addition, within each topographical zone or environment type, the foliar biogeochemical niche partitioning

  20. Biogeochemical and Ecomorphological Niche Segregation of Mediterranean Woody Species along a Local Gradient.

    Science.gov (United States)

    de la Riva, Enrique G; Marañón, Teodoro; Violle, Cyrille; Villar, Rafael; Pérez-Ramos, Ignacio M

    2017-01-01

    According with niche theory the species are specialized in different ecological niches, being able to coexist as result of a differential use of resources. In this context, the biogeochemical niche hypothesis proposes that species have an optimal elemental composition which results from the link between the chemical and morphological traits for the optimum plant functioning. Thus, and attending to the limiting similarity concept, different elemental composition and plant structure among co-occurring species may reduce competition, promoting different functional niches. Different functional habits associated with leaf life-span or growth forms are associated with different strategies for resource uptake, which could promote niche partitioning. In the present study, based on the biogeochemical niche concept and the use of resources in different proportions, we have focused on leaf traits (morphological and chemical) associated with resource uptake, and explored the niche partitioning among functional habits: leaf life-span (deciduous, evergreen, and semideciduous) and growth (tree, shrub, and arborescent-shrub). To this end, we have quantified the hypervolume of the leaf functional trait space (both structure and chemical composition) in a sample of 45 Mediterranean woody species from Sierra Morena Mountains (Spain) growing along a local soil resource gradient. Our results show consistent variation in functional space for woody communities distributed along the environmental gradient. Thus, communities dominated by deciduous trees with faster growth and a predominant acquisitive strategy were characteristic of bottom forests and showed highest leaf biogeochemical space. While semideciduous shrubs and evergreen (arborescent, trees) species, characterized by a conservative strategy, dominated ridge forests and showed smaller functional space. In addition, within each topographical zone or environment type, the foliar biogeochemical niche partitioning would underlie the

  1. Intersexual trophic niche partitioning in an ant-eating spider (Araneae: Zodariidae.

    Directory of Open Access Journals (Sweden)

    Stano Pekár

    2011-01-01

    Full Text Available Divergence in trophic niche between the sexes may function to reduce competition between the sexes ("intersexual niche partitioning hypothesis", or may be result from differential selection among the sexes on maximizing reproductive output ("sexual selection hypothesis". The latter may lead to higher energy demands in females driven by fecundity selection, while males invest in mate searching. We tested predictions of the two hypotheses underlying intersexual trophic niche partitioning in a natural population of spiders. Zodarion jozefienae spiders specialize on Messor barbarus ants that are polymorphic in body size and hence comprise potential trophic niches for the spider, making this system well-suited to study intersexual trophic niche partitioning.Comparative analysis of trophic morphology (the chelicerae and body size of males, females and juveniles demonstrated highly female biased SSD (Sexual Size Dimorphism in body size, body weight, and in the size of chelicerae, the latter arising from sex-specific growth patterns in trophic morphology. In the field, female spiders actively selected ant sub-castes that were larger than the average prey size, and larger than ants captured by juveniles and males. Female fecundity was highly positively correlated with female body mass, which reflects foraging success during the adult stage. Females in laboratory experiments preferred the large ant sub-castes and displayed higher capture efficiency. In contrast, males occupied a different trophic niche and showed reduced foraging effort and reduced prey capture and feeding efficiency compared with females and juveniles.Our data indicate that female-biased dimorphism in trophic morphology and body size correlate with sex-specific reproductive strategies. We propose that intersexual trophic niche partitioning is shaped primarily by fecundity selection in females, and results from sex-differences in the route to successful reproduction where females are

  2. Trophic Niche Differentiation in Rodents and Marsupials Revealed by Stable Isotopes.

    Directory of Open Access Journals (Sweden)

    Mauro Galetti

    Full Text Available Tropical rainforests support the greatest diversity of small mammals in the world, yet we have little understanding about the mechanisms that promote the coexistence of species. Diet partitioning can favor coexistence by lessening competition, and interspecific differences in body size and habitat use are usually proposed to be associated with trophic divergence. However, the use of classic dietary methods (e.g. stomach contents is challenging in small mammals, particularly in community-level studies, thus we used stable isotopes (δ13C and δ15N to infer about trophic niche. We investigated i how trophic niche is partitioned among rodent and marsupial species in three Atlantic forest sites and ii if interspecific body size and locomotor habit inequalities can constitute mechanisms underlying the isotopic niche partitioning. We found that rodents occupied a broad isotopic niche space with species distributed in different trophic levels and relying on diverse basal carbon sources (C3 and C4 plants. Surprisingly, on the other hand, marsupials showed a narrow isotopic niche, both in δ13C and δ15N dimensions, which is partially overlapped with rodents, contradicting their description as omnivores and generalists proposed classic dietary studies. Although body mass differences did not explained the divergence in isotopic values among species, groups of species with different locomotor habit presented clear differences in the position of the isotopic niche space, indicating that the use of different forest strata can favor trophic niche partitioning in small mammals communities. We suggest that anthropogenic impacts, such as habitat modification (logging, harvesting, can simplify the vertical structure of ecosystems and collapse the diversity of basal resources, which might affect negatively small mammals communities in Atlantic forests.

  3. Commodifying snow, taming the waters. Socio-ecological niche construction in an Alpine village.

    Science.gov (United States)

    Gross, Robert; Winiwarter, Verena

    White belts of snow clad mountains all over the world each winter. Even if there is no snow, the tourism industry is able to produce the white finery at the push of the button, thereby consuming large amounts of water. Studying Damüls, a well-known ski resort in Austria's westernmost province Vorarlberg, we can show that the development of a service sector within agro-pastoral landscapes was connected with novel water uses and massive interventions into Alpine landscapes. Human niche construction theory offers a unique avenue for studying the development of Alpine communities, but also highlights side effects accompanying the change from agrarian to tourism livelihoods. One aim of this paper is to broaden the scope of human niche construction theory. Inceptive, counteractive and relocational niche construction activities were coupled to the differentiation of actor groups. To incorporate social dynamics, indispensable for studies in environmental history, we propose the concept of socio-ecological niche construction. The paper investigates how villagers balanced resource limitations typical for an agrarian society with the differentiation of sub-niches, mediating selective forces on the population. When the valleys were industrialized, Damüls was almost given up as a permanent settlement. Then, tourists entered the stage, by and by turning the wheel of local development into a different direction. A tourism niche based on natural snow evolved from the 1930s onwards. While the socio-ecological niches of agriculture and tourism coexisted in the interwar years, this changed when ski lifts were built, embedded into a debt-based economy that made the tourism niche vulnerable to snow availability. Snow-dependency became a powerful selective force. It was mediated by the ski lift companies through a range of niche construction activities that turned water into an important resource of snowmaking systems.

  4. Improved Predictions of the Geographic Distribution of Invasive Plants Using Climatic Niche Models

    Science.gov (United States)

    Ramírez-Albores, Jorge E.; Bustamante, Ramiro O.

    2016-01-01

    Climatic niche models for invasive plants are usually constructed with occurrence records taken from literature and collections. Because these data neither discriminate among life-cycle stages of plants (adult or juvenile) nor the origin of individuals (naturally established or man-planted), the resulting models may mispredict the distribution ranges of these species. We propose that more accurate predictions could be obtained by modelling climatic niches with data of naturally established individuals, particularly with occurrence records of juvenile plants because this would restrict the predictions of models to those sites where climatic conditions allow the recruitment of the species. To test this proposal, we focused on the Peruvian peppertree (Schinus molle), a South American species that has largely invaded Mexico. Three climatic niche models were constructed for this species using high-resolution dataset gathered in the field. The first model included all occurrence records, irrespective of the life-cycle stage or origin of peppertrees (generalized niche model). The second model only included occurrence records of naturally established mature individuals (adult niche model), while the third model was constructed with occurrence records of naturally established juvenile plants (regeneration niche model). When models were compared, the generalized climatic niche model predicted the presence of peppertrees in sites located farther beyond the climatic thresholds that naturally established individuals can tolerate, suggesting that human activities influence the distribution of this invasive species. The adult and regeneration climatic niche models concurred in their predictions about the distribution of peppertrees, suggesting that naturally established adult trees only occur in sites where climatic conditions allow the recruitment of juvenile stages. These results support the proposal that climatic niches of invasive plants should be modelled with data of

  5. Tug of war in the haematopoietic stem cell niche: do myeloma plasma cells compete for the HSC niche?

    Science.gov (United States)

    Noll, J E; Williams, S A; Purton, L E; Zannettino, A C W

    2012-09-14

    In the adult mammal, normal haematopoiesis occurs predominantly in the bone marrow, where primitive haematopoietic stem cells (HSC) and their progeny reside in specialised microenvironments. The bone marrow microenvironment contains specific anatomical areas (termed niches) that are highly specialised for the development of certain blood cell types, for example HSCs. The HSC niche provides important cell-cell interactions and signalling molecules that regulate HSC self-renewal and differentiation processes. These same signals and interactions are also important in the progression of haematological malignancies, such as multiple myeloma (MM). This review provides an overview of the bone marrow microenvironment and its involvement in normal, physiological HSC maintenance and plasma cell growth throughout MM disease progression.

  6. Biogeographical diversity of leaf-associated microbial communities from salt-secreting Tamarix trees of the Dead Sea region.

    Science.gov (United States)

    Qvit-Raz, Noga; Finkel, Omri M; Al-Deeb, Taghleb M; Malkawi, Hanan I; Hindiyeh, Muna Y; Jurkevitch, Edouard; Belkin, Shimshon

    2012-02-01

    The leaves of Tamarix, a salt-secreting desert tree, form an extreme niche that harbors a unique microbial community. In view of the global distribution of this tree, its island-like phyllosphere is highly suitable for studying microbial diversity along geographical gradients. Here we present an analysis of microbial community diversity using leaf surface samples collected at six different sites, on both sides of the Dead Sea, over a period of one year. Biodiversity analysis of denaturing gradient gel electrophoresis (DGGE) patterns of the bacterial 16S rRNA gene revealed a significant degree of bacterial community similarity within trees sampled at the same site, much higher than the similarity between trees from different geographical locations. Statistical analysis indicated that the degree of similarity was negatively correlated with the distance between sampling sites, and that a weak correlation existed between diversity and leaf pH. Copyright © 2011 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  7. Socializing with the neighbors: stem cells and their niche.

    Science.gov (United States)

    Fuchs, Elaine; Tumbar, Tudorita; Guasch, Geraldine

    2004-03-19

    The potential of stem cells in regenerative medicine relies upon removing them from their natural habitat, propagating them in culture, and placing them into a foreign tissue environment. To do so, it is essential to understand how stem cells interact with their microenvironment, the so-called stem cell niche, to establish and maintain their properties. In this review, we examine adult stem cell niches and their impact on stem cell biology.

  8. The influence of social niche on cultural niche construction: modelling changes in belief about marriage form in Taiwan

    Science.gov (United States)

    Lipatov, Mikhail; Brown, Melissa J.; Feldman, Marcus W.

    2011-01-01

    With introduction of social niche effects into a model of cultural change, the frequency of a practice cannot predict the frequency of its underlying belief. The combination of a general model with empirical data from a specific case illustrates the importance of collaboration between modellers and field researchers, and identifies the type of quantitative data necessary for analysing case studies. Demographic data from colonial-period household registers in Taiwan document a shift in marriage form within 40 years, from a mixture of uxorilocal marriages and virilocal marriages to the latter's dominance. Ethnographic data indicate marriage-related beliefs, costs, ethnic effects and colonial policies as well as the importance of horizontal cultural transmission. We present a formal model for the effects of moral beliefs about marriage and a population economic index on the decline of uxorilocal marriage. We integrate empirical marriage rates and an estimated economic index to produce five projections of the historical frequencies of one belief. These projections demonstrate how economic development may affect a cultural niche. They also indicate the need for future research on the relationship between wealth and cultural variability, the motivational force of cultural versus social factors, and the process of cultural niche construction. PMID:21320903

  9. Citizen-science, Geoethics and Human Niche

    Science.gov (United States)

    Bohle, Martin

    2017-04-01

    The anthropogenic biogeosphere or 'human niche' is the intersection of the biogeosphere and the sphere of human activities of social, economic, cultural and political nature. The application case for geoethics, namely "appropriate behaviours and practices, wherever human activities interact with the Earth system" [1], is about niche building. Geoethics is about the conduct of people and geoscientists, respectively their ordinary lifestyles and professional activities. Geoscience professionals notice the diverse economic, social and cultural living conditions of people, and the application cases of geosciences mirror the diversity of the global social sphere. Subsequently it is argued: A) when considering the ethical dimensions of global niche building then geosciences should feature 'citizen geoscience'; and B) when considering the functioning of a knowledge-based society under conditions of anthropogenic global change then 'citizen geoscience' facilitates applying that knowledge base. (A) Regarding 'niche building': The design of production systems and consumption patterns embeds geoscience know-how and relates it to the everyday life. Any citizen's activities purposefully interconnect to the biogeosphere for well-being, care-taking, and reproduction, although habitually without involving a geoscientist in professional capacity. In that implicit manner the everyday behaviours and practices of people influence Earth system dynamic. This renders their inherent geoscience know-how a public good as it makes their ignorance a public risk. A comfortable human niche for billions of people requires a global biogeosphere that is disrupted little by citizens' activities and exposes them to hazards that can be tamed. Quite the reverse, anthropogenic global change will disturb living conditions for many citizen. Much geoscience know-how will have to be deployed to tame disturbances in a socially sustainable manner. Sustainability in turn needs involvement of citizens in

  10. Microbial community composition and endolith colonization at an Arctic thermal spring are driven by calcite precipitation

    Science.gov (United States)

    Starke, Verena; Kirshtein, Julie; Fogel, Marilyn L.; Steele, Andrew

    2013-01-01

    Environmental conditions shape community composition. Arctic thermal springs provide an opportunity to study how environmental gradients can impose strong selective pressures on microbial communities and provide a continuum of niche opportunities. We use microscopic and molecular methods to conduct a survey of microbial community composition at Troll Springs on Svalbard, Norway, in the high Arctic. Microorganisms there exist under a wide range of environmental conditions: in warm water as periphyton, in moist granular materials, and in cold, dry rock as endoliths. Troll Springs has two distinct ecosystems, aquatic and terrestrial, together in close proximity, with different underlying environmental factors shaping each microbial community. Periphyton are entrapped during precipitation of calcium carbonate from the spring's waters, providing microbial populations that serve as precursors for the development of endolithic communities. This process differs from most endolith colonization, in which the rock predates the communities that colonize it. Community composition is modulated as environmental conditions change within the springs. At Troll, the aquatic environments show a small number of dominant operational taxonomic units (OTUs) that are specific to each sample. The terrestrial environments show a more even distribution of OTUs common to multiple samples.

  11. The multi-niche crowding genetic algorithm: Analysis and applications

    Energy Technology Data Exchange (ETDEWEB)

    Cedeno, Walter [Univ. of California, Davis, CA (United States)

    1995-09-01

    The ability of organisms to evolve and adapt to the environment has provided mother nature with a rich and diverse set of species. Only organisms well adapted to their environment can survive from one generation to the next, transferring on the traits, that made them successful, to their offspring. Competition for resources and the ever changing environment drives some species to extinction and at the same time others evolve to maintain the delicate balance in nature. In this disertation we present the multi-niche crowding genetic algorithm, a computational metaphor to the survival of species in ecological niches in the face of competition. The multi-niche crowding genetic algorithm maintains stable subpopulations of solutions in multiple niches in multimodal landscapes. The algorithm introduces the concept of crowding selection to promote mating among members with qirnilar traits while allowing many members of the population to participate in mating. The algorithm uses worst among most similar replacement policy to promote competition among members with similar traits while allowing competition among members of different niches as well. We present empirical and theoretical results for the success of the multiniche crowding genetic algorithm for multimodal function optimization. The properties of the algorithm using different parameters are examined. We test the performance of the algorithm on problems of DNA Mapping, Aquifer Management, and the File Design Problem. Applications that combine the use of heuristics and special operators to solve problems in the areas of combinatorial optimization, grouping, and multi-objective optimization. We conclude by presenting the advantages and disadvantages of the algorithm and describing avenues for future investigation to answer other questions raised by this study.

  12. Early colonization of thermal niches in a silica-depositing hot spring in central Tibet.

    Science.gov (United States)

    Lau, C Y; Aitchison, J C; Pointing, S B

    2008-03-01

    Thermophilic microbial mats dominated by the anoxygenic phototroph Roseiflexus castenholzii commonly develop around sinter-depositing geysers in the Daggyai Tso geothermal field of central Tibet. In this study we used morphological and molecular genetic techniques to reveal a diverse pioneer biofilm community including both archaea and bacteria involved in early colonization of such thermal niches at temperatures ranging from 46 to 77 degrees C. Sinter precipitation and biomineralization were evident at all locations, but the latter was selective between taxa and most evident on filamentous cells. Evidence for possible indirect biosignatures from biofilms overwhelmed by sinter deposition was found. Succession to a mature community appeared to relate to the growth rate for key taxa outpacing that of silicification within an optimum temperature range of 54-61 degrees C. The thin surface layer of silicification-resistant cyanobacteria that developed on the surface of mature mats may play a role in preventing biomineralization of the susceptible R. castenholzii beneath within these communities.

  13. Renewable energies and the poor: niche or nexus?

    International Nuclear Information System (INIS)

    Bhattacharyya, Subhes C.

    2006-01-01

    Renewable energies are considered as an essential element of any strategy for sustainable energy development. The poor in the developing world without access to modern energies are regarded as a major market for renewable energies. This short paper attempts to analyse whether such a niche is backed by any economic logic and whether renewable energy and the poor nexus could be a strategy for success. The paper suggests that contrary to the common belief, the economic logic behind the niche is unsound and that the nexus is not a recipe for success

  14. Evolution of the Jatropha Biofuel Niche in Ghana

    DEFF Research Database (Denmark)

    Nygaard, Ivan; Bolwig, Simon

    spanning the period 1995–2004 and including detailed company case studies. Relating to the MLP framework the factors analysed influencing internal niche processes are alignment of expectations, network formation, and learning and knowledge sharing, while those relating to the GVC framework are value chain......, which contributed to the collapse of the jatropha sector in Ghana and thus to the failure to capitalise on the initially high expectations of biofuel production. We also found a low level of learning and knowledgesharing between jatropha niche actors in Ghana, which, alongside weak public R&D support...

  15. Mineralogic control on abundance and diversity of surface-adherent microbial communities

    Science.gov (United States)

    Mauck, Brena S.; Roberts, Jennifer A.

    2007-01-01

    In this study, we investigated the role of mineral-bound P and Fe in defining microbial abundance and diversity in a carbon-rich groundwater. Field colonization experiments of initially sterile mineral surfaces were combined with community structure characterization of the attached microbial population. Silicate minerals containing varying concentrations of P (∼1000 ppm P) and Fe (∼4 wt % Fe 2 O3), goethite (FeOOH), and apatite [Ca5(PO4)3(OH)] were incubated for 14 months in three biogeochemically distinct zones within a petroleum-contaminated aquifer. Phospholipid fatty acid analysis of incubated mineral surfaces and groundwater was used as a measure of microbial community structure and biomass. Microbial biomass on minerals exhibited distinct trends as a function of mineralogy depending on the environment of incubation. In the carbon-rich, aerobic groundwater attached biomass did not correlate to the P- or Fe- content of the mineral. In the methanogenic groundwater, however, biomass was most abundant on P-containing minerals. Similarly, in the Fe-reducing groundwater a correlation between Fe-content and biomass was observed. The community structure of the mineral-adherent microbial population was compared to the native groundwater community. These two populations were significantly different regardless of mineralogy, suggesting differentiation of the planktonic community through attachment, growth, and death of colonizing cells. Biomarkers specific for dissimilatory Fe-reducing bacteria native to the aquifer were identified only on Fe-containing minerals in the Fe-reducing groundwater. These results demonstrate that the trace nutrient content of minerals affects both the abundance and diversity of surface-adherent microbial communities. This behavior may be a means to access limiting nutrients from the mineral, creating a niche for a particular microbial population. These results suggest that heterogeneity of microbial populations and their associated

  16. Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia.

    Science.gov (United States)

    Ben Said, Sami; Or, Dani

    2017-01-01

    The metabolic diversity present in microbial communities enables cooperation toward accomplishing more complex tasks than possible by a single organism. Members of a consortium communicate by exchanging metabolites or signals that allow them to coordinate their activity through division of labor. In contrast with monocultures, evidence suggests that microbial consortia self-organize to form spatial patterns, such as observed in biofilms or in soil aggregates, that enable them to respond to gradient, to improve resource interception and to exchange metabolites more effectively. Current biotechnological applications of microorganisms remain rudimentary, often relying on genetically engineered monocultures (e.g., pharmaceuticals) or mixed-cultures of partially known composition (e.g., wastewater treatment), yet the vast potential of "microbial ecological power" observed in most natural environments, remains largely underused. In line with the Unified Microbiome Initiative (UMI) which aims to "discover and advance tools to understand and harness the capabilities of Earth's microbial ecosystems," we propose in this concept paper to capitalize on ecological insights into the spatial and modular design of interlinked microbial consortia that would overcome limitations of natural systems and attempt to optimize the functionality of the members and the performance of the engineered consortium. The topology of the spatial connections linking the various members and the regulated fluxes of media between those modules, while representing a major engineering challenge, would allow the microbial species to interact. The modularity of such spatially linked microbial consortia (SLMC) could facilitate the design of scalable bioprocesses that can be incorporated as parts of a larger biochemical network. By reducing the need for a compatible growth environment for all species simultaneously, SLMC will dramatically expand the range of possible combinations of microorganisms and their

  17. AN ANALYSIS OF FUNDING DECISIONS FOR NICHE AGRICULTURAL PRODUCTS

    OpenAIRE

    HOWARD VAN AUKEN; SHAWN CARRAHER

    2012-01-01

    This paper examines the flow of funds from providers of capital to niche agricultural users of capital. Various programs through the US government, state/local economic development and private agencies work to improve the flow of capital to the niche agricultural sector. However, despite the expansion of programs aimed at providing financial resources to the agricultural sector, many sectors remain poorly served. Previous studies have suggested that agencies need to facilitate the flow of cap...

  18. Ontogenetic specialism in predators with multiple niche shifts prevents predator population recovery and establishment

    NARCIS (Netherlands)

    van Leeuwen, A.; Huss, M.; Gårdmark, A.; de Roos, A.M.

    2014-01-01

    The effects of ontogenetic niche shifts on community structure and dynamics are underexplored, despite the occurrence of such shifts in the majority of animal species. We studied the form of niche shifts in a predator that exhibits multiple ontogenetic niche shifts, and analyzed how this life

  19. Targeting the vascular and perivascular niches as a regenerative therapy for lung and liver fibrosis.

    Science.gov (United States)

    Cao, Zhongwei; Ye, Tinghong; Sun, Yue; Ji, Gaili; Shido, Koji; Chen, Yutian; Luo, Lin; Na, Feifei; Li, Xiaoyan; Huang, Zhen; Ko, Jane L; Mittal, Vivek; Qiao, Lina; Chen, Chong; Martinez, Fernando J; Rafii, Shahin; Ding, Bi-Sen

    2017-08-30

    The regenerative capacity of lung and liver is sometimes impaired by chronic or overwhelming injury. Orthotopic transplantation of parenchymal stem cells to damaged organs might reinstate their self-repair ability. However, parenchymal cell engraftment is frequently hampered by the microenvironment in diseased recipient organs. We show that targeting both the vascular niche and perivascular fibroblasts establishes "hospitable soil" to foster the incorporation of "seed," in this case, the engraftment of parenchymal cells in injured organs. Specifically, ectopic induction of endothelial cell (EC)-expressed paracrine/angiocrine hepatocyte growth factor (HGF) and inhibition of perivascular NOX4 [NADPH (reduced form of nicotinamide adenine dinucleotide phosphate) oxidase 4] synergistically enabled reconstitution of mouse and human parenchymal cells in damaged organs. Reciprocally, genetic knockout of Hgf in mouse ECs ( Hgf iΔEC/iΔEC ) aberrantly up-regulated perivascular NOX4 during liver and lung regeneration. Dysregulated HGF and NOX4 pathways subverted the function of vascular and perivascular cells from an epithelially inductive niche to a microenvironment that inhibited parenchymal reconstitution. Perivascular NOX4 induction in Hgf iΔEC/iΔEC mice recapitulated the phenotype of human and mouse liver and lung fibrosis. Consequently, EC-directed HGF and NOX4 inhibitor GKT137831 stimulated regenerative integration of mouse and human parenchymal cells in chronically injured lung and liver. Our data suggest that targeting dysfunctional perivascular and vascular cells in diseased organs can bypass fibrosis and enable reparative cell engraftment to reinstate lung and liver regeneration. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  20. Environmental niche models for riverine desert fishes and their similarity according to phylogeny and functionality

    Science.gov (United States)

    Whitney, James E.; Whittier, Joanna B.; Paukert, Craig P.

    2017-01-01

    Environmental filtering and competitive exclusion are hypotheses frequently invoked in explaining species' environmental niches (i.e., geographic distributions). A key assumption in both hypotheses is that the functional niche (i.e., species traits) governs the environmental niche, but few studies have rigorously evaluated this assumption. Furthermore, phylogeny could be associated with these hypotheses if it is predictive of functional niche similarity via phylogenetic signal or convergent evolution, or of environmental niche similarity through phylogenetic attraction or repulsion. The objectives of this study were to investigate relationships between environmental niches, functional niches, and phylogenies of fishes of the Upper (UCRB) and Lower (LCRB) Colorado River Basins of southwestern North America. We predicted that functionally similar species would have similar environmental niches (i.e., environmental filtering) and that closely related species would be functionally similar (i.e., phylogenetic signal) and possess similar environmental niches (i.e., phylogenetic attraction). Environmental niches were quantified using environmental niche modeling, and functional similarity was determined using functional trait data. Nonnatives in the UCRB provided the only support for environmental filtering, which resulted from several warmwater nonnatives having dam number as a common predictor of their distributions, whereas several cool- and coldwater nonnatives shared mean annual air temperature as an important distributional predictor. Phylogenetic signal was supported for both natives and nonnatives in both basins. Lastly, phylogenetic attraction was only supported for native fishes in the LCRB and for nonnative fishes in the UCRB. Our results indicated that functional similarity was heavily influenced by evolutionary history, but that phylogenetic relationships and functional traits may not always predict the environmental distribution of species. However, the

  1. Comparison of Hematopoietic and Spermatogonial Stem Cell Niches from the Regenerative Medicine Aspect.

    Science.gov (United States)

    Köse, Sevil; Yersal, Nilgün; Önen, Selin; Korkusuz, Petek

    2018-06-08

    Recent advances require a dual evaluation of germ and somatic stem cell niches with a regenerative medicine perspective. For a better point of view of the niche concept, it is needed to compare the microenvironments of those niches in respect to several components. The cellular environment of spermatogonial stem cells' niche consists of Sertoli cells, Leydig cells, vascular endothelial cells, epididymal fat cells, peritubular myoid cells while hematopoietic stem cells have mesenchymal stem cells, osteoblasts, osteoclasts, megacaryocytes, macrophages, vascular endothelial cells, pericytes and adipocytes in their microenvironment. Not only those cells', but also the effect of the other factors such as hormones, growth factors, chemokines, cytokines, extracellular matrix components, biomechanical forces (like shear stress, tension or compression) and physical environmental elements such as temperature, oxygen level and pH will be clarified during the chapter. Because it is known that the microenvironment has an important role in the stem cell homeostasis and disease conditions, it is crucial to understand the details of the microenvironment and to be able to compare the niche concepts of the different types of stem cells from each other, for the regenerative interventions. Indeed, the purpose of this chapter is to point out the usage of niche engineering within the further studies in the regenerative medicine field. Decellularized, synthetic or non-synthetic scaffolds may help to mimic the stem cell niche. However, the shared or different characteristics of germ and somatic stem cell microenvironments are necessary to constitute a proper niche model. When considered from this aspect, it is possible to produce some strategies on the personalized medicine by using those artificial models of stem cell microenvironment.

  2. Global thermal niche models of two European grasses show high invasion risks in Antarctica.

    Science.gov (United States)

    Pertierra, Luis R; Aragón, Pedro; Shaw, Justine D; Bergstrom, Dana M; Terauds, Aleks; Olalla-Tárraga, Miguel Ángel

    2017-07-01

    The two non-native grasses that have established long-term populations in Antarctica (Poa pratensis and Poa annua) were studied from a global multidimensional thermal niche perspective to address the biological invasion risk to Antarctica. These two species exhibit contrasting introduction histories and reproductive strategies and represent two referential case studies of biological invasion processes. We used a multistep process with a range of species distribution modelling techniques (ecological niche factor analysis, multidimensional envelopes, distance/entropy algorithms) together with a suite of thermoclimatic variables, to characterize the potential ranges of these species. Their native bioclimatic thermal envelopes in Eurasia, together with the different naturalized populations across continents, were compared next. The potential niche of P. pratensis was wider at the cold extremes; however, P. annua life history attributes enable it to be a more successful colonizer. We observe that particularly cold summers are a key aspect of the unique Antarctic environment. In consequence, ruderals such as P. annua can quickly expand under such harsh conditions, whereas the more stress-tolerant P. pratensis endures and persist through steady growth. Compiled data on human pressure at the Antarctic Peninsula allowed us to provide site-specific biosecurity risk indicators. We conclude that several areas across the region are vulnerable to invasions from these and other similar species. This can only be visualized in species distribution models (SDMs) when accounting for founder populations that reveal nonanalogous conditions. Results reinforce the need for strict management practices to minimize introductions. Furthermore, our novel set of temperature-based bioclimatic GIS layers for ice-free terrestrial Antarctica provide a mechanism for regional and global species distribution models to be built for other potentially invasive species. © 2017 John Wiley & Sons Ltd.

  3. The muscle stem cell niche : regulation of satellite cells during regeneration

    NARCIS (Netherlands)

    Boonen, K.J.M.; Post, M.J.

    2008-01-01

    Satellite cells are considered to be adult skeletal muscle stem cells. Their ability to regenerate large muscle defects is highly dependent on their specific niche. When these cells are cultured in vitro, the loss of this niche leads to a loss of proliferative capacity and defective regeneration

  4. CROSS DRIFT ALCOVE/NICHE UTILITIES ANALYSIS

    International Nuclear Information System (INIS)

    S. Goodin

    1999-01-01

    The purpose of this analysis is to provide the design basis and general arrangement requirements of the non-potable water, waste water, compressed air and ventilation (post excavation) utilities required in support of the Cross Drift alcoves and niches

  5. Making Blood: The Haematopoietic Niche throughout Ontogeny

    Directory of Open Access Journals (Sweden)

    Mohammad A. Al-Drees

    2015-01-01

    Full Text Available Approximately one-quarter of all cells in the adult human body are blood cells. The haematopoietic system is therefore massive in scale and requires exquisite regulation to be maintained under homeostatic conditions. It must also be able to respond when needed, such as during infection or following blood loss, to produce more blood cells. Supporting cells serve to maintain haematopoietic stem and progenitor cells during homeostatic and pathological conditions. This coalition of supportive cell types, organised in specific tissues, is termed the haematopoietic niche. Haematopoietic stem and progenitor cells are generated in a number of distinct locations during mammalian embryogenesis. These stem and progenitor cells migrate to a variety of anatomical locations through the conceptus until finally homing to the bone marrow shortly before birth. Under stress, extramedullary haematopoiesis can take place in regions that are typically lacking in blood-producing activity. Our aim in this review is to examine blood production throughout the embryo and adult, under normal and pathological conditions, to identify commonalities and distinctions between each niche. A clearer understanding of the mechanism underlying each haematopoietic niche can be applied to improving ex vivo cultures of haematopoietic stem cells and potentially lead to new directions for transplantation medicine.

  6. Microbial genome-wide association studies: lessons from human GWAS.

    Science.gov (United States)

    Power, Robert A; Parkhill, Julian; de Oliveira, Tulio

    2017-01-01

    The reduced costs of sequencing have led to whole-genome sequences for a large number of microorganisms, enabling the application of microbial genome-wide association studies (GWAS). Given the successes of human GWAS in understanding disease aetiology and identifying potential drug targets, microbial GWAS are likely to further advance our understanding of infectious diseases. These advances include insights into pressing global health problems, such as antibiotic resistance and disease transmission. In this Review, we outline the methodologies of GWAS, the current state of the field of microbial GWAS, and how lessons from human GWAS can direct the future of the field.

  7. Vikodak--A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets.

    Directory of Open Access Journals (Sweden)

    Sunil Nagpal

    Full Text Available The overall metabolic/functional potential of any given environmental niche is a function of the sum total of genes/proteins/enzymes that are encoded and expressed by various interacting microbes residing in that niche. Consequently, prior (collated information pertaining to genes, enzymes encoded by the resident microbes can aid in indirectly (reconstructing/ inferring the metabolic/ functional potential of a given microbial community (given its taxonomic abundance profile. In this study, we present Vikodak--a multi-modular package that is based on the above assumption and automates inferring and/ or comparing the functional characteristics of an environment using taxonomic abundance generated from one or more environmental sample datasets. With the underlying assumptions of co-metabolism and independent contributions of different microbes in a community, a concerted effort has been made to accommodate microbial co-existence patterns in various modules incorporated in Vikodak.Validation experiments on over 1400 metagenomic samples have confirmed the utility of Vikodak in (a deciphering enzyme abundance profiles of any KEGG metabolic pathway, (b functional resolution of distinct metagenomic environments, (c inferring patterns of functional interaction between resident microbes, and (d automating statistical comparison of functional features of studied microbiomes. Novel features incorporated in Vikodak also facilitate automatic removal of false positives and spurious functional predictions.With novel provisions for comprehensive functional analysis, inclusion of microbial co-existence pattern based algorithms, automated inter-environment comparisons; in-depth analysis of individual metabolic pathways and greater flexibilities at the user end, Vikodak is expected to be an important value addition to the family of existing tools for 16S based function prediction.A web implementation of Vikodak can be publicly accessed at: http

  8. Ecological Niche Modelling of Bank Voles in Western Europe

    Directory of Open Access Journals (Sweden)

    Sara Amirpour Haredasht

    2013-01-01

    Full Text Available The bank vole (Myodes glareolus is the natural host of Puumala virus (PUUV in vast areas of Europe. PUUV is one of the hantaviruses which are transmitted to humans by infected rodents. PUUV causes a general mild form of hemorrhagic fever with renal syndrome (HFRS called nephropathia epidemica (NE. Vector-borne and zoonotic diseases generally display clear spatial patterns due to different space-dependent factors. Land cover influences disease transmission by controlling both the spatial distribution of vectors or hosts, as well as by facilitating the human contact with them. In this study the use of ecological niche modelling (ENM for predicting the geographical distribution of bank vole population on the basis of spatial climate information is tested. The Genetic Algorithm for Rule-set Prediction (GARP is used to model the ecological niche of bank voles in Western Europe. The meteorological data, land cover types and geo-referenced points representing the locations of the bank voles (latitude/longitude in the study area are used as the primary model input value. The predictive accuracy of the bank vole ecologic niche model was significant (training accuracy of 86%. The output of the GARP models based on the 50% subsets of points used for testing the model showed an accuracy of 75%. Compared with random models, the probability of such high predictivity was low (χ2 tests, p < 10−6. As such, the GARP models were predictive and the used ecologic niche model indeed indicates the ecologic requirements of bank voles. This approach successfully identified the areas of infection risk across the study area. The result suggests that the niche modelling approach can be implemented in a next step towards the development of new tools for monitoring the bank vole’s population.

  9. Ecological niche modelling of bank voles in Western Europe.

    Science.gov (United States)

    Amirpour Haredasht, Sara; Barrios, Miguel; Farifteh, Jamshid; Maes, Piet; Clement, Jan; Verstraeten, Willem W; Tersago, Katrien; Van Ranst, Marc; Coppin, Pol; Berckmans, Daniel; Aerts, Jean-Marie

    2013-01-28

    The bank vole (Myodes glareolus) is the natural host of Puumala virus (PUUV) in vast areas of Europe. PUUV is one of the hantaviruses which are transmitted to humans by infected rodents. PUUV causes a general mild form of hemorrhagic fever with renal syndrome (HFRS) called nephropathia epidemica (NE). Vector-borne and zoonotic diseases generally display clear spatial patterns due to different space-dependent factors. Land cover influences disease transmission by controlling both the spatial distribution of vectors or hosts, as well as by facilitating the human contact with them. In this study the use of ecological niche modelling (ENM) for predicting the geographical distribution of bank vole population on the basis of spatial climate information is tested. The Genetic Algorithm for Rule-set Prediction (GARP) is used to model the ecological niche of bank voles in Western Europe. The meteorological data, land cover types and geo-referenced points representing the locations of the bank voles (latitude/longitude) in the study area are used as the primary model input value. The predictive accuracy of the bank vole ecologic niche model was significant (training accuracy of 86%). The output of the GARP models based on the 50% subsets of points used for testing the model showed an accuracy of 75%. Compared with random models, the probability of such high predictivity was low (χ(2) tests, p < 10(-6)). As such, the GARP models were predictive and the used ecologic niche model indeed indicates the ecologic requirements of bank voles. This approach successfully identified the areas of infection risk across the study area. The result suggests that the niche modelling approach can be implemented in a next step towards the development of new tools for monitoring the bank vole's population.

  10. Microbial Communities in Sunken Wood Are Structured by Wood-Boring Bivalves and Location in a Submarine Canyon

    Science.gov (United States)

    Fagervold, Sonja K.; Romano, Chiara; Kalenitchenko, Dimitri; Borowski, Christian; Nunes-Jorge, Amandine; Martin, Daniel; Galand, Pierre E.

    2014-01-01

    The cornerstones of sunken wood ecosystems are microorganisms involved in cellulose degradation. These can either be free-living microorganisms in the wood matrix or symbiotic bacteria associated with wood-boring bivalves such as emblematic species of Xylophaga, the most common deep-sea woodborer. Here we use experimentally submerged pine wood, placed in and outside the Mediterranean submarine Blanes Canyon, to compare the microbial communities on the wood, in fecal pellets of Xylophaga spp. and associated with the gills of these animals. Analyses based on tag pyrosequencing of the 16S rRNA bacterial gene showed that sunken wood contained three distinct microbial communities. Wood and pellet communities were different from each other suggesting that Xylophaga spp. create new microbial niches by excreting fecal pellets into their burrows. In turn, gills of Xylophaga spp. contain potential bacterial symbionts, as illustrated by the presence of sequences closely related to symbiotic bacteria found in other wood eating marine invertebrates. Finally, we found that sunken wood communities inside the canyon were different and more diverse than the ones outside the canyon. This finding extends to the microbial world the view that submarine canyons are sites of diverse marine life. PMID:24805961

  11. Drosophila Glypicans Regulate Follicle Stem Cell Maintenance and Niche Competition.

    Science.gov (United States)

    Su, Tsu-Yi; Nakato, Eriko; Choi, Pui Yee; Nakato, Hiroshi

    2018-04-09

    Adult stem cells reside in specialized microenvironments, called niches, which provide signals for stem cells to maintain their undifferentiated and self-renewing state. To maintain stem cell quality, several types of stem cells are known to be regularly replaced by progenitor cells through niche competition. However, the cellular and molecular bases for stem cell competition for niche occupancy are largely unknown. Here, we show that two Drosophila members of the glypican family of heparan sulfate proteoglycans (HSPGs), Dally and Dally-like (Dlp), differentially regulate follicle stem cell (FSC) maintenance and FSC competitiveness for niche occupancy. Lineage analyses of glypican mutant FSC clones showed that dally is essential for normal FSC maintenance. In contrast, dlp is a hyper-competitive mutation: dlp mutant FSC progenitors often eventually occupy the entire epithelial sheet. RNAi knockdown experiments showed that Dally and Dlp play both partially redundant and distinct roles in regulating Jak/Stat, Wg and Hh signaling in FSCs. The Drosophila FSC system offers a powerful genetic model to study the mechanisms by which HSPGs exert specific functions in stem cell replacement and competition. Copyright © 2018, Genetics.

  12. Environmental filtering drives the shape and breadth of the seed germination niche in coastal plant communities.

    Science.gov (United States)

    Fernández-Pascual, Eduardo; Pérez-Arcoiza, Adrián; Prieto, José Alberto; Díaz, Tomás E

    2017-05-01

    A phylogenetic comparative analysis of the seed germination niche was conducted in coastal plant communities of western Europe. Two hypotheses were tested, that (1) the germination niche shape (i.e. the preference for a set of germination cues as opposed to another) would differ between beaches and cliffs to prevent seedling emergence in the less favourable season (winter and summer, respectively); and (2) the germination niche breadth (i.e. the amplitude of germination cues) would be narrower in the seawards communities, where environmental filtering is stronger. Seeds of 30 specialist species of coastal plant communities were collected in natural populations of northern Spain. Their germination was measured in six laboratory treatments based on field temperatures. Germination niche shape was estimated as the best germination temperature. Germination niche breadth was calculated using Pielou's evenness index. Differences between plant communities in their germination niche shape and breadth were tested using phylogenetic generalized least squares regression (PGLS). Germination niche shape differed between communities, being warm-cued in beaches (best germination temperature = 20 °C) and cold-cued in cliffs (14 °C). Germination niche was narrowest in seawards beaches (Pielou's index = 0·89) and broadest in landwards beaches (0·99). Cliffs had an intermediate germination niche breadth (0·95). The relationship between niche and plant community had a positive phylogenetic signal for shape (Pagel's λ = 0·64) and a negative one for breadth (Pagel's λ = -1·71). Environmental filters shape the germination niche to prevent emergence in the season of highest threat for seedling establishment. The germination niche breadth is narrower in the communities with stronger environmental filters, but only in beaches. This study provides empirical support to a community-level generalization of the hypotheses about the environmental drivers of the germination

  13. Evolution is a cooperative process: the biodiversity-related niches differentiation theory (BNDT) can explain why.

    Science.gov (United States)

    Gatti, Roberto Cazzolla

    2011-01-01

    A. McFayden and G.E. Hutchinson defined a niche as a multidimensional space or hypervolume within the environment that allows an individual or a species to survive, we consider niches as a fundamental ecological variable that regulate species' composition and relation in ecosystems. Successively the niche concept has been associated to the genetic term "phenotype" by MacArthurstressing the importance on what a species or a genome can show outside, either in the environmental functions or in body characteristics. Several indexes have been developed to evaluate the grade of overlapping and similarities of species' niches, even utilizing the theory of information. However, which are the factors that determine the number of species that can coexist in a determinate environment and why a generalist species do not compete until the exclusion of the remaining species to maximize its fitness, is still quite unknown. Moreover, there are few studies and theories that clearly explain why the number of niches is so variable through ecosystems and how can several species live in the same basal niche, intended in a comprehensive sense as the range of basic conditions (temperature, humidity, food-guild, etc.). Here I show that the number of niches in an ecosystem depends on the number of species present in a particular moment and that the species themselves allow the enhancement of niches in terms of space and number. I found that using a three-dimensional model as hypervolume and testing the theory on a Mediterranean, temperate and tropical forest ecosystem it is possible to demonstrate that each species plays a fundamental role in facilitating the colonization by other species by simply modifying the environment and exponentially increasing the available niches' space and number. I resumed these hypothesis, after some preliminary empiric tests, in the Biodiversity-related Niches Differentiation Theory (BNDT), stressing with these definition that the process of niches

  14. Soil microbial community composition is correlated to soil carbon processing along a boreal wetland formation gradient

    Science.gov (United States)

    Chapman, Eric; Cadillo-Quiroz, Hinsby; Childers, Daniel L.; Turetsky, Merritt R.; Waldrop, Mark P.

    2017-01-01

    Climate change is modifying global biogeochemical cycles. Microbial communities play an integral role in soil biogeochemical cycles; knowledge about microbial composition helps provide a mechanistic understanding of these ecosystem-level phenomena. Next generation sequencing approaches were used to investigate changes in microbial functional groups during ecosystem development, in response to climate change, in northern boreal wetlands. A gradient of wetlands that developed following permafrost degradation was used to characterize changes in the soil microbial communities that mediate C cycling: a bog representing an “undisturbed” system with intact permafrost, and a younger bog and an older bog that formed following the disturbance of permafrost thaw. Reference 16S rRNA databases and several diversity indices were used to assess structural differences among these communities, to assess relationships between soil microbial community composition and various environmental variables including redox potential and pH. Rates of potential CO2 and CH4 gas production were quantified to correlate sequence data with gas flux. The abundance of organic C degraders was highest in the youngest bog, suggesting higher rates of microbial processes, including potential CH4 production. In addition, alpha diversity was also highest in the youngest bog, which seemed to be related to a more neutral pH and a lower redox potential. These results could potentially be driven by increased niche differentiation in anaerobic soils. These results suggest that ecosystem structure, which was largely driven by changes in edaphic and plant community characteristics between the “undisturbed” permafrost bog and the two bogs formed following permafrost thaw, strongly influenced microbial function.

  15. Differential cytokine contributions of perivascular haematopoietic stem cell niches.

    Science.gov (United States)

    Asada, Noboru; Kunisaki, Yuya; Pierce, Halley; Wang, Zichen; Fernandez, Nicolas F; Birbrair, Alexander; Ma'ayan, Avi; Frenette, Paul S

    2017-03-01

    Arterioles and sinusoids of the bone marrow (BM) are accompanied by stromal cells that express nerve/glial antigen 2 (NG2) and leptin receptor (LepR), and constitute specialized niches that regulate quiescence and proliferation of haematopoietic stem cells (HSCs). However, how niche cells differentially regulate HSC functions remains unknown. Here, we show that the effects of cytokines regulating HSC functions are dependent on the producing cell sources. Deletion of chemokine C-X-C motif ligand 12 (Cxcl12) or stem cell factor (Scf) from all perivascular cells marked by nestin-GFP dramatically depleted BM HSCs. Selective Cxcl12 deletion from arteriolar NG2 + cells, but not from sinusoidal LepR + cells, caused HSC reductions and altered HSC localization in BM. By contrast, deletion of Scf in LepR + cells, but not NG2 + cells, led to reductions in BM HSC numbers. These results uncover distinct contributions of cytokines derived from perivascular cells in separate vascular niches to HSC maintenance.

  16. Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics

    Energy Technology Data Exchange (ETDEWEB)

    Gobler, C J; Grigoriev, I V; Berry, D L; Dyhrman, S T; Wilhelm, S W; Salamov, A; Lobanov, A V; Zhang, Y; Collier, J L; Wurch, L L; Kustka, A B; Dill, B D; Shah, M; VerBerkomes, N C; Kuo, A; Terry, A; Pangilinan, J; Lindquist, E A; Lucas, S; Paulsen, I; Hattenrath-Lehmann, T K; Talmage, S; Walker, E A; Koch, F; Burson, A M; Marcoval, M A; Tang, Y; LeCleir, G R; Coyne, K J; Berg, G M; Bertrand, E M; Saito, M A; Gladyshev, V N

    2011-03-02

    Harmful algal blooms (HABs) cause significant economic and ecological damage worldwide. Despite considerable efforts, a comprehensive understanding of the factors that promote these blooms has been lacking because the biochemical pathways that facilitate their dominance relative to other phytoplankton within specific environments have not been identified. Here, biogeochemical measurements demonstrated that the harmful alga Aureococcus anophagefferens outcompeted co-occurring phytoplankton in estuaries with elevated levels of dissolved organic matter and turbidity and low levels of dissolved inorganic nitrogen. We subsequently sequenced the first HAB genome (A. anophagefferens) and compared its gene complement to those of six competing phytoplankton species identified via metaproteomics. Using an ecogenomic approach, we specifically focused on the gene sets that may facilitate dominance within the environmental conditions present during blooms. A. anophagefferens possesses a larger genome (56 mbp) and more genes involved in light harvesting, organic carbon and nitrogen utilization, and encoding selenium- and metal-requiring enzymes than competing phytoplankton. Genes for the synthesis of microbial deterrents likely permit the proliferation of this species with reduced mortality losses during blooms. Collectively, these findings suggest that anthropogenic activities resulting in elevated levels of turbidity, organic matter, and metals have opened a niche within coastal ecosystems that ideally suits the unique genetic capacity of A. anophagefferens and thus has facilitated the proliferation of this and potentially other HABs.

  17. Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor; Gobler, Christopher; Salamov, Asaf; Kuo, Alan; Terry, Astrid; Pangillian, Jasmyn; Lindquist, Erika; Lucas, Susan; Berry, Dianna; Dyhrman, Sonya; Wilhelm, Steven; Lobanov, Alexei; Zhang, Yan; Collier, Jackie; Wurch, Louie; Kusta, Adam; Dill, Brian; Shsh, Manesh; VerBerkmoes, Nathan; Paulsen, Ian; Hattenrath-Lehmann, Theresa; Talmage, Stephanie; Walker, Elyse; Koch, Florian; Burson, Amanda; Marcoval, Maria; Tang, Yin-Zhong; LeCleir, Gary; Coyne, Kathyrn; Berg, Gry; Bertrand, Erin; Saito, Mak; Gladyshev, Vadim

    2011-02-18

    Harmful algal blooms (HABs) cause significant economic and ecological damage worldwide. Despite considerable efforts, a comprehensive understanding of the factors that promote these blooms has been lacking, because the biochemical pathways that facilitate their dominance relative to other phytoplankton within specific environments have not been identified. Here, biogeochemical measurements showed that the harmful alga Aureococcus anophagefferens outcompeted co-occurring phytoplankton in estuaries with elevated levels of dissolved organic matter and turbidity and low levels of dissolved inorganic nitrogen. We subsequently sequenced the genome of A. anophagefferens and compared its gene complement with those of six competing phytoplankton species identified through metaproteomics. Using an ecogenomic approach, we specifically focused on gene sets that may facilitate dominance within the environmental conditions present during blooms. A. anophagefferens possesses a larger genome (56 Mbp) and has more genes involved in light harvesting, organic carbon and nitrogen use, and encoding selenium- and metal-requiring enzymes than competing phytoplankton. Genes for the synthesis of microbial deterrents likely permit the proliferation of this species, with reduced mortality losses during blooms. Collectively, these findings suggest that anthropogenic activities resulting in elevated levels of turbidity, organic matter, and metals have opened a niche within coastal ecosystems that ideally suits the unique genetic capacity of A. anophagefferens and thus, has facilitated the proliferation of this and potentially other HABs.

  18. Biogeochemical and Ecomorphological Niche Segregation of Mediterranean Woody Species along a Local Gradient

    OpenAIRE

    Enrique G. de la Riva; Enrique G. de la Riva; Teodoro Marañón; Cyrille Violle; Rafael Villar; Ignacio M. Pérez-Ramos

    2017-01-01

    According with niche theory the species are specialized in different ecological niches, being able to coexist as result of a differential use of resources. In this context, the biogeochemical niche hypothesis proposes that species have an optimal elemental composition which results from the link between the chemical and morphological traits for the optimum plant functioning. Thus, and attending to the limiting similarity concept, different elemental composition and plant structure among co-oc...

  19. Protection from UV light is an evolutionarily conserved feature of the haematopoietic niche

    Science.gov (United States)

    Kapp, Friedrich G.; Perlin, Julie R.; Hagedorn, Elliott J.; Gansner, John M.; Schwarz, Daniel E.; O'Connell, Lauren A.; Johnson, Nicholas; Amemiya, Chris; Fisher, David E.; Wolfle, Ute; Trompouki, Eirini; Niemeyer, Charlotte M.; Driever, Wolfgang; Zon, Leonard I.

    2018-01-01

    Haematopoietic stem and progenitor cells (HSPCs) require a specific microenvironment, the haematopoietic niche, which regulates HSPC behaviour. The location of this niche varies across species, but the evolutionary pressures that drive HSPCs to different microenvironments remain unknown. The niche is located in the bone marrow in adult mammals, whereas it is found in other locations in non-mammalian vertebrates, for example, in the kidney marrow in teleost fish. Here we show that a melanocyte umbrella above the kidney marrow protects HSPCs against ultraviolet light in zebrafish. Because mutants that lack melanocytes have normal steady-state haematopoiesis under standard laboratory conditions, we hypothesized that melanocytes above the stem cell niche protect HSPCs against ultraviolet-light-induced DNA damage. Indeed, after ultraviolet-light irradiation, unpigmented larvae show higher levels of DNA damage in HSPCs, as indicated by staining of cyclobutane pyrimidine dimers and have reduced numbers of HSPCs, as shown by cmyb (also known as myb) expression. The umbrella of melanocytes associated with the haematopoietic niche is highly evolutionarily conserved in aquatic animals, including the sea lamprey, a basal vertebrate. During the transition from an aquatic to a terrestrial environment, HSPCs relocated into the bone marrow, which is protected from ultraviolet light by the cortical bone around the marrow. Our studies reveal that melanocytes above the haematopoietic niche protect HSPCs from ultraviolet-light-induced DNA damage in aquatic vertebrates and suggest that during the transition to terrestrial life, ultraviolet light was an evolutionary pressure affecting the location of the haematopoietic niche.

  20. Microbial Interactions and the Ecology and Evolution of Hawaiian Drosophilidae

    Directory of Open Access Journals (Sweden)

    Timothy eO'Connor

    2014-12-01

    Full Text Available Adaptive radiations are characterized by an increased rate of speciation and expanded range of habitats and ecological niches exploited by those species. The Hawaiian Drosophilidae is a classic adaptive radiation; a single ancestral species colonized Hawaii approximately 25 million years ago and gave rise to two monophyletic lineages, the Hawaiian Drosophila and the genus Scaptomyza. The Hawaiian Drosophila are largely saprophagous and rely on approximately 40 endemic plant families and their associated microbes to complete development. Scaptomyza are even more diverse in host breadth. While many species of Scaptomyza utilize decomposing plant substrates, some species have evolved to become herbivores, parasites on spider egg masses, and exploit microbes on living plant tissue. Understanding the origin of the ecological diversity encompassed by these nearly 700 described species has been a challenge. The central role of microbes in drosophilid ecology suggests bacterial and fungal associates may have played a role in the diversification of the Hawaiian Drosophilidae. Here we synthesize recent ecological and microbial community data from the Hawaiian Drosophilidae to examine the forces that may have led to this adaptive radiation. We propose that the evolutionary success of the Hawaiian Drosophilidae is due to a combination of factors, including adaptation to novel ecological niches facilitated by microbes.

  1. Evolutionary dynamics of ecological niche in three Rhinogobio fishes from the upper Yangtze River inferred from morphological traits

    Science.gov (United States)

    Wang, Meirong; Liu, Fei; Lin, Pengcheng; Yang, Shaorong; Liu, Huanzhang

    2015-01-01

    In the past decades, it has been debated whether ecological niche should be conserved among closely related species (phylogenetic niche conservatism, PNC) or largely divergent (traditional ecological niche theory and ecological speciation) and whether niche specialist and generalist might remain in equilibrium or niche generalist could not appear. In this study, we employed morphological traits to describe ecological niche and test whether different niche dimensions exhibit disparate evolutionary patterns. We conducted our analysis on three Rhinogobio fish species (R. typus,R. cylindricus, and R. ventralis) from the upper Yangtze River, China. Among the 32 measured morphological traits except body length, PCA extracted the first four principal components with their loading scores >1.000. To find the PNC among species, Mantel tests were conducted with the Euclidean distances calculated from the four principal components (representing different niche dimensions) against the pairwise distances calculated from mitochondrial cytochrome b sequence variations. The results showed that the second and the third niche dimension, both related to swimming ability and behavior, exhibited phylogenetic conservatism. Further comparison on niche breadth among these three species revealed that the fourth dimension of R. typus showed the greatest width, indicating that this dimension exhibited niche generalism. In conclusion, our results suggested that different niche dimensions could show different evolutionary dynamic patterns: they may exhibit PNC or not, and some dimensions may evolve generalism. PMID:25691981

  2. Global Microbial Identifier

    DEFF Research Database (Denmark)

    Wielinga, Peter; Hendriksen, Rene S.; Aarestrup, Frank Møller

    2017-01-01

    ) will likely also enable a much better understanding of the pathogenesis of the infection and the molecular basis of the host response to infection. But the full potential of these advances will only transpire if the data in this area become transferable and thereby comparable, preferably in open-source...... of microorganisms, for the identification of relevant genes and for the comparison of genomes to detect outbreaks and emerging pathogens. To harness the full potential of WGS, a shared global database of genomes linked to relevant metadata and the necessary software tools needs to be generated, hence the global...... microbial identifier (GMI) initiative. This tool will ideally be used in amongst others in the diagnosis of infectious diseases in humans and animals, in the identification of microorganisms in food and environment, and to track and trace microbial agents in all arenas globally. This will require...

  3. Notch signaling mediates the age-associated decrease in adhesion of germline stem cells to the niche.

    Directory of Open Access Journals (Sweden)

    Chen-Yuan Tseng

    2014-12-01

    Full Text Available Stem cells have an innate ability to occupy their stem cell niche, which in turn, is optimized to house stem cells. Organ aging is associated with reduced stem cell occupancy in the niche, but the mechanisms involved are poorly understood. Here, we report that Notch signaling is increased with age in Drosophila female germline stem cells (GSCs, and this results in their removal from the niche. Clonal analysis revealed that GSCs with low levels of Notch signaling exhibit increased adhesiveness to the niche, thereby out-competing their neighbors with higher levels of Notch; adhesiveness is altered through regulation of E-cadherin expression. Experimental enhancement of Notch signaling in GSCs hastens their age-dependent loss from the niche, and such loss is at least partially mediated by Sex lethal. However, disruption of Notch signaling in GSCs does not delay GSC loss during aging, and nor does it affect BMP signaling, which promotes self-renewal of GSCs. Finally, we show that in contrast to GSCs, Notch activation in the niche (which maintains niche integrity, and thus mediates GSC retention is reduced with age, indicating that Notch signaling regulates GSC niche occupancy both intrinsically and extrinsically. Our findings expose a novel role of Notch signaling in controlling GSC-niche adhesion in response to aging, and are also of relevance to metastatic cancer cells, in which Notch signaling suppresses cell adhesion.

  4. Genome-enabled Modeling of Microbial Biogeochemistry using a Trait-based Approach. Does Increasing Metabolic Complexity Increase Predictive Capabilities?

    Science.gov (United States)

    King, E.; Karaoz, U.; Molins, S.; Bouskill, N.; Anantharaman, K.; Beller, H. R.; Banfield, J. F.; Steefel, C. I.; Brodie, E.

    2015-12-01

    The biogeochemical functioning of ecosystems is shaped in part by genomic information stored in the subsurface microbiome. Cultivation-independent approaches allow us to extract this information through reconstruction of thousands of genomes from a microbial community. Analysis of these genomes, in turn, gives an indication of the organisms present and their functional roles. However, metagenomic analyses can currently deliver thousands of different genomes that range in abundance/importance, requiring the identification and assimilation of key physiologies and metabolisms to be represented as traits for successful simulation of subsurface processes. Here we focus on incorporating -omics information into BioCrunch, a genome-informed trait-based model that represents the diversity of microbial functional processes within a reactive transport framework. This approach models the rate of nutrient uptake and the thermodynamics of coupled electron donors and acceptors for a range of microbial metabolisms including heterotrophs and chemolithotrophs. Metabolism of exogenous substrates fuels catabolic and anabolic processes, with the proportion of energy used for cellular maintenance, respiration, biomass development, and enzyme production based upon dynamic intracellular and environmental conditions. This internal resource partitioning represents a trade-off against biomass formation and results in microbial community emergence across a fitness landscape. Biocrunch was used here in simulations that included organisms and metabolic pathways derived from a dataset of ~1200 non-redundant genomes reflecting a microbial community in a floodplain aquifer. Metagenomic data was directly used to parameterize trait values related to growth and to identify trait linkages associated with respiration, fermentation, and key enzymatic functions such as plant polymer degradation. Simulations spanned a range of metabolic complexities and highlight benefits originating from simulations

  5. Introducing SONS, a Tool for Operational Taxonomic Unit-Based Comparisons of Microbial Community Memberships and Structures

    OpenAIRE

    Schloss, Patrick D.; Handelsman, Jo

    2006-01-01

    The recent advent of tools enabling statistical inferences to be drawn from comparisons of microbial communities has enabled the focus of microbial ecology to move from characterizing biodiversity to describing the distribution of that biodiversity. Although statistical tools have been developed to compare community structures across a phylogenetic tree, we lack tools to compare the memberships and structures of two communities at a particular operational taxonomic unit (OTU) definition. Furt...

  6. Individual diet variation in a marine fish assemblage: Optimal Foraging Theory, Niche Variation Hypothesis and functional identity

    Science.gov (United States)

    Cachera, M.; Ernande, B.; Villanueva, M. C.; Lefebvre, S.

    2017-02-01

    Individual diet variation (i.e. diet variation among individuals) impacts intra- and inter-specific interactions. Investigating its sources and relationship with species trophic niche organization is important for understanding community structure and dynamics. Individual diet variation may increase with intra-specific phenotypic (or "individual state") variation and habitat variability, according to Optimal Foraging Theory (OFT), and with species trophic niche width, according to the Niche Variation Hypothesis (NVH). OFT proposes "proximate sources" of individual diet variation such as variations in habitat or size whereas NVH relies on "ultimate sources" related to the competitive balance between intra- and inter-specific competitions. The latter implies as a corollary that species trophic niche overlap, taken as inter-specific competition measure, decreases as species niche width and individual niche variation increase. We tested the complementary predictions of OFT and NVH in a marine fish assemblage using stomach content data and associated trophic niche metrics. The NVH predictions were tested between species of the assemblage and decomposed into a between- and a within-functional group component to assess the potential influence of species' ecological function. For most species, individual diet variation and niche overlap were consistently larger than expected. Individual diet variation increased with intra-specific variability in individual state and habitat, as expected from OFT. It also increased with species niche width but in compliance with the null expectation, thus not supporting the NVH. In contrast, species niche overlap increased significantly less than null expectation with both species niche width and individual diet variation, supporting NVH corollary. The between- and within-functional group components of the NVH relationships were consistent with those between species at the assemblage level. Changing the number of prey categories used to

  7. Individual and species-specific traits explain niche size and functional role in spiders as generalist predators.

    Science.gov (United States)

    Sanders, Dirk; Vogel, Esther; Knop, Eva

    2015-01-01

    The function of a predator within a community is greatly based on its trophic niche, that is the number and the strength of feeding links. In generalist predators, which feed on a wide range of prey, the size and position of the trophic niche is likely determined by traits such as hunting mode, the stratum they occur in, their body size and age. We used stable isotope analyses ((13)C and (15)N) to measure the trophic niche size of nine spider species within a forest hedge community and tested for species traits and individual traits that influence stable isotope enrichment, niche size and resource use. The spiders Enoplognatha, Philodromus, Floronia, and Heliophanus had large isotopic niches, which correspond to a more generalistic feeding behaviour. In contrast, Araneus, Metellina and Agelena, as top predators in the system, had rather narrow niches. We found a negative correlation between trophic position and niche size. Differences in trophic position in spiders were explained by body size, hunting modes and stratum, while niche size was influenced by hunting mode. In Philodromus, the size of the trophic niche increased significantly with age. Fitting spiders to functional groups according to their mean body size, hunting mode and their habitat domain resulted in largely separated niches, which indicates that these traits are meaningful for separating functional entities in spiders. Functional groups based on habitat domain (stratum) caught the essential functional differences between the species with species higher up in the vegetation feeding on flying insects and herb and ground species also preying on forest floor decomposers. Interestingly, we found a gradient from large species using a higher habitat domain and having a smaller niche to smaller species foraging closer to the ground and having a larger niche. This shows that even within generalist predators, such as spiders, there is a gradient of specialism that can be predicted by functional traits.

  8. Convergent and divergent learning in photovoltaic pilot projects and subsequent niche development

    NARCIS (Netherlands)

    Mierlo, van B.

    2012-01-01

    A proposed strategy to facilitate the use and development of radical new sustainable technologies is the creation of niches. Learning in these niches and the social embedding of learning experiences can stimulate changes in existing sociotechnological regimes. Pilot projects in which new

  9. Niche construction through phenological plasticity: life history dynamics and ecological consequences.

    Science.gov (United States)

    Donohue, Kathleen

    2005-04-01

    The ability of an organism to alter the environment that it experiences has been termed 'niche construction'. Plants have several ways whereby they can determine the environment to which they are exposed at different life stages. This paper discusses three of these: plasticity in dispersal, flowering timing and germination timing. It reviews pathways through which niche construction alters evolutionary and ecological trajectories by altering the selective environment to which organisms are exposed, the phenotypic expression of plastic characters, and the expression of genetic variation. It provides examples whereby niche construction creates positive or negative feedbacks between phenotypes and environments, which in turn cause novel evolutionary constraints and novel life-history expression. Copyright New Phytologist (2005).

  10. Niche separation and reproduction of Clausocalanus species (Copepoda, Calanoida) in the Atlantic Ocean

    Science.gov (United States)

    Peralba, Àurea; Mazzocchi, Maria Grazia; Harris, Roger P.

    2017-11-01

    The distribution and reproductive traits of copepods of the genus Clausocalanus were investigated during the Atlantic Meridional Transect cruise AMT-15, in September-October 2004 to estimate their ecological niches and secondary production in the epipelagic layer along a latitudinal cline (48°N-40°S). The distribution patterns of selected environmental parameters, i.e., temperature, salinity and chlorophyll a concentration, enabled eco-provinces to be identified as described by Longhurst (2006). Clausocalanus represented on average 34% of total copepod abundance, with a large predominance of adult females and copepodites over males. Among the eleven Clausocalanus species found during the survey, eight species showed a wide distributional range, i.e.,C. paululus, C. pergens, C. furcatus, C. arcuicornis, C. jobei, C. parapergens, C. lividus, and C. mastigophorus, while C. ingens, C. brevipes, and C. laticeps were recorded only in the South Atlantic. The smallest C. furcatus, C. paululus, and C. pergens together accounted for 85% of total Clausocalanus adult abundance. The ecological niches were clearly separated among congeners of similar size and largely overlapped in congeners whose size differed. The small- and medium-sized species, which are egg-sac-spawners, had smaller clutch size and lower egg-production rate than the larger broadcaster congeners. Nevertheless, embryo viability was lower in broadcasters, which may explain their low abundance in terms of lower recruitment. A sex ratio largely skewed toward females in all Clausocalanus species and the observation of viable eggs in successive clutches from isolated females seem to indicate that re-mating is not necessary in this genus. Broadcast-spawners showed the highest weight-specific fecundity rates in the genus but similar secondary production to sac-spawners despite the fact that they never occurred at high abundance. In light of their abundant occurrence in oceanic waters and well-defined ecological

  11. Sulfur metabolizing microbes dominate microbial communities in Andesite-hosted shallow-sea hydrothermal systems.

    Directory of Open Access Journals (Sweden)

    Yao Zhang

    Full Text Available To determine microbial community composition, community spatial structure and possible key microbial processes in the shallow-sea hydrothermal vent systems off NE Taiwan's coast, we examined the bacterial and archaeal communities of four samples collected from the water column extending over a redoxocline gradient of a yellow and four from a white hydrothermal vent. Ribosomal tag pyrosequencing based on DNA and RNA showed statistically significant differences between the bacterial and archaeal communities of the different hydrothermal plumes. The bacterial and archaeal communities from the white hydrothermal plume were dominated by sulfur-reducing Nautilia and Thermococcus, whereas the yellow hydrothermal plume and the surface water were dominated by sulfide-oxidizing Thiomicrospira and Euryarchaeota Marine Group II, respectively. Canonical correspondence analyses indicate that methane (CH(4 concentration was the only statistically significant variable that explains all community cluster patterns. However, the results of pyrosequencing showed an essential absence of methanogens and methanotrophs at the two vent fields, suggesting that CH(4 was less tied to microbial processes in this shallow-sea hydrothermal system. We speculated that mixing between hydrothermal fluids and the sea or meteoric water leads to distinctly different CH(4 concentrations and redox niches between the yellow and white vents, consequently influencing the distribution patterns of the free-living Bacteria and Archaea. We concluded that sulfur-reducing and sulfide-oxidizing chemolithoautotrophs accounted for most of the primary biomass synthesis and that microbial sulfur metabolism fueled microbial energy flow and element cycling in the shallow hydrothermal systems off the coast of NE Taiwan.

  12. Sulfur metabolizing microbes dominate microbial communities in Andesite-hosted shallow-sea hydrothermal systems.

    Science.gov (United States)

    Zhang, Yao; Zhao, Zihao; Chen, Chen-Tung Arthur; Tang, Kai; Su, Jianqiang; Jiao, Nianzhi

    2012-01-01

    To determine microbial community composition, community spatial structure and possible key microbial processes in the shallow-sea hydrothermal vent systems off NE Taiwan's coast, we examined the bacterial and archaeal communities of four samples collected from the water column extending over a redoxocline gradient of a yellow and four from a white hydrothermal vent. Ribosomal tag pyrosequencing based on DNA and RNA showed statistically significant differences between the bacterial and archaeal communities of the different hydrothermal plumes. The bacterial and archaeal communities from the white hydrothermal plume were dominated by sulfur-reducing Nautilia and Thermococcus, whereas the yellow hydrothermal plume and the surface water were dominated by sulfide-oxidizing Thiomicrospira and Euryarchaeota Marine Group II, respectively. Canonical correspondence analyses indicate that methane (CH(4)) concentration was the only statistically significant variable that explains all community cluster patterns. However, the results of pyrosequencing showed an essential absence of methanogens and methanotrophs at the two vent fields, suggesting that CH(4) was less tied to microbial processes in this shallow-sea hydrothermal system. We speculated that mixing between hydrothermal fluids and the sea or meteoric water leads to distinctly different CH(4) concentrations and redox niches between the yellow and white vents, consequently influencing the distribution patterns of the free-living Bacteria and Archaea. We concluded that sulfur-reducing and sulfide-oxidizing chemolithoautotrophs accounted for most of the primary biomass synthesis and that microbial sulfur metabolism fueled microbial energy flow and element cycling in the shallow hydrothermal systems off the coast of NE Taiwan.

  13. Fuel cells niche market applications and design studies

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-07-01

    Mainstream fuel cell markets such as stationary power and transport propulsion have already received considerable attention. However, the niche areas considered in this report also offer considerable markets that are considered potentially ready for exploitation. This report examines those markets and considers the broad issues for exploitation. This programme of work has been funded under the DTI's Advanced Fuel Cell Programme. The overall aim of this project was to identify and evaluate niche market applications that have the potential to provide early commercially competitive market opportunities for fuel cell systems. Battery replacement, portable, mobile auxiliary power and stationary applications for non-standard generation are covered. (author)

  14. Are neural crest stem cells the missing link between hematopoietic and neurogenic niches?

    Directory of Open Access Journals (Sweden)

    Cécile eCoste

    2015-06-01

    Full Text Available Hematopoietic niches are defined as cellular and molecular microenvironments that regulate hematopoietic stem cell (HSC function together with stem cell autonomous mechanisms. Many different cell types have been characterized as contributors to the formation of HSC niches, such as osteoblasts, endothelial cells, Schwann cells, and mesenchymal progenitors. These mesenchymal progenitors have themselves been classified as CXC chemokine ligand (CXCL12-abundant reticular (CAR cells, stem cell factor expressing cells, or nestin-positive mesenchymal stem cells (MSCs, which have been recently identified as neural crest-derived cells (NCSCs. Together, these cells are spatially associated with HSCs and believed to provide appropriate microenvironments for HSC self-renewal, differentiation, mobilization and hibernation both by cell-to-cell contact and soluble factors. Interestingly, it appears that regulatory pathways governing the hematopoietic niche homeostasis are operating in the neurogenic niche as well. Therefore, this review paper aims to compare both the regulation of hematopoietic and neurogenic niches, in order to highlight the role of NCSCs and nervous system components in the development and the regulation of the hematopoietic system.

  15. Are neural crest stem cells the missing link between hematopoietic and neurogenic niches?

    Science.gov (United States)

    Coste, Cécile; Neirinckx, Virginie; Gothot, André; Wislet, Sabine; Rogister, Bernard

    2015-01-01

    Hematopoietic niches are defined as cellular and molecular microenvironments that regulate hematopoietic stem cell (HSC) function together with stem cell autonomous mechanisms. Many different cell types have been characterized as contributors to the formation of HSC niches, such as osteoblasts, endothelial cells, Schwann cells, and mesenchymal progenitors. These mesenchymal progenitors have themselves been classified as CXC chemokine ligand (CXCL) 12-abundant reticular (CAR) cells, stem cell factor expressing cells, or nestin-positive mesenchymal stem cells (MSCs), which have been recently identified as neural crest-derived cells (NCSCs). Together, these cells are spatially associated with HSCs and believed to provide appropriate microenvironments for HSC self-renewal, differentiation, mobilization and hibernation both by cell-cell contact and soluble factors. Interestingly, it appears that regulatory pathways governing the hematopoietic niche homeostasis are operating in the neurogenic niche as well. Therefore, this review paper aims to compare both the regulation of hematopoietic and neurogenic niches, in order to highlight the role of NCSCs and nervous system components in the development and the regulation of the hematopoietic system.

  16. Ecological niche dimensionality and the evolutionary diversification of stick insects.

    Directory of Open Access Journals (Sweden)

    Patrik Nosil

    Full Text Available The degree of phenotypic divergence and reproductive isolation between taxon pairs can vary quantitatively, and often increases as evolutionary divergence proceeds through various stages, from polymorphism to population differentiation, ecotype and race formation, speciation, and post-speciational divergence. Although divergent natural selection promotes divergence, it does not always result in strong differentiation. For example, divergent selection can fail to complete speciation, and distinct species pairs sometimes collapse ('speciation in reverse'. Widely-discussed explanations for this variability concern genetic architecture, and the geographic arrangement of populations. A less-explored possibility is that the degree of phenotypic and reproductive divergence between taxon pairs is positively related to the number of ecological niche dimensions (i.e., traits subject to divergent selection. Some data supporting this idea stem from laboratory experimental evolution studies using Drosophila, but tests from nature are lacking. Here we report results from manipulative field experiments in natural populations of herbivorous Timema stick insects that are consistent with this 'niche dimensionality' hypothesis. In such insects, divergent selection between host plants might occur for cryptic colouration (camouflage to evade visual predation, physiology (to detoxify plant chemicals, or both of these niche dimensions. We show that divergent selection on the single niche dimension of cryptic colouration can result in ecotype formation and intermediate levels of phenotypic and reproductive divergence between populations feeding on different hosts. However, greater divergence between a species pair involved divergent selection on both niche dimensions. Although further replication of the trends reported here is required, the results suggest that dimensionality of selection may complement genetic and geographic explanations for the degree of

  17. New directions in coral reef microbial ecology.

    Science.gov (United States)

    Garren, Melissa; Azam, Farooq

    2012-04-01

    Microbial processes largely control the health and resilience of coral reef ecosystems, and new technologies have led to an exciting wave of discovery regarding the mechanisms by which microbial communities support the functioning of these incredibly diverse and valuable systems. There are three questions at the forefront of discovery: What mechanisms underlie coral reef health and resilience? How do environmental and anthropogenic pressures affect ecosystem function? What is the ecology of microbial diseases of corals? The goal is to understand the functioning of coral reefs as integrated systems from microbes and molecules to regional and ocean-basin scale ecosystems to enable accurate predictions of resilience and responses to perturbations such as climate change and eutrophication. This review outlines recent discoveries regarding the microbial ecology of different microenvironments within coral ecosystems, and highlights research directions that take advantage of new technologies to build a quantitative and mechanistic understanding of how coral health is connected through microbial processes to its surrounding environment. The time is ripe for natural resource managers and microbial ecologists to work together to create an integrated understanding of coral reef functioning. In the context of long-term survival and conservation of reefs, the need for this work is immediate. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

  18. Megakaryocytes promote murine osteoblastic HSC niche expansion and stem cell engraftment after radioablative conditioning.

    Science.gov (United States)

    Olson, Timothy S; Caselli, Anna; Otsuru, Satoru; Hofmann, Ted J; Williams, Richard; Paolucci, Paolo; Dominici, Massimo; Horwitz, Edwin M

    2013-06-27

    Successful hematopoietic stem cell (HSC) transplantation requires donor HSC engraftment within specialized bone marrow microenvironments known as HSC niches. We have previously reported a profound remodeling of the endosteal osteoblastic HSC niche after total body irradiation (TBI), defined as relocalization of surviving megakaryocytes to the niche site and marked expansion of endosteal osteoblasts. We now demonstrate that host megakaryocytes function critically in expansion of the endosteal niche after preparative radioablation and in the engraftment of donor HSC. We show that TBI-induced migration of megakaryocytes to the endosteal niche depends on thrombopoietin signaling through the c-MPL receptor on megakaryocytes, as well as CD41 integrin-mediated adhesion. Moreover, niche osteoblast proliferation post-TBI required megakaryocyte-secreted platelet-derived growth factor-BB. Furthermore, blockade of c-MPL-dependent megakaryocyte migration and function after TBI resulted in a significant decrease in donor HSC engraftment in primary and competitive secondary transplantation assays. Finally, we administered thrombopoietin to mice beginning 5 days before marrow radioablation and ending 24 hours before transplant to enhance megakaryocyte function post-TBI, and found that this strategy significantly enhanced donor HSC engraftment, providing a rationale for improving hematopoietic recovery and perhaps overall outcome after clinical HSC transplantation.

  19. Ecological divergence and conservatism: spatiotemporal patterns of niche evolution in a genus of livebearing fishes (Poeciliidae: Xiphophorus).

    Science.gov (United States)

    Culumber, Zachary W; Tobler, Michael

    2016-02-19

    Ecological factors often have a strong impact on spatiotemporal patterns of biodiversity. The integration of spatial ecology and phylogenetics allows for rigorous tests of whether speciation is associated with niche conservatism (constraints on ecological divergence) or niche divergence. We address this question in a genus of livebearing fishes for which the role of sexual selection in speciation has long been studied, but in which the potential role of ecological divergence during speciation has not been tested. By combining reconstruction of ancestral climate tolerances and disparity indices, we show that the earliest evolutionary split in Xiphophorus was associated with significant divergence for temperature variables. Niche evolution and present day niches were most closely associated with each species' geographic distribution relative to a biogeographic barrier, the Trans-Mexican Volcanic Belt. Tests for similarity of the environmental backgrounds of closely related species suggested that the relative importance of niche conservatism and divergence during speciation varied among the primary clades of Xiphophorus. Closely related species in the two swordtail clades exhibited higher levels of niche overlap than expected given environmental background similarity indicative of niche conservatism. In contrast, almost all species of platyfish had significantly divergent niches compared to environmental backgrounds, which is indicative of niche divergence. The results suggest that the relative importance of niche conservatism and divergence differed among the clades of Xiphophorus and that traits associated with niche evolution may be more evolutionarily labile in the platyfishes. Our results ultimately suggest that the taxonomic scale of tests for conservatism and divergence could greatly influence inferences of their relative importance in the speciation process.

  20. Intestinal Stem Cell Niche: The Extracellular Matrix and Cellular Components

    Directory of Open Access Journals (Sweden)

    Laween Meran

    2017-01-01

    Full Text Available The intestinal epithelium comprises a monolayer of polarised columnar cells organised along the crypt-villus axis. Intestinal stem cells reside at the base of crypts and are constantly nourished by their surrounding niche for maintenance, self-renewal, and differentiation. The cellular microenvironment including the adjacent Paneth cells, stromal cells, smooth muscle cells, and neural cells as well as the extracellular matrix together constitute the intestinal stem cell niche. A dynamic regulatory network exists among the epithelium, stromal cells, and the matrix via complex signal transduction to maintain tissue homeostasis. Dysregulation of these biological or mechanical signals could potentially lead to intestinal injury and disease. In this review, we discuss the role of different intestinal stem cell niche components and dissect the interaction between dynamic matrix factors and regulatory signalling during intestinal stem cell homeostasis.

  1. Development and aging of a brain neural stem cell niche.

    Science.gov (United States)

    Conover, Joanne C; Todd, Krysti L

    2017-08-01

    In the anterior forebrain, along the lateral wall of the lateral ventricles, a neurogenic stem cell niche is found in a region referred to as the ventricular-subventricular zone (V-SVZ). In rodents, robust V-SVZ neurogenesis provides new neurons to the olfactory bulb throughout adulthood; however, with increasing age stem cell numbers are reduced and neurogenic capacity is significantly diminished, but new olfactory bulb neurons continue to be produced even in old age. Humans, in contrast, show little to no new neurogenesis after two years of age and whether V-SVZ neural stem cells persist in the adult human brain remains unclear. Here, we review functional and organizational differences in the V-SVZ stem cell niche of mice and humans, and examine how aging affects the V-SVZ niche and its associated functions. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Niche differentiation and expansion of plant species are associated with mycorrhizal symbiosis

    NARCIS (Netherlands)

    Gerz, Maret; Guillermo Bueno, C.; Ozinga, Wim A.; Zobel, Martin; Moora, Mari

    2018-01-01

    Mycorrhizal symbiosis is a widespread association between plant roots and mycorrhizal fungi, which is thought to contribute to plant niche differentiation and expansion. However, this has so far not been explicitly tested. To address the effect of mycorrhizal symbiosis on plants’ realized niches, we

  3. Disjunct populations of European vascular plant species keep the same climatic niches

    DEFF Research Database (Denmark)

    Wasof, Safaa; Lenoir, Jonathan; Aarrestad, Per Arild

    2015-01-01

    separated for thousands of years. Location: European Alps and Fennoscandia. Methods: Of the studied pool of 888 terrestrial vascular plant species occurring in both the Alps and Fennoscandia, we used two complementary approaches to test and quantify climatic-niche shifts for 31 species having strictly......Aim: Previous research on how climatic niches vary across species ranges has focused on a limited number of species, mostly invasive, and has not, to date, been very conclusive. Here we assess the degree of niche conservatism between distant populations of native alpine plant species that have been...... to be largely valid for arctic-alpine plants....

  4. Doctoral education in a successful ecological niche

    DEFF Research Database (Denmark)

    Christensen, Mette Krogh; Lund, Ole

    2014-01-01

    Scholarly communities are dependent on and often measured by their ability to attract and develop doctoral students. Recent literature suggests that most scholarly communities entail ecological niches in which the doctoral students learn the codes and practices of research. In this article, we...... successful doctoral education because it: 1) fleshes out the professional attitude that is necessary for becoming a successful researcher in the department, 2) shapes and adapts the doctoral students’ desires to grasp and identify with the department’s practices, and 3) provides the doctoral students...... explore the microclimate in an ecological niche of doctoral education. Based on a theoretical definition of microclimate as the emotional atmosphere that ties group members together and affects their actions, we conducted a case study that aimed to describe the key features of the microclimate...

  5. Visualization for genomics: the Microbial Genome Viewer.

    NARCIS (Netherlands)

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a

  6. Classification and comparison of niche services for developing strategy of medical tourism in Asian countries.

    Science.gov (United States)

    Chen, Hung-chi; Kuo, Hsin-chih; Chung, Kuo-Piao; Chang, Sophia; Su, Syi; Yang, Ming-chin

    2010-01-01

    Medical tourism is a new trend in medical service. It is booming not only in Asian countries but also in European and South American countries. Worldwide competition of medical service is expected in the future, and niche service will be a "trademark" for the promotion of global medicine. Niche service also functions for market segmentation. Niche services are usually surgical procedures. A study was carried out to compare different strategies for developing medical tourism in Asian countries. The role of a niche service is evaluated in the initiation and further development of medical tourism for individual countries. From this study, a general classification was proposed in terms of treatment procedures. It can be used as a useful guideline for additional studies in medical tourism. Niche service plays the following roles in the development of medical tourism: (1) It attracts attention in the mass media and helps in subsequent promotion of business, (2) it exerts pressure on the hospital, which must improve the quality of health care provided in treating foreign patients, especially the niche services, and (3) it is a tool for setting up the business model. E-Da Hospital is an example for developing medical tourism in Taiwan. A side effect is that niche service brings additional foreign patients, which will contribute to the benefit of the hospital, but this leaves less room for treating domestic patients. A niche service is a means of introduction for entry into the market of medical tourism. How to create a successful story is important for the development of a niche service. When a good reputation has been established, the information provided on the Internet can last for a long time and can spread internationally to form a distinguished mark for further development. Niche services can be classified into 3 categories: (1) Low-risk procedures with large price differences and long stay after retirement; (2) high-risk procedures with less of a price difference

  7. Bluetooth-enabled teleradiology: applications and complications.

    Science.gov (United States)

    Hura, Angela M

    2002-01-01

    Wireless personal area networks and local area networks are becoming increasingly more prevalent in the teleradiology and telemedicine industry. Although there has been much debate about the role that Bluetooth will play in the future of wireless technology, both promoters and doubters acknowledge that Bluetooth will have an impact on networking, even if only as a "niche" product. This article provides an overview of the Bluetooth standard and highlights current and future areas of inclusion for use in a teleradiology environment. The possibilities for Bluetooth in a teleradiology environment without wires are nearly boundless and an overview of current and proposed Bluetooth-enabled radiology equipment and vendors is provided. A comparison of Bluetooth and other wireless technologies is provided, including areas of similarity and potential conflict. Bluetooth and other wireless technologies can not only peacefully coexist but also complement each other and provide enhanced teleradiology services.

  8. A communal catalogue reveals Earth's multiscale microbial diversity.

    Science.gov (United States)

    Thompson, Luke R; Sanders, Jon G; McDonald, Daniel; Amir, Amnon; Ladau, Joshua; Locey, Kenneth J; Prill, Robert J; Tripathi, Anupriya; Gibbons, Sean M; Ackermann, Gail; Navas-Molina, Jose A; Janssen, Stefan; Kopylova, Evguenia; Vázquez-Baeza, Yoshiki; González, Antonio; Morton, James T; Mirarab, Siavash; Zech Xu, Zhenjiang; Jiang, Lingjing; Haroon, Mohamed F; Kanbar, Jad; Zhu, Qiyun; Jin Song, Se; Kosciolek, Tomasz; Bokulich, Nicholas A; Lefler, Joshua; Brislawn, Colin J; Humphrey, Gregory; Owens, Sarah M; Hampton-Marcell, Jarrad; Berg-Lyons, Donna; McKenzie, Valerie; Fierer, Noah; Fuhrman, Jed A; Clauset, Aaron; Stevens, Rick L; Shade, Ashley; Pollard, Katherine S; Goodwin, Kelly D; Jansson, Janet K; Gilbert, Jack A; Knight, Rob

    2017-11-23

    Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

  9. Discovery of enzymes for toluene synthesis from anoxic microbial communities

    DEFF Research Database (Denmark)

    Beller, Harry R.; Rodrigues, Andria V.; Zargar, Kamrun

    2018-01-01

    Microbial toluene biosynthesis was reported in anoxic lake sediments more than three decades ago, but the enzyme catalyzing this biochemically challenging reaction has never been identified. Here we report the toluene-producing enzyme PhdB, a glycyl radical enzyme of bacterial origin that catalyzes...... phenylacetate decarboxylation, and its cognate activating enzyme PhdA, a radical S-adenosylmethionine enzyme, discovered in two distinct anoxic microbial communities that produce toluene. The unconventional process of enzyme discovery from a complex microbial community (>300,000 genes), rather than from...... a microbial isolate, involved metagenomics- and metaproteomics-enabled biochemistry, as well as in vitro confirmation of activity with recombinant enzymes. This work expands the known catalytic range of glycyl radical enzymes (only seven reaction types had been characterized previously) and aromatic...

  10. Stem Cell Spheroids and Ex Vivo Niche Modeling: Rationalization and Scaling-Up.

    Science.gov (United States)

    Chimenti, Isotta; Massai, Diana; Morbiducci, Umberto; Beltrami, Antonio Paolo; Pesce, Maurizio; Messina, Elisa

    2017-04-01

    Improved protocols/devices for in vitro culture of 3D cell spheroids may provide essential cues for proper growth and differentiation of stem/progenitor cells (S/PCs) in their niche, allowing preservation of specific features, such as multi-lineage potential and paracrine activity. Several platforms have been employed to replicate these conditions and to generate S/PC spheroids for therapeutic applications. However, they incompletely reproduce the niche environment, with partial loss of its highly regulated network, with additional hurdles in the field of cardiac biology, due to debated resident S/PCs therapeutic potential and clinical translation. In this contribution, the essential niche conditions (metabolic, geometric, mechanical) that allow S/PCs maintenance/commitment will be discussed. In particular, we will focus on both existing bioreactor-based platforms for the culture of S/PC as spheroids, and on possible criteria for the scaling-up of niche-like spheroids, which could be envisaged as promising tools for personalized cardiac regenerative medicine, as well as for high-throughput drug screening.

  11. Removal of Microbial Contamination from Surface by Plasma

    Science.gov (United States)

    Feng, Xinxin; Liu, Hongxia; Shen, Zhenxing; Wang, Taobo

    2018-01-01

    Microbial contamination is closely associated with human and environmental health, they can be tested on food surfaces, medical devices, packing material and so on. In this paper the removal of the microbial contamination from surface using plasma treatment is investigated. The Escherichia coli (E. coli) has been chosen as a bio-indicator enabling to evaluate the effect of plasma assisted microbial inactivation. Oxygen gas was as the working gas. The plasma RF power, plasma exposition time, gas flow and the concentration of organic pollutant were varied in order to see the effect of the plasma treatment on the Gram-negative germ removal. After the treatment, the microbial abatement was evaluated by the standard plate count method. This proved a positive effect of the plasma treatment on Gram-negative germ removal. The kinetics and mathematical model of removal were studied after plasma treatment, and then the removing course of E. coli was analyzed. This work is meaningful for deepening our understanding of the fundamental scientific principles regarding microbial contamination from surface by plasma.

  12. Novel Microbial Electrochemical Technologies and Microorganisms for Power Generation and Desalination

    KAUST Repository

    Chehab, Noura A.

    2014-12-01

    Global increases in water demand and decreases in both the quantity and quality of fresh water resources have served as the major driving forces to develop sustainable use of water resources. One viable alternative is to explore non-traditional (impaired quality) water sources such as wastewater and seawater. The current paradigm for wastewater treatment is based on technologies that are energy intensive and fail to recover the potential resources (water and energy) in wastewater. Also, conventional desalination technologies like reverse osmosis (RO) are energy intensive. Therefore, there is a need for the development of sustainable wastewater treatment and desalination technologies for practical applications. Processes based on microbial electrochemical technologies (METs) such as microbial fuel cells (MFCs), microbial electrolysis cells (MECs) and microbial desalination cells (MDCs) hold promise for the treatment of wastewater with recovery of the inherent energy, and MDCs could be used for both desalination of seawater and energy recovery. METs use anaerobic bacteria, referred to as exoelectrogens, that are capable of transferring electrons exogenously to convert soluble organic matter present in the wastewater directly into an electrical current to produce electrical power (MFC and MDC) or biogas (MEC). In my dissertation, I investigated the three types of METs mentioned above to: 1) have a better insight on the effect of 4 oxygen intrusion on the microbial community structure and performance of air-cathode MFCs; 2) improve the desalination efficiency of air-cathode MDCs using ion exchange resins (IXRs); and 3) enrich for extremophilic exoelectrogens from the Red Sea brine pool using MECs. The findings from these studies can shape further research aimed at developing more efficient air-cathode MFCs for practical applications, a more efficient integrated IXRMDC configuration that can be used as a pre-treatment to RO, and exploring extreme environments as a

  13. The thermal niche of Neotropical nectar-feeding bats: Its evolution and application to predict responses to global warming.

    Science.gov (United States)

    Ortega-García, Stephanie; Guevara, Lázaro; Arroyo-Cabrales, Joaquín; Lindig-Cisneros, Roberto; Martínez-Meyer, Enrique; Vega, Ernesto; Schondube, Jorge E

    2017-09-01

    The thermal niche of a species is one of the main determinants of its ecology and biogeography. In this study, we determined the thermal niche of 23 species of Neotropical nectar-feeding bats of the subfamily Glossophaginae (Chiroptera, Phyllostomidae). We calculated their thermal niches using temperature data obtained from collection records, by generating a distribution curve of the maximum and minimum temperatures per locality, and using the inflection points of the temperature distributions to estimate the species optimal (STZ) and suboptimal (SRZ) zones of the thermal niche. Additionally, by mapping the values of the STZ and SRZ on a phylogeny of the group, we generated a hypothesis of the evolution of the thermal niches of this clade of nectar-feeding bats. Finally, we used the characteristics of their thermal niches to predict the responses of these organisms to climate change. We found a large variation in the width and limits of the thermal niches of nectar-feeding bats. Additionally, while the upper limits of the thermal niches varied little among species, their lower limits differ wildly. The ancestral reconstruction of the thermal niche indicated that this group of Neotropical bats evolved under cooler temperatures. The two clades inside the Glossophaginae differ in the evolution of their thermal niches, with most members of the clade Choeronycterines evolving "colder" thermal niches, while the majority of the species in the clade Glossophagines evolving "warmer" thermal niches. By comparing thermal niches with climate change models, we found that all species could be affected by an increase of 1°C in temperature at the end of this century. This suggests that even nocturnal species could suffer important physiological costs from global warming. Our study highlights the value of scientific collections to obtain ecologically significant physiological data for a large number of species.

  14. Niche Extracellular Matrix Components and Their Influence on HSC.

    Science.gov (United States)

    Domingues, Mélanie J; Cao, Huimin; Heazlewood, Shen Y; Cao, Benjamin; Nilsson, Susan K

    2017-08-01

    Maintenance of hematopoietic stem cells (HSC) takes place in a highly specialized microenvironment within the bone marrow. Technological improvements, especially in the field of in vivo imaging, have helped unravel the complexity of the niche microenvironment and have completely changed the classical concept from what was previously believed to be a static supportive platform, to a dynamic microenvironment tightly regulating HSC homeostasis through the complex interplay between diverse cell types, secreted factors, extracellular matrix molecules, and the expression of different transmembrane receptors. To add to the complexity, non-protein based metabolites have also been recognized as a component of the bone marrow niche. The objective of this review is to discuss the current understanding on how the different extracellular matrix components of the niche regulate HSC fate, both during embryonic development and in adulthood. Special attention will be provided to the description of non-protein metabolites, such as lipids and metal ions, which contribute to the regulation of HSC behavior. J. Cell. Biochem. 118: 1984-1993, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  15. Emerging mass spectrometry techniques for the direct analysis of microbial colonies

    OpenAIRE

    Fang, Jinshu; Dorrestein, Pieter C.

    2014-01-01

    One of the emerging areas in microbiology is detecting specialized metabolites produced by microbial colonies and communities with mass spectrometry. In this review/perspective, we illustrate the emerging mass spectrometry methodologies that enable the interrogation of specialized metabolites directly from microbial colonies. Mass spectrometry techniques such as imaging mass spectrometry and real-time mass spectrometry allow two and three dimensional visualization of the distri...

  16. Toward a microbial Neolithic revolution in buildings.

    Science.gov (United States)

    Thaler, David S

    2016-03-29

    The Neolithic revolution--the transition of our species from hunter and gatherer to cultivator--began approximately 14,000 years ago and is essentially complete for macroscopic food. Humans remain largely pre-Neolithic in our relationship with microbes but starting with the gut we continue our hundred-year project of approaching the ability to assess and cultivate benign microbiomes in our bodies. Buildings are analogous to the body and it is time to ask what it means to cultivate benign microbiomes in our built environment. A critical distinction is that we have not found, or invented, niches in buildings where healthful microbial metabolism occurs and/or could be cultivated. Key events affecting the health and healthfulness of buildings such as a hurricane leading to a flood or a burst pipe occur only rarely and unpredictably. The cause may be transient but the effects can be long lasting and, e.g., for moisture damage, cumulative. Non-invasive "building tomography" could find moisture and "sentinel microbes" could record the integral of transient growth. "Seed" microbes are metabolically inert cells able to grow when conditions allow. All microbes and their residue present actinic molecules including immunological epitopes (molecular shapes). The fascinating hygiene and microbial biodiversity hypotheses propose that a healthy immune system requires exposure to a set of microbial epitopes that is rich in diversity. A particular conjecture is that measures of the richness of diversity derived from microbiome next-generation sequencing (NGS) can be mechanistically coupled to--rather than merely correlated with some measures of--human health. These hypotheses and conjectures inspire workers and funders but an alternative is also consequent to the first Neolithic revolution: That the genetic uniformity of contemporary foods may also decrease human exposure to molecular biodiversity in a heath-relevant manner. Understanding the consequences--including the unintended

  17. Synthetic Klebsiella pneumoniae-Shewanella oneidensis Consortium Enables Glycerol-Fed High-Performance Microbial Fuel Cells.

    Science.gov (United States)

    Li, Feng; Yin, Changji; Sun, Liming; Li, Yuanxiu; Guo, Xuewu; Song, Hao

    2018-05-01

    Microbial fuel cell (MFC) is an eco-friendly bio-electrochemical sys-tem that uses microorganism as biocatalyst to convert biomass into electricity. Glycerol, as a waste in the biodiesel refinery processes, is an appealing substrate for MFC. Nevertheless, glycerol cannot be utilized as carbon source by well-known exoelectrogens such as Shewanella oneidensis. Herein, to generate electricity by rapidly harnessing glycerol, the authors rationally constructed a Klebsiella pneumoniae-Shewanella oneidensis microbial consortium to efficiently harvest electricity from glyc-erol, in which K. pneumoniae converted glycerol into lactate, fed to S. oneidensis as carbon source and electron donor. To improve electricity output, the authors systematically engineered the consortium in terms of carbon flux distribution and efficiency of extracellular electron transfer (EET). To direct more carbon flux to lactate biosynthesis in K. pneumoniae, the authors eliminated the ethanol pathway by knocking out the alcohol dehydrogenase gene (adhE), and enhanced lactate biosynthesis by heterologously expressing a lactate dehydrogen-ase gene (ldhD) from Lactobacillus bulgaricus and a lactate transporter gene (lldP) from Escherichia coli. To facilitate EET between S. oneidensis and anode surfaces, a biosynthetic flavins pathway from Bacillus subtilis is introduced into S. oneidensis. The author further optimized the glycerol concentration, thus S. oneidensis could be continuously fed with lactate synthesized from K. pneumoniae at a constant rate. Our glycerol-fed MFC generated a maximum power density of 19.9 mW/m 2 , significantly higher than that of the wild-type consor-tium. This work suggested that engineering microbial consortia is an effi-cient strategy to expand the spectrum of usable carbon sources and promote electricity power production in MFCs. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Mechanistic species distribution modeling reveals a niche shift during invasion.

    Science.gov (United States)

    Chapman, Daniel S; Scalone, Romain; Štefanić, Edita; Bullock, James M

    2017-06-01

    Niche shifts of nonnative plants can occur when they colonize novel climatic conditions. However, the mechanistic basis for niche shifts during invasion is poorly understood and has rarely been captured within species distribution models. We quantified the consequence of between-population variation in phenology for invasion of common ragweed (Ambrosia artemisiifolia L.) across Europe. Ragweed is of serious concern because of its harmful effects as a crop weed and because of its impact on public health as a major aeroallergen. We developed a forward mechanistic species distribution model based on responses of ragweed development rates to temperature and photoperiod. The model was parameterized and validated from the literature and by reanalyzing data from a reciprocal common garden experiment in which native and invasive populations were grown within and beyond the current invaded range. It could therefore accommodate between-population variation in the physiological requirements for flowering, and predict the potentially invaded ranges of individual populations. Northern-origin populations that were established outside the generally accepted climate envelope of the species had lower thermal requirements for bud development, suggesting local adaptation of phenology had occurred during the invasion. The model predicts that this will extend the potentially invaded range northward and increase the average suitability across Europe by 90% in the current climate and 20% in the future climate. Therefore, trait variation observed at the population scale can trigger a climatic niche shift at the biogeographic scale. For ragweed, earlier flowering phenology in established northern populations could allow the species to spread beyond its current invasive range, substantially increasing its risk to agriculture and public health. Mechanistic species distribution models offer the possibility to represent niche shifts by varying the traits and niche responses of individual

  19. [Niche and interspecific association of the dominant fish in the south coastal waters of Wenzhou, China].

    Science.gov (United States)

    Dong, Jing Rui; Shui, Bo Nian; Hu, Cheng Ye; Shui, Yu Yue; DU, Xiao; Tian, Kuo

    2017-05-18

    The studies about the niche and interspecific association in China were mainly focused on the plants, birds and marine animals, and seldom on fish. Based on the fishery resources survey in spring (May) and autumn (September) in 2015, the associations among major fish species in south coastal waters of Wenzhou were investigated. The methods including niche breadth, niche overlap, variance ratio (VR), Χ 2 -test, association coefficient (AC), percentage of co-occurrence (PC) and point correlation coefficients (Ф) were used. The results showed that 47 fish species were identified, including 9 orders, 27 families and 41 genera. Four species were dominant species and 9 were important species, which together accounted for 17%. The niche breadth cluster analysis demonstrated two clearly identifiable ecological niches. The first one referred to wide niche that included Harpodon nehereus, Collichthys lucidus, Engraulis japonicas, Pampus echinogaster, Argyrosomus argentatus, Polynemus sextarius, Decapterus maruadsi and Trichiurus haumela, and the second one was narrow niche that included Muraenesox cinereus, Amblychaeturichthys hexanema, Cunoglossus robustus, Pseudosciaena polyactis and Ilisha elongate. The niche overlap value of the main fish was 0-0.90, indicating that there was difference in the resource utilization among the species. The ecological niche widths of C. robustus and M. cinereus were narrow, and the overlap values were high. This indicated that there was competition between these two species. The VR analysis revealed significant positive correlation among the main fish species. In view of the advantages of Ф value, which could reduce the impact of the analysis results of Χ 2 -test, AC and PC to the interspecific association, the Ф value method was selected in this study, and the association of 63 couples were positive. Both the interspecific association and ecological niche had different degrees of correlation with the stability of community structure

  20. Divergence is not enough: the use of ecological niche models for the validation of taxon boundaries.

    Science.gov (United States)

    Dagnino, D; Minuto, L; Casazza, G

    2017-11-01

    Delimiting taxon boundaries is crucial for any evolutionary research and conservation regulation. In order to avoid mistaken description of species, the approach of integrative taxonomy recommends considering multidisciplinary lines of evidence, including ecology. Unfortunately, ecological data are often difficult to quantify objectively. Here we test and discuss the potential use of ecological niche models for validating taxon boundaries, using three pairs of closely related plant taxa endemic to the south-western Alps as a case study. We also discuss the application of ecological niche models for species delimitation and the implementation of different approaches. Niche overlap, niche equivalency and niche similarity were assessed both in multidimensional environmental space and in geographic space to look for differences in the niche of three pairs of closely related plant taxa. We detected a high degree of niche differentiation between taxa although this result seems not due to differences in habitat selection. The different statistical tests gave contrasting outcomes between environmental and geographic spaces. According to our results, niche divergence does not seem to support taxon boundaries at species level, but may have had important consequences for local adaptation and in generating phenotypic diversity at intraspecific level. Environmental space analysis should be preferred to geographic space as it provides more clear results. Even if the different analyses widely disagree in their conclusions about taxon boundaries, our study suggests that ecological niche models may help taxonomists to reach a decision. © 2017 German Botanical Society and The Royal Botanical Society of the Netherlands.

  1. A hybrid niched-island genetic algorithm applied to a nuclear core optimization problem

    International Nuclear Information System (INIS)

    Pereira, Claudio M.N.A.

    2005-01-01

    Diversity maintenance is a key-feature in most genetic-based optimization processes. The quest for such characteristic, has been motivating improvements in the original genetic algorithm (GA). The use of multiple populations (called islands) has demonstrating to increase diversity, delaying the genetic drift. Island Genetic Algorithms (IGA) lead to better results, however, the drift is only delayed, but not avoided. An important advantage of this approach is the simplicity and efficiency for parallel processing. Diversity can also be improved by the use of niching techniques. Niched Genetic Algorithms (NGA) are able to avoid the genetic drift, by containing evolution in niches of a single-population GA, however computational cost is increased. In this work it is investigated the use of a hybrid Niched-Island Genetic Algorithm (NIGA) in a nuclear core optimization problem found in literature. Computational experiments demonstrate that it is possible to take advantage of both, performance enhancement due to the parallelism and drift avoidance due to the use of niches. Comparative results shown that the proposed NIGA demonstrated to be more efficient and robust than an IGA and a NGA for solving the proposed optimization problem. (author)

  2. Single-cell analyses identify bioengineered niches for enhanced maintenance of hematopoietic stem cells.

    Science.gov (United States)

    Roch, Aline; Giger, Sonja; Girotra, Mukul; Campos, Vasco; Vannini, Nicola; Naveiras, Olaia; Gobaa, Samy; Lutolf, Matthias P

    2017-08-09

    The in vitro expansion of long-term hematopoietic stem cells (HSCs) remains a substantial challenge, largely because of our limited understanding of the mechanisms that control HSC fate choices. Using single-cell multigene expression analysis and time-lapse microscopy, here we define gene expression signatures and cell cycle hallmarks of murine HSCs and the earliest multipotent progenitors (MPPs), and analyze systematically single HSC fate choices in culture. Our analysis revealed twelve differentially expressed genes marking the quiescent HSC state, including four genes encoding cell-cell interaction signals in the niche. Under basal culture conditions, most HSCs rapidly commit to become early MPPs. In contrast, when we present ligands of the identified niche components such as JamC or Esam within artificial niches, HSC cycling is reduced and long-term multipotency in vivo is maintained. Our approach to bioengineer artificial niches should be useful in other stem cell systems.Haematopoietic stem cell (HSC) self-renewal is not sufficiently understood to recapitulate in vitro. Here, the authors generate gene signature and cell cycle hallmarks of single murine HSCs, and use identified endothelial receptors Esam and JamC as substrates to enhance HSC growth in engineered niches.

  3. When should we expect microbial phenotypic traits to predict microbial abundances?

    Directory of Open Access Journals (Sweden)

    Jeremy W. Fox

    2012-08-01

    Full Text Available Species’ phenotypic traits may predict their relative abundances. Intuitively, this is because locally-abundant species have traits making them well adapted to local abiotic and biotic conditions, while locally-rare species are not as well-adapted. But this intuition may not be valid. If competing species vary in how well-adapted they are to local conditions, why doesn’t the best-adapted species simply exclude the others entirely? But conversely, if species exhibit niche differences that allow them to coexist, then by definition there is no single best adapted species. Rather, demographic rates depend on species’ relative abundances, so that phenotypic traits conferring high adaptedness do not necessarily confer high abundance. I illustrate these points using a simple theoretical model incorporating adjustable levels of "adaptedness" and "niche differences". Even very small niche differences can weaken or even reverse the expected correlation between adaptive traits and abundance. Conversely, adaptive traits confer high abundance when niche differences are very strong. Future work should be directed towards understanding the link between phenotypic traits and frequency-dependence of demographic rates.

  4. When should we expect microbial phenotypic traits to predict microbial abundances?

    Science.gov (United States)

    Fox, Jeremy W

    2012-01-01

    Species' phenotypic traits may predict their relative abundances. Intuitively, this is because locally abundant species have traits making them well-adapted to local abiotic and biotic conditions, while locally rare species are not as well-adapted. But this intuition may not be valid. If competing species vary in how well-adapted they are to local conditions, why doesn't the best-adapted species simply exclude the others entirely? But conversely, if species exhibit niche differences that allow them to coexist, then by definition there is no single best adapted species. Rather, demographic rates depend on species' relative abundances, so that phenotypic traits conferring high adaptedness do not necessarily confer high abundance. I illustrate these points using a simple theoretical model incorporating adjustable levels of "adaptedness" and "niche differences." Even very small niche differences can weaken or even reverse the expected correlation between adaptive traits and abundance. Conversely, adaptive traits confer high abundance when niche differences are very strong. Future work should be directed toward understanding the link between phenotypic traits and frequency-dependence of demographic rates.

  5. Urban niche dynamics of Kaifeng city%开封市的城市生态位变化分析

    Institute of Scientific and Technical Information of China (English)

    丁圣彦; 李志恒

    2007-01-01

    Niche theory is one of the most important ecological theories. It is widely applied to analyzing such phenomena as competition among, and evolution of, urban ecosystem functional modules. This paper describes a study concerningdifferent functional modules of Kaifeng city urban ecosystem. Niche theory and techniques were used to analyze the changes of these functional modules in the period 1994-2003. The results showed that, in the period 1994-2003: (1) Niche value of the atmospheric environment and urban virescence modules increased, while niche value of the water environment and sound environment modules decreased; (2) niche value of the tertiary industry module increased, niche value of the secondary industry module decreased, while niche value of the primary industry module showed little change; and (3) niche value of the infrastructure, resource distribution, and production & social security modules increased, while niche value of the population module decreased. This study may contribute to macroscopic planning of urban functional modules,economic development, and environmental protection.

  6. Bridging the Service Divide: Dual Labor Niches and Embedded Opportunities in Restaurant Work

    Directory of Open Access Journals (Sweden)

    Eli R. Wilson

    2018-01-01

    Full Text Available Restaurants and other interactive service workplaces in the United States serve as labor niches for two very different kinds of workers doing different tasks. Immigrant Latinos primarily work “back-of-the-house” jobs doing manual tasks, while class-privileged whites work “front-of-the-house” jobs performing customer-facing tasks. How do these social and structural cleavages between dual labor niches affect the workplace dynamic? Drawing on ethnographic research in upscale Los Angeles restaurants, I describe the closed boundaries between these distinct labor niches and the valuable bridging between them performed by certain workers who are able to ease social tensions and buffer the service labor process. I discuss the implications of these findings for the study of contemporary immigrant labor niches and the nature of the opportunities within them and between them.

  7. Identification of hepatic niche harboring human acute lymphoblastic leukemic cells via the SDF-1/CXCR4 axis.

    Directory of Open Access Journals (Sweden)

    Itaru Kato

    Full Text Available In acute lymphoblastic leukemia (ALL patients, the bone marrow niche is widely known to be an important element of treatment response and relapse. Furthermore, a characteristic liver pathology observed in ALL patients implies that the hepatic microenvironment provides an extramedullary niche for leukemic cells. However, it remains unclear whether the liver actually provides a specific niche. The mechanism underlying this pathology is also poorly understood. Here, to answer these questions, we reconstituted the histopathology of leukemic liver by using patients-derived primary ALL cells into NOD/SCID/Yc (null mice. The liver pathology in this model was similar to that observed in the patients. By using this model, we clearly demonstrated that bile duct epithelial cells form a hepatic niche that supports infiltration and proliferation of ALL cells in the liver. Furthermore, we showed that functions of the niche are maintained by the SDF-1/CXCR4 axis, proposing a novel therapeutic approach targeting the extramedullary niche by inhibition of the SDF-1/CXCR4 axis. In conclusion, we demonstrated that the liver dissemination of leukemia is not due to nonselective infiltration, but rather systematic invasion and proliferation of leukemic cells in hepatic niche. Although the contribution of SDF-1/CXCR4 axis is reported in some cancer cells or leukemic niches such as bone marrow, we demonstrated that this axis works even in the extramedullary niche of leukemic cells. Our findings form the basis for therapeutic approaches that target the extramedullary niche by inhibiting the SDF-1/CXCR4 axis.

  8. Secreted protein Del-1 regulates myelopoiesis in the hematopoietic stem cell niche.

    Science.gov (United States)

    Mitroulis, Ioannis; Chen, Lan-Sun; Singh, Rashim Pal; Kourtzelis, Ioannis; Economopoulou, Matina; Kajikawa, Tetsuhiro; Troullinaki, Maria; Ziogas, Athanasios; Ruppova, Klara; Hosur, Kavita; Maekawa, Tomoki; Wang, Baomei; Subramanian, Pallavi; Tonn, Torsten; Verginis, Panayotis; von Bonin, Malte; Wobus, Manja; Bornhäuser, Martin; Grinenko, Tatyana; Di Scala, Marianna; Hidalgo, Andres; Wielockx, Ben; Hajishengallis, George; Chavakis, Triantafyllos

    2017-10-02

    Hematopoietic stem cells (HSCs) remain mostly quiescent under steady-state conditions but switch to a proliferative state following hematopoietic stress, e.g., bone marrow (BM) injury, transplantation, or systemic infection and inflammation. The homeostatic balance between quiescence, self-renewal, and differentiation of HSCs is strongly dependent on their interactions with cells that constitute a specialized microanatomical environment in the BM known as the HSC niche. Here, we identified the secreted extracellular matrix protein Del-1 as a component and regulator of the HSC niche. Specifically, we found that Del-1 was expressed by several cellular components of the HSC niche, including arteriolar endothelial cells, CXCL12-abundant reticular (CAR) cells, and cells of the osteoblastic lineage. Del-1 promoted critical functions of the HSC niche, as it regulated long-term HSC (LT-HSC) proliferation and differentiation toward the myeloid lineage. Del-1 deficiency in mice resulted in reduced LT-HSC proliferation and infringed preferentially upon myelopoiesis under both steady-state and stressful conditions, such as hematopoietic cell transplantation and G-CSF- or inflammation-induced stress myelopoiesis. Del-1-induced HSC proliferation and myeloid lineage commitment were mediated by β3 integrin on hematopoietic progenitors. This hitherto unknown Del-1 function in the HSC niche represents a juxtacrine homeostatic adaptation of the hematopoietic system in stress myelopoiesis.

  9. Niche conservatism and dispersal limitation cause large-scale phylogenetic structure in the New World palm flora

    DEFF Research Database (Denmark)

    Eiserhardt, Wolf L.; Svenning, J.-C.; Baker, William J.

    similarity decays after speciation depends on the rates of niche evolution and dispersal. If dispersal is slow compared to the tempo of lineage diversification, distributions change little during clade diversification. Phylogenetic niche conservatism precludes distributional shifts in environmental space......, and to the degree that distributions are limited by the niche, also in geographic space. Using phylogenetic turnover methods, we simultaneously analysed the distributions of all New World palms (n=547) and inferred to which degree phylogenetic niche conservatism and dispersal limitation, respectively, caused...

  10. Current and future niche of North and Central American sand flies (Diptera: psychodidae in climate change scenarios.

    Directory of Open Access Journals (Sweden)

    David Moo-Llanes

    Full Text Available Ecological niche models are useful tools to infer potential spatial and temporal distributions in vector species and to measure epidemiological risk for infectious diseases such as the Leishmaniases. The ecological niche of 28 North and Central American sand fly species, including those with epidemiological relevance, can be used to analyze the vector's ecology and its association with transmission risk, and plan integrated regional vector surveillance and control programs. In this study, we model the environmental requirements of the principal North and Central American phlebotomine species and analyze three niche characteristics over future climate change scenarios: i potential change in niche breadth, ii direction and magnitude of niche centroid shifts, iii shifts in elevation range. Niche identity between confirmed or incriminated Leishmania vector sand flies in Mexico, and human cases were analyzed. Niche models were constructed using sand fly occurrence datapoints from Canada, USA, Mexico, Guatemala and Belize. Nine non-correlated bioclimatic and four topographic data layers were used as niche components using GARP in OpenModeller. Both B2 and A2 climate change scenarios were used with two general circulation models for each scenario (CSIRO and HadCM3, for 2020, 2050 and 2080. There was an increase in niche breadth to 2080 in both scenarios for all species with the exception of Lutzomyia vexator. The principal direction of niche centroid displacement was to the northwest (64%, while the elevation range decreased greatest for tropical, and least for broad-range species. Lutzomyia cruciata is the only epidemiologically important species with high niche identity with that of Leishmania spp. in Mexico. Continued landscape modification in future climate change will provide an increased opportunity for the geographic expansion of NCA sand flys' ENM and human exposure to vectors of Leishmaniases.

  11. Current and Future Niche of North and Central American Sand Flies (Diptera: Psychodidae) in Climate Change Scenarios

    Science.gov (United States)

    Moo-Llanes, David; Ibarra-Cerdeña, Carlos N.; Rebollar-Téllez, Eduardo A.; Ibáñez-Bernal, Sergio; González, Camila; Ramsey, Janine M.

    2013-01-01

    Ecological niche models are useful tools to infer potential spatial and temporal distributions in vector species and to measure epidemiological risk for infectious diseases such as the Leishmaniases. The ecological niche of 28 North and Central American sand fly species, including those with epidemiological relevance, can be used to analyze the vector's ecology and its association with transmission risk, and plan integrated regional vector surveillance and control programs. In this study, we model the environmental requirements of the principal North and Central American phlebotomine species and analyze three niche characteristics over future climate change scenarios: i) potential change in niche breadth, ii) direction and magnitude of niche centroid shifts, iii) shifts in elevation range. Niche identity between confirmed or incriminated Leishmania vector sand flies in Mexico, and human cases were analyzed. Niche models were constructed using sand fly occurrence datapoints from Canada, USA, Mexico, Guatemala and Belize. Nine non-correlated bioclimatic and four topographic data layers were used as niche components using GARP in OpenModeller. Both B2 and A2 climate change scenarios were used with two general circulation models for each scenario (CSIRO and HadCM3), for 2020, 2050 and 2080. There was an increase in niche breadth to 2080 in both scenarios for all species with the exception of Lutzomyia vexator. The principal direction of niche centroid displacement was to the northwest (64%), while the elevation range decreased greatest for tropical, and least for broad-range species. Lutzomyia cruciata is the only epidemiologically important species with high niche identity with that of Leishmania spp. in Mexico. Continued landscape modification in future climate change will provide an increased opportunity for the geographic expansion of NCA sand flys' ENM and human exposure to vectors of Leishmaniases. PMID:24069478

  12. COREMIC: a web-tool to search for a niche associated CORE MICrobiome

    Directory of Open Access Journals (Sweden)

    Richard R. Rodrigues

    2018-02-01

    Full Text Available Microbial diversity on earth is extraordinary, and soils alone harbor thousands of species per gram of soil. Understanding how this diversity is sorted and selected into habitat niches is a major focus of ecology and biotechnology, but remains only vaguely understood. A systems-biology approach was used to mine information from databases to show how it can be used to answer questions related to the core microbiome of habitat-microbe relationships. By making use of the burgeoning growth of information from databases, our tool “COREMIC” meets a great need in the search for understanding niche partitioning and habitat-function relationships. The work is unique, furthermore, because it provides a user-friendly statistically robust web-tool (http://coremic2.appspot.com or http://core-mic.com, developed using Google App Engine, to help in the process of database mining to identify the “core microbiome” associated with a given habitat. A case study is presented using data from 31 switchgrass rhizosphere community habitats across a diverse set of soil and sampling environments. The methodology utilizes an outgroup of 28 non-switchgrass (other grasses and forbs to identify a core switchgrass microbiome. Even across a diverse set of soils (five environments, and conservative statistical criteria (presence in more than 90% samples and FDR q-val <0.05% for Fisher’s exact test a core set of bacteria associated with switchgrass was observed. These included, among others, closely related taxa from Lysobacter spp., Mesorhizobium spp, and Chitinophagaceae. These bacteria have been shown to have functions related to the production of bacterial and fungal antibiotics and plant growth promotion. COREMIC can be used as a hypothesis generating or confirmatory tool that shows great potential for identifying taxa that may be important to the functioning of a habitat (e.g. host plant. The case study, in conclusion, shows that COREMIC can identify key habitat

  13. Strategic niche management and sustainable innovation journeys : theory, findings, research agenda, and policy

    NARCIS (Netherlands)

    Schot, J.W.; Geels, F.W.

    2008-01-01

    This article discusses empirical findings and conceptual elaborations of the last 10 years in strategic niche management research (SNM). The SNM approach suggests that sustainable innovation journeys can be facilitated by creating technological niches, i.e. protected spaces that allow the

  14. Intersexual Trophic Niche Partitioning in an Ant-Eating spider (Araneae: Zodariidae)

    DEFF Research Database (Denmark)

    Pekár, Stanislav; Martisová, Martina; Bilde, T.

    2011-01-01

    lead to higher energy demands in females driven by fecundity selection, while males invest in mate searching. We tested predictions of the two hypotheses underlying intersexual trophic niche partitioning in a natural population of spiders. Zodarion jozefienae spiders specialize on Messor barbarus ants...... that are polymorphic in body size and hence comprise potential trophic niches for the spider, making this system well-suited to study intersexual trophic niche partitioning. Methodology/Principal Findings Comparative analysis of trophic morphology (the chelicerae) and body size of males, females and juveniles...... demonstrated highly female biased SSD (Sexual Size Dimorphism) in body size, body weight, and in the size of chelicerae, the latter arising from sex-specific growth patterns in trophic morphology. In the field, female spiders actively selected ant sub-castes that were larger than the average prey size...

  15. A Mosaic of Geothermal and Marine Features Shapes Microbial Community Structure on Deception Island Volcano, Antarctica

    Directory of Open Access Journals (Sweden)

    Amanda G. Bendia

    2018-05-01

    Full Text Available Active volcanoes in Antarctica contrast with their predominantly cold surroundings, resulting in environmental conditions capable of selecting for versatile and extremely diverse microbial communities. This is especially true on Deception Island, where geothermal, marine, and polar environments combine to create an extraordinary range of environmental conditions. Our main goal in this study was to understand how microbial community structure is shaped by gradients of temperature, salinity, and geochemistry in polar marine volcanoes. Thereby, we collected surface sediment samples associated with fumaroles and glaciers at two sites on Deception, with temperatures ranging from 0 to 98°C. Sequencing of the 16S rRNA gene was performed to assess the composition and diversity of Bacteria and Archaea. Our results revealed that Deception harbors a combination of taxonomic groups commonly found both in cold and geothermal environments of continental Antarctica, and also groups normally identified at deep and shallow-sea hydrothermal vents, such as hyperthermophilic archaea. We observed a clear separation in microbial community structure across environmental gradients, suggesting that microbial community structure is strongly niche driven on Deception. Bacterial community structure was significantly associated with temperature, pH, salinity, and chemical composition; in contrast, archaeal community structure was strongly associated only with temperature. Our work suggests that Deception represents a peculiar “open-air” laboratory to elucidate central questions regarding molecular adaptability, microbial evolution, and biogeography of extremophiles in polar regions.

  16. Macrophages Contribute to the Spermatogonial Niche in the Adult Testis

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    Tony DeFalco

    2015-08-01

    Full Text Available The testis produces sperm throughout the male reproductive lifespan by balancing self-renewal and differentiation of spermatogonial stem cells (SSCs. Part of the SSC niche is thought to lie outside the seminiferous tubules of the testis; however, specific interstitial components of the niche that regulate spermatogonial divisions and differentiation remain undefined. We identified distinct populations of testicular macrophages, one of which lies on the surface of seminiferous tubules, in close apposition to areas of tubules enriched for undifferentiated spermatogonia. These macrophages express spermatogonial proliferation- and differentiation-inducing factors, such as colony-stimulating factor 1 (CSF1 and enzymes involved in retinoic acid (RA biosynthesis. We show that transient depletion of macrophages leads to a disruption in spermatogonial differentiation. These findings reveal an unexpected role for macrophages in the spermatogonial niche in the testis and raise the possibility that macrophages play previously unappreciated roles in stem/progenitor cell regulation in other tissues.

  17. The extraocular muscle stem cell niche is resistant to ageing and disease

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    Luigi eFormicola

    2014-12-01

    Full Text Available Specific muscles are spared in many degenerative myopathies. Most notably, the extraocular muscles (EOMs do not show clinical signs of late stage myopathies including the accumulation of fibrosis and fat. It has been proposed that an altered stem cell niche underlies the resistance of EOMs in these pathologies, however, to date, no reports have provided a detailed characterization of the EOM stem cell niche. PW1/Peg3 is expressed in progenitor cells in all adult tissues including satellite cells and a subset of interstitial non-satellite cell progenitors in muscle. These PW1-positive interstitial cells (PICs include a fibroadipogenic progenitor population (FAPs that give rise to fat and fibrosis in late stage myopathies. PICs/FAPs are mobilized following injury and FAPs exert a promyogenic role upon myoblasts in vitro but require the presence of a minimal population of satellite cells in vivo. We and others recently described that FAPs express promyogenic factors while satellite cells express antimyogenic factors suggesting that PICs/FAPs act as support niche cells in skeletal muscle through paracrine interactions. We analyzed the EOM stem cell niche in young adult and aged wild-type mice and found that the balance between PICs and satellite cells within the EOM stem cell niche is maintained throughout life. Moreover, in the adult mdx mouse model for Duchenne muscular dystrophy, the EOM stem cell niche is unperturbed compared to normal mice, in contrast to Tibialis Anterior (TA muscle, which displays signs of ongoing degeneration/regeneration. Regenerating mdx TA shows increased levels of both PICs and satellite cells, comparable to normal unaffected EOMs. We propose that the increase in PICs that we observe in normal EOMs contributes to preserving the integrity of the myofibers and satellite cells. Our data suggest that molecular cues regulating muscle regeneration are intrinsic properties of EOMs.

  18. Niche versus neutrality: a dynamical analysis

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    Michael Kalyuzhny; Efrat Seri; Rachel Chocron; Curtis H. Flather; Ronen Kadmon; Nadav M. Shnerb

    2014-01-01

    Understanding the forces shaping ecological communities is of crucial importance for basic science and conservation. After 50 years in which ecological theory has focused on either stable communities driven by niche-based forces or nonstable “neutral” communities driven by demographic stochasticity, contemporary theories suggest that ecological communities are driven...

  19. Aligning the Measurement of Microbial Diversity with Macroecological Theory

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    James C. Stegen

    2016-09-01

    Full Text Available The number of microbial operational taxonomic units (OTUs within a community is akin to species richness within plant/animal (‘macrobial’ systems. A large literature documents OTU richness patterns, drawing comparisons to macrobial theory. There is, however, an unrecognized fundamental disconnect between OTU richness and macrobial theory: OTU richness is commonly estimated on a per-individual basis, while macrobial richness is estimated per-area. Furthermore, the range or extent of sampled environmental conditions can strongly influence a study’s outcomes and conclusions, but this is not commonly addressed when studying OTU richness. Here we (i propose a new sampling approach that estimates OTU richness per-mass of soil, which results in strong support for species energy theory, (ii use data reduction to show how support for niche conservatism emerges when sampling across a restricted range of environmental conditions, and (iii show how additional insights into drivers of OTU richness can be generated by combining different sampling methods while simultaneously considering patterns that emerge by restricting the range of environmental conditions. We propose that a more rigorous connection between microbial ecology and macrobial theory can be facilitated by exploring how changes in OTU richness units and environmental extent influence outcomes of data analysis. While fundamental differences between microbial and macrobial systems persist (e.g., species concepts, we suggest that closer attention to units and scale provide tangible and immediate improvements to our understanding of the processes governing OTU richness and how those processes relate to drivers of macrobial species richness.

  20. The niche construction of cultural complexity: interactions between innovations, population size and the environment.

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    Fogarty, Laurel; Creanza, Nicole

    2017-12-05

    Niche construction is a process through which organisms alter their environments and, in doing so, influence or change the selective pressures to which they are subject. 'Cultural niche construction' refers specifically to the effect of cultural traits on the selective environments of other biological or cultural traits and may be especially important in human evolution. In addition, the relationship between population size and cultural accumulation has been the subject of extensive debate, in part because anthropological studies have demonstrated a significant association between population size and toolkit complexity in only a subset of studied cultures. Here, we review the role of cultural innovation in constructing human evolutionary niches and introduce a new model to describe the accumulation of human cultural traits that incorporates the effects of cultural niche construction. We consider the results of this model in light of available data on human toolkit sizes across populations to help elucidate the important differences between food-gathering societies and food-producing societies, in which niche construction may be a more potent force. These results support the idea that a population's relationship with its environment, represented here by cultural niche construction, should be considered alongside population size in studies of cultural complexity.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'. © 2017 The Author(s).

  1. The malignant niche: safe spaces for toxic stem cell marketing.

    Science.gov (United States)

    Sipp, Douglas

    2017-01-01

    Many tumors are sustained by microenvironments, or niches, that support and protect malignant cells, thus conferring a competitive advantage against both healthy cells and therapeutic interventions (for a brief review, see Yao and Link (Stem Cells 35: 3-8, 2017)). The global industry engaged in the commercial promotion of unproven and scientifically implausible cell-based "regenerative" therapies has developed a number of self-protective strategies that support its survival and growth in ways that are broadly analogous to the functions of the malignant niche.

  2. The Microbial Contamination of Mobile Communication Devices

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    Joanna Verran

    2012-02-01

    Full Text Available This tip describes a simple laboratory exercise to assess the microbial contamination of mobile phones, and suggests extension work that enables additional exploration of the topic. At its most basic, it is suitable for the school classroom; more advanced development of the suggested activities are suitable for undergraduate project work.

  3. Niche construction and the evolution of leadership

    NARCIS (Netherlands)

    Spisak, B.R.; O'Brien, M.; Nicholson, N.; van Vugt, M.

    2015-01-01

    We use the concept of niche construction - the process whereby individuals, through their activities, interactions, and choices, modify their own and each other's environments - as an example of how biological evolution and cultural evolution interacted to form an integrative foundation of modern

  4. Niche tracking and rapid establishment of distributional equilibrium in the house sparrow show potential responsiveness of species to climate change.

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    William B Monahan

    Full Text Available The ability of species to respond to novel future climates is determined in part by their physiological capacity to tolerate climate change and the degree to which they have reached and continue to maintain distributional equilibrium with the environment. While broad-scale correlative climatic measurements of a species' niche are often described as estimating the fundamental niche, it is unclear how well these occupied portions actually approximate the fundamental niche per se, versus the fundamental niche that exists in environmental space, and what fitness values bounding the niche are necessary to maintain distributional equilibrium. Here, we investigate these questions by comparing physiological and correlative estimates of the thermal niche in the introduced North American house sparrow (Passer domesticus. Our results indicate that occupied portions of the fundamental niche derived from temperature correlations closely approximate the centroid of the existing fundamental niche calculated on a fitness threshold of 50% population mortality. Using these niche measures, a 75-year time series analysis (1930-2004 further shows that: (i existing fundamental and occupied niche centroids did not undergo directional change, (ii interannual changes in the two niche centroids were correlated, (iii temperatures in North America moved through niche space in a net centripetal fashion, and consequently, (iv most areas throughout the range of the house sparrow tracked the existing fundamental niche centroid with respect to at least one temperature gradient. Following introduction to a new continent, the house sparrow rapidly tracked its thermal niche and established continent-wide distributional equilibrium with respect to major temperature gradients. These dynamics were mediated in large part by the species' broad thermal physiological tolerances, high dispersal potential, competitive advantage in human-dominated landscapes, and climatically induced

  5. Niche divergence builds the case for ecological speciation in skinks of the Plestiodon skiltonianus species complex

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    Wogan, Guinevere O.U.; Richmond, Jonathan Q.

    2015-01-01

    Adaptation to different thermal environments has the potential to cause evolutionary changes that are sufficient to drive ecological speciation. Here, we examine whether climate-based niche divergence in lizards of the Plestiodon skiltonianus species complex is consistent with the outcomes of such a process. Previous work on this group shows that a mechanical sexual barrier has evolved between species that differ mainly in body size and that the barrier may be a by-product of selection for increased body size in lineages that have invaded xeric environments; however, baseline information on niche divergence among members of the group is lacking. We quantified the climatic niche using mechanistic physiological and correlative niche models and then estimated niche differences among species using ordination techniques and tests of niche overlap and equivalency. Our results show that the thermal niches of size-divergent, reproductively isolated morphospecies are significantly differentiated and that precipitation may have been as important as temperature in causing increased shifts in body size in xeric habitats. While these findings alone do not demonstrate thermal adaptation or identify the cause of speciation, their integration with earlier genetic and behavioral studies provides a useful test of phenotype–environment associations that further support the case for ecological speciation in these lizards.

  6. Visualization for genomics: the Microbial Genome Viewer.

    Science.gov (United States)

    Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

    2004-07-22

    A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

  7. Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond.

    Science.gov (United States)

    Hiraoka, Satoshi; Yang, Ching-Chia; Iwasaki, Wataru

    2016-09-29

    Metagenomic approaches are now commonly used in microbial ecology to study microbial communities in more detail, including many strains that cannot be cultivated in the laboratory. Bioinformatic analyses make it possible to mine huge metagenomic datasets and discover general patterns that govern microbial ecosystems. However, the findings of typical metagenomic and bioinformatic analyses still do not completely describe the ecology and evolution of microbes in their environments. Most analyses still depend on straightforward sequence similarity searches against reference databases. We herein review the current state of metagenomics and bioinformatics in microbial ecology and discuss future directions for the field. New techniques will allow us to go beyond routine analyses and broaden our knowledge of microbial ecosystems. We need to enrich reference databases, promote platforms that enable meta- or comprehensive analyses of diverse metagenomic datasets, devise methods that utilize long-read sequence information, and develop more powerful bioinformatic methods to analyze data from diverse perspectives.

  8. Mesenchymal stem cells in human placental chorionic villi reside in a vascular Niche

    NARCIS (Netherlands)

    Castrechini, N. M.; Murthi, P.; Gude, N. M.; Erwich, J. J. H. M.; Gronthos, S.; Zannettino, A.; Brennecke, S. R.; Kalionis, B.; Brennecke, S.P.

    The chorionic villi of human term placentae are a rich source of mesenchymal stem cells (PMSCs) The stem cell "niche" within the chorionic villi regulates how PMSCs participate in placental tissue generation, maintenance and repair, but the anatomic location of the niche has not been defined A

  9. When does it pay to invest in a patch? The evolution of intentional niche construction.

    Science.gov (United States)

    Mohlenhoff, Kathryn A; Codding, Brian F

    2017-09-01

    Humans modify their environments in ways that significantly transform the earth's ecosystems. Recent research suggests that such niche-constructing behaviors are not passive human responses to environmental variation, but instead should be seen as active and intentional management of the environment. Although such research is useful in highlighting the interactive dynamics between humans and their natural world, the niche-construction framework, as currently applied, fails to explain why people would decide to modify their environments in the first place. To help resolve this problem, we use a model of technological intensification to analyze the cost-benefit trade-offs associated with niche construction as a form of patch investment. We use this model to assess the costs and benefits of three paradigmatic cases of intentional niche construction in Western North America: the application of fire in acorn groves, the manufacture of fishing weirs, and the adoption of maize agriculture. Intensification models predict that investing in patch modification (niche construction) only provides a net benefit when the amount of resources needed crosses a critical threshold that makes the initial investment worthwhile. From this, it follows that low-cost investments, such as burning in oak groves, should be quite common, while more costly investments, such as maize agriculture, should be less common and depend on the alternatives available in the local environment. We examine how patterns of mobility, risk management, territoriality, and private property also co-evolve with the costs and benefits of niche construction. This approach illustrates that explaining niche-constructing behavior requires understanding the economic trade-offs involved in patch investment. Integrating concepts from niche construction and technological intensification models within a behavioral ecological framework provides insights into the coevolution and active feedback between adaptive behaviors and

  10. β3-Adrenergic Regulation of EPC Features Through Manipulation of the Bone Marrow MSC Niche.

    Science.gov (United States)

    Vafaei, Rana; Nassiri, Seyed Mahdi; Siavashi, Vahid

    2017-12-01

    Mesenchymal stem cells (MSCs) reside in a specific niche in the bone marrow, however, biological features of this niche are still not fully understood. Given the interactions of MSCs with endothelial cells in different tissues, bone marrow MSC niche may influence the biological features of endothelial progenitor cells (EPCs). To understand the role of the sympathetic nervous system in regulation of the MSC niche, we examined whether the manipulation of the MSC niche via β3-adrenergic signals will affect EPC features. A selective β3 agonist (BRL37344) or a β3 antagonist (SR59230A) was administered in mice for 2 weeks to determine the potential effects of these regimens on the population of CD133 + stem cells in the bone marrow. Then, bone marrow-derived MSCs and EPCs were harvested and expanded from the mice to examine the effect of changes in the MSC niche on EPC features. Improved MSC colony forming potency with increased bone marrow stromal cell-derived factor 1 (SDF-1) (also known as C-X-C motif chemokine 12 [CXCL12]) expression was shown as a result of intensification of the bone marrow adrenergic signals through BRL37344 injection. On the other hand, the blockage of these signals limited the expression level of SDF-1 and resulted in bone marrow enrichment of CD133 + cells. Manipulation of the MSC niche and decreased SDF-1 expression via SR59230A injection also prompted EPCs to form more colonies with augmented proliferation and differentiation capacity. Overall, our results indicate that the β3-adrenergic signals regulate the MSC niche, thereby resulting in modulation of EPC biological features. J. Cell. Biochem. 118: 4753-4761, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  11. A Stromal Cell Niche for Human and Mouse Type 3 Innate Lymphoid Cells.

    Science.gov (United States)

    Hoorweg, Kerim; Narang, Priyanka; Li, Zhi; Thuery, Anne; Papazian, Natalie; Withers, David R; Coles, Mark C; Cupedo, Tom

    2015-11-01

    Adaptive immunity critically depends on the functional compartmentalization of secondary lymphoid organs. Mesenchymal stromal cells create and maintain specialized niches that support survival, activation, and expansion of T and B cells, and integrated analysis of lymphocytes and their niche has been instrumental in understanding adaptive immunity. Lymphoid organs are also home to type 3 innate lymphoid cells (ILC3), innate effector cells essential for barrier immunity. However, a specialized stromal niche for ILC3 has not been identified. A novel lineage-tracing approach now identifies a subset of murine fetal lymphoid tissue organizer cells that gives rise exclusively to adult marginal reticular cells. Moreover, both cell types are conserved from mice to humans and colocalize with ILC3 in secondary lymphoid tissues throughout life. In sum, we provide evidence that fetal stromal organizers give rise to adult marginal reticular cells and form a dedicated stromal niche for innate ILC3 in adaptive lymphoid organs. Copyright © 2015 by The American Association of Immunologists, Inc.

  12. Evolution of niche preference in Sphagnum peat mosses.

    Science.gov (United States)

    Johnson, Matthew G; Granath, Gustaf; Tahvanainen, Teemu; Pouliot, Remy; Stenøien, Hans K; Rochefort, Line; Rydin, Håkan; Shaw, A Jonathan

    2015-01-01

    Peat mosses (Sphagnum) are ecosystem engineers-species in boreal peatlands simultaneously create and inhabit narrow habitat preferences along two microhabitat gradients: an ionic gradient and a hydrological hummock-hollow gradient. In this article, we demonstrate the connections between microhabitat preference and phylogeny in Sphagnum. Using a dataset of 39 species of Sphagnum, with an 18-locus DNA alignment and an ecological dataset encompassing three large published studies, we tested for phylogenetic signal and within-genus changes in evolutionary rate of eight niche descriptors and two multivariate niche gradients. We find little to no evidence for phylogenetic signal in most component descriptors of the ionic gradient, but interspecific variation along the hummock-hollow gradient shows considerable phylogenetic signal. We find support for a change in the rate of niche evolution within the genus-the hummock-forming subgenus Acutifolia has evolved along the multivariate hummock-hollow gradient faster than the hollow-inhabiting subgenus Cuspidata. Because peat mosses themselves create some of the ecological gradients constituting their own habitats, the classic microtopography of Sphagnum-dominated peatlands is maintained by evolutionary constraints and the biological properties of related Sphagnum species. The patterns of phylogenetic signal observed here will instruct future study on the role of functional traits in peatland growth and reconstruction. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

  13. Microbial-immune cross-talk and regulation of the immune system.

    Science.gov (United States)

    Cahenzli, Julia; Balmer, Maria L; McCoy, Kathy D

    2013-01-01

    We are all born germ-free. Following birth we enter into a lifelong relationship with microbes residing on our body's surfaces. The lower intestine is home to the highest microbial density in our body, which is also the highest microbial density known on Earth (up to 10(12) /g of luminal contents). With our indigenous microbial cells outnumbering our human cells by an order of magnitude our body is more microbial than human. Numerous immune adaptations confine these microbes within the mucosa, enabling most of us to live in peaceful homeostasis with our intestinal symbionts. Intestinal epithelial cells not only form a physical barrier between the bacteria-laden lumen and the rest of the body but also function as multi-tasking immune cells that sense the prevailing microbial (apical) and immune (basolateral) milieus, instruct the underlying immune cells, and adapt functionally. In the constant effort to ensure intestinal homeostasis, the immune system becomes educated to respond appropriately and in turn immune status can shape the microbial consortia. Here we review how the dynamic immune-microbial dialogue underlies maturation and regulation of the immune system and discuss recent findings on the impact of diet on both microbial ecology and immune function. © 2012 The Authors. Immunology © 2012 Blackwell Publishing Ltd.

  14. Microbial diversity in ikaite tufa columns: an alkaline, cold ecological niche in Greenland.

    Science.gov (United States)

    Stougaard, Peter; Jørgensen, Flemming; Johnsen, Mads G; Hansen, Ole C

    2002-08-01

    Ikaite tufa columns from the Ikka Fjord in south-western Greenland constitute a natural, stable environment at low temperature and with a pH ranging from neutral at the exterior to very alkaline (pH 10.4) at the interior of the column. Phylogenetic analysis of culturable organisms revealed ten different isolates representing three of the major bacterial divisions. Nine of the isolates showed 94-99% similarity to known sequences, whereas one isolate displayed a low degree of similarity (less than 90%) to a Cyclobacterium species. Seven of the isolates were shown to be cold active alkaliphiles, whereas three isolates showed optimal growth at neutral pH. Phylogenetic analysis of DNA isolated directly from the ikaite material demonstrated the presence of a microbial flora more diverse than the culturable isolates. Whereas approximately half of the phylotypes showed 90-99% similarity to known meso- or thermophilic alkaliphiles, the rest of the sequences displayed less than 90% similarity when compared to known 16S rRNA gene sequences in databases. Thus, in the present paper, we demonstrate that ikaite columns that host a specialized macroscopic flora and fauna also contain a unique, cold active, alkaliphilic microflora.

  15. Subsurface microbial diversity in deep-granitic-fracture water in Colorado

    Science.gov (United States)

    Sahl, J.W.; Schmidt, R.; Swanner, E.D.; Mandernack, K.W.; Templeton, A.S.; Kieft, Thomas L.; Smith, R.L.; Sanford, W.E.; Callaghan, R.L.; Mitton, J.B.; Spear, J.R.

    2008-01-01

    A microbial community analysis using 16S rRNA gene sequencing was performed on borehole water and a granite rock core from Henderson Mine, a >1,000-meter-deep molybdenum mine near Empire, CO. Chemical analysis of borehole water at two separate depths (1,044 m and 1,004 m below the mine entrance) suggests that a sharp chemical gradient exists, likely from the mixing of two distinct subsurface fluids, one metal rich and one relatively dilute; this has created unique niches for microorganisms. The microbial community analyzed from filtered, oxic borehole water indicated an abundance of sequences from iron-oxidizing bacteria (Gallionella spp.) and was compared to the community from the same borehole after 2 weeks of being plugged with an expandable packer. Statistical analyses with UniFrac revealed a significant shift in community structure following the addition of the packer. Phospholipid fatty acid (PLFA) analysis suggested that Nitrosomonadales dominated the oxic borehole, while PLFAs indicative of anaerobic bacteria were most abundant in the samples from the plugged borehole. Microbial sequences were represented primarily by Firmicutes, Proteobacteria, and a lineage of sequences which did not group with any identified bacterial division; phylogenetic analyses confirmed the presence of a novel candidate division. This "Henderson candidate division" dominated the clone libraries from the dilute anoxic fluids. Sequences obtained from the granitic rock core (1,740 m below the surface) were represented by the divisions Proteobacteria (primarily the family Ralstoniaceae) and Firmicutes. Sequences grouping within Ralstoniaceae were also found in the clone libraries from metal-rich fluids yet were absent in more dilute fluids. Lineage-specific comparisons, combined with phylogenetic statistical analyses, show that geochemical variance has an important effect on microbial community structure in deep, subsurface systems. Copyright ?? 2008, American Society for Microbiology

  16. Landscape heterogeneity drives intra-population niche variation and reproduction in an arctic top predator.

    Science.gov (United States)

    L'hérault, Vincent; Franke, Alastair; Lecomte, Nicolas; Alogut, Adam; Bêty, Joël

    2013-09-01

    While intra-population variability in resource use is ubiquitous, little is known of how this measure of niche diversity varies in space and its role in population dynamics. Here we examined how heterogeneous breeding environments can structure intra-population niche variation in both resource use and reproductive output. We investigated intra-population niche variation in the Arctic tundra ecosystem, studying peregrine falcon (Falco peregrinus tundrius, White) breeding within a terrestrial-marine gradient near Rankin Inlet, Nunavut, Canada. Using stable isotope analysis, we found that intra-population niches varied at the individual level; we examined within-nest and among-nest variation, though only the latter varied along the terrestrial-marine gradient (i.e., increased among-nest variability among birds nesting within the marine environment, indicating higher degree of specialization). Terrestrial prey species (small herbivores and insectivores) were consumed by virtually all falcons. Falcons nesting within the marine environment made use of marine prey (sea birds), but depended heavily on terrestrial prey (up to 90% of the diet). Using 28-years of peregrine falcon nesting data, we found a positive relationship between the proportion of terrestrial habitat surrounding nest sites and annual nestling production, but no relationship with the likelihood of successfully rearing at least one nestling reaching 25 days old. Annually, successful inland breeders raised 0.47 more young on average compared to offshore breeders, which yields potential fitness consequences for this long-living species. The analyses of niche and reproductive success suggest a potential breeding cost for accessing distant terrestrial prey, perhaps due to additional traveling costs, for those individuals with marine nest site locations. Our study indicates how landscape heterogeneity can generate proximate (niche variation) and ultimate (reproduction) consequences on a population of generalist

  17. Untangling the relationships among regional occupancy, species traits, and niche characteristics in stream invertebrates

    Science.gov (United States)

    Heino, Jani; Grönroos, Mira

    2014-01-01

    The regional occupancy and local abundance of species are affected by various species traits, but their relative effects are poorly understood. We studied the relationships between species traits and occupancy (i.e., proportion of sites occupied) or abundance (i.e., mean local abundance at occupied sites) of stream invertebrates using small-grained data (i.e., local stream sites) across a large spatial extent (i.e., three drainage basins). We found a significant, yet rather weak, linear relationship between occupancy and abundance. However, occupancy was strongly related to niche position (NP), but it showed a weaker relationship with niche breadth (NB). Abundance was at best weakly related to these explanatory niche-based variables. Biological traits, including feeding modes, habit traits, dispersal modes and body size classes, were generally less important in accounting for variation in occupancy and abundance. Our findings showed that the regional occupancy of stream invertebrate species is mostly related to niche characteristics, in particular, NP. However, the effects of NB on occupancy were affected by the measure itself. We conclude that niche characteristics determine the regional occupancy of species at relatively large spatial extents, suggesting that species distributions are determined by environmental variation among sites. PMID:24963387

  18. The hidden Niemann-Pick type C patient: clinical niches for a rare inherited metabolic disease.

    Science.gov (United States)

    Hendriksz, Christian J; Anheim, Mathieu; Bauer, Peter; Bonnot, Olivier; Chakrapani, Anupam; Corvol, Jean-Christophe; de Koning, Tom J; Degtyareva, Anna; Dionisi-Vici, Carlo; Doss, Sarah; Duning, Thomas; Giunti, Paola; Iodice, Rosa; Johnston, Tracy; Kelly, Dierdre; Klünemann, Hans-Hermann; Lorenzl, Stefan; Padovani, Alessandro; Pocovi, Miguel; Synofzik, Matthis; Terblanche, Alta; Then Bergh, Florian; Topçu, Meral; Tranchant, Christine; Walterfang, Mark; Velten, Christian; Kolb, Stefan A

    2017-05-01

    Niemann-Pick disease type C (NP-C) is a rare, inherited neurodegenerative disease of impaired intracellular lipid trafficking. Clinical symptoms are highly heterogeneous, including neurological, visceral, or psychiatric manifestations. The incidence of NP-C is under-estimated due to under-recognition or misdiagnosis across a wide range of medical fields. New screening and diagnostic methods provide an opportunity to improve detection of unrecognized cases in clinical sub-populations associated with a higher risk of NP-C. Patients in these at-risk groups ("clinical niches") have symptoms that are potentially related to NP-C, but go unrecognized due to other, more prevalent clinical features, and lack of awareness regarding underlying metabolic causes. Twelve potential clinical niches identified by clinical experts were evaluated based on a comprehensive, non-systematic review of literature published to date. Relevant publications were identified by targeted literature searches of EMBASE and PubMed using key search terms specific to each niche. Articles published in English or other European languages up to 2016 were included. Several niches were found to be relevant based on available data: movement disorders (early-onset ataxia and dystonia), organic psychosis, early-onset cholestasis/(hepato)splenomegaly, cases with relevant antenatal findings or fetal abnormalities, and patients affected by family history, consanguinity, and endogamy. Potentially relevant niches requiring further supportive data included: early-onset cognitive decline, frontotemporal dementia, parkinsonism, and chronic inflammatory CNS disease. There was relatively weak evidence to suggest amyotrophic lateral sclerosis or progressive supranuclear gaze palsy as potential niches. Several clinical niches have been identified that harbor patients at increased risk of NP-C.

  19. Microbial mineral illization of montmorillonite in low-permeability oil reservoirs for microbial enhanced oil recovery.

    Science.gov (United States)

    Cui, Kai; Sun, Shanshan; Xiao, Meng; Liu, Tongjing; Xu, Quanshu; Dong, Honghong; Wang, Di; Gong, Yejing; Sha, Te; Hou, Jirui; Zhang, Zhongzhi; Fu, Pengcheng

    2018-05-11

    Microbial mineral illization has been investigated for its role in the extraction and recovery of metals from ores. Here we report our application of mineral bioillization for the microbial enhanced oil recovery in low-permeability oil reservoirs. It aimed to reveal the etching mechanism of the four Fe (III)-reducing microbial strains under anaerobic growth conditions on the Ca-montmorillonite. The mineralogical characterization of the Ca-montmorillonite was performed by Fourier transform infrared spectroscopy, X-ray powder diffraction, scanning electron microscopy and energy dispersive spectrometer. Results showed that the microbial strains could efficiently reduce Fe (III) at an optimal rate of 71 %, and alter the crystal lattice structure of the lamella to promote the interlayer cation exchange, and to efficiently inhibit the Ca-montmorillonite swelling at an inhibitory rate of 48.9 %. Importance Microbial mineral illization is ubiquitous in the natural environment. Microbes in low-permeability reservoirs are able to enable the alteration of the structure and phase of the Fe-poor minerals by reducing Fe (III) and inhibiting clay swelling which is still poorly studied. This study aimed to reveal the interaction mechanism between Fe (III)-reducing bacterial strains and Ca-montmorillonite under anaerobic atmosphere, and to investigate the extent and rates of Fe (III) reduction and phase changes with their activities. Application of Fe (III)-reducing bacteria will provide a new way to inhibit clay swelling, to elevate reservoir permeability, and to reduce pore throat resistance after water flooding for enhanced oil recovery in low-permeability reservoirs. Copyright © 2018 American Society for Microbiology.

  20. Flow cytometric analysis of microbial contamination in food industry technological lines--initial study.

    Science.gov (United States)

    Józwa, Wojciech; Czaczyk, Katarzyna

    2012-04-02

    Flow cytometry constitutes an alternative for traditional methods of microorganisms identification and analysis, including methods requiring cultivation step. It enables the detection of pathogens and other microorganisms contaminants without the need to culture microbial cells meaning that the sample (water, waste or food e.g. milk, wine, beer) may be analysed directly. This leads to a significant reduction of time required for analysis allowing monitoring of production processes and immediate reaction in case of contamination or any disruption occurs. Apart from the analysis of raw materials or products on different stages of manufacturing process, the flow cytometry seems to constitute an ideal tool for the assessment of microbial contamination on the surface of technological lines. In the present work samples comprising smears from 3 different surfaces of technological lines from fruit and vegetable processing company from Greater Poland were analysed directly with flow cytometer. The measured parameters were forward and side scatter of laser light signals allowing the estimation of microbial cell contents in each sample. Flow cytometric analysis of the surface of food industry production lines enable the preliminary evaluation of microbial contamination within few minutes from the moment of sample arrival without the need of sample pretreatment. The presented method of fl ow cytometric initial evaluation of microbial state of food industry technological lines demonstrated its potential for developing a robust, routine method for the rapid and labor-saving detection of microbial contamination in food industry.

  1. Introducing MERGANSER: A Flexible Framework for Ecological Niche Modeling

    Science.gov (United States)

    Klawonn, M.; Dow, E. M.

    2015-12-01

    Ecological Niche Modeling (ENM) is a collection of techniques to find a "fundamental niche", the range of environmental conditions suitable for a species' survival in the absence of inter-species interactions, given a set of environmental parameters. Traditional approaches to ENM face a number of obstacles including limited data accessibility, data management problems, computational costs, interface usability, and model validation. The MERGANSER system, which stands for Modeling Ecological Residency Given A Normalized Set of Environmental Records, addresses these issues through powerful data persistence and flexible data access, coupled with a clear presentation of results and fine-tuned control over model parameters. MERGANSER leverages data measuring 72 weather related phenomena, land cover, soil type, population, species occurrence, general species information, and elevation, totaling over 1.5 TB of data. To the best of the authors' knowledge, MERGANSER uses higher-resolution spatial data sets than previously published models. Since MERGANSER stores data in an instance of Apache SOLR, layers generated in support of niche models are accessible to users via simplified Apache Lucene queries. This is made even simpler via an HTTP front end that generates Lucene queries automatically. Specifically, a user need only enter the name of a place and a species to run a model. Using this approach to synthesizing model layers, the MERGANSER system has successfully reproduced previously published niche model results with a simplified user experience. Input layers for the model are generated dynamically using OpenStreetMap and SOLR's spatial search functionality. Models are then run using either user-specified or automatically determined parameters after normalizing them into a common grid. Finally, results are visualized in the web interface, which allows for quick validation. Model results and all surrounding metadata are also accessible to the user for further study.

  2. The nutritional nexus: linking niche, habitat variability and prey composition in a generalist marine predator.

    Science.gov (United States)

    Machovsky-Capuska, Gabriel E; Miller, Mark G R; Silva, Fabiola R O; Amiot, Christophe; Stockin, Karen A; Senior, Alistair M; Schuckard, Rob; Melville, David; Raubenheimer, David

    2018-06-05

    1.Our understanding of the niche concept will remain limited while the quantity and range of different food types eaten remains a dominant proxy for niche breadth, as this does not account for the broad ecological context that governs diet. Linking nutrition, physiology and behaviour are critical to predict the extent to which a species adjusts its nutritional niche breadth at the levels of prey ("prey composition niche", defined as the range of prey compositions eaten), and diet ("realized nutritional niche" is the range of diets composed through feeding on the prey). 2.Here we studied adult-chick rearing Australasian gannets (Morus serrator) to propose an integrative approach using sea surface temperature anomalies (SSTa), geographic location and bathymetry over different years, to explore their relationship with the nutritional composition of prey and diets (i.e., prey composition and nutritional niche breadth), habitat use and foraging behavior. 3.We found that gannets feed on prey that varied widely in their nutritional composition (have a broad prey composition niche), and composed diets from these prey that likewise varied in composition (have a broad realized nutritional niche), suggesting generalism at two levels of macronutrient selection. 4.Across seasons, we established "nutritional landscapes" (hereafter nutriscapes), linking the nutritional content of prey (wet mass protein to-lipid ratio -P:L-) to the most likely geographic area of capture and bathymetry. Nutriscapes varied in their P:L from 6.06 to 15.28, over time, space and bathymetry (0 to 150 m). 5.During warm water events (strong positive SSTa), gannets expanded their foraging habitat, increased their foraging trip duration and consumed prey and diets with low macronutrient content (wet mass proportions of P and L). They were also constrained to the smallest prey composition and realized nutritional niche breadths. 6.Our findings are consistent with previous suggestions that dietary generalism

  3. Effect of environmental conditions on the fatty acid fingerprint of microbial communities

    Science.gov (United States)

    Biryukov, Mikhail; Dippold, Michaela; Kuzyakov, Yakov

    2014-05-01

    information was gained from the analysis of intact polar lipids. Ethanolamines and cholines were the most abundant head groups within bacteria and are mainly combined with one specific and one unspecific fatty acid. Reactions on changing environmental conditions occurred mainly by modifications of fatty acids and rarely by a change of the headgroup fingerprint. This approach thus enables to categorize a certain amount of formerly unspecific fatty acids towards a specific microbial group. Ecological understanding for the interface between surrounding environment and cellular metabolism could be deepened by investigating the intact compounds e.g. intact phospholipids of microbial membranes. However, data from further organisms as well as diverse microbial communities are needed to continue the databases of intact phospholipids. Further investigations of diverse microbial communities under changing environmental conditions have to follow these first studies to 1) assess the effects of soil environment on microbial membranes (e.g. associations in biofilms) and 2) assess the effect of interspecific microbial interactions on their membrane properties and lipid fingerprints. Thus, combination of various lipid biomarkers as well as their intact characterization enables a more detailed look into microbial community structure and their respond on environmental conditions, improves our understanding of microbial functioning in ecosystems and enables a more specific estimation of biomass of various microbial groups.

  4. A practical guideline for examining a uterine niche using ultrasonography in non-pregnant women: a modified Delphi method amongst European experts.

    Science.gov (United States)

    Jordans, I P M; de Leeuw, R; Stegwee, S I; Amso, N N; Barri-Soldevila, P N; van den Bosch, T; Bourne, T; Brolmann, H A M; Donnez, O; Dueholm, M; Hehenkamp, W J K; Jastrow, N; Jurkovic, D; Mashiach, R; Naji, O; Streuli, I; Timmerman, D; Vd Voet, L F; Huirne, J A F

    2018-03-14

    To generate a uniform, internationally recognized guideline for detailed uterine niche evaluation by ultrasonography in non-pregnant women using a modified Delphi method amongst international experts. Fifteen international gynecological experts were recruited by their membership of the European niche taskforce group. All experts were physicians with extensive experience in niche evaluation in clinical practice and/or authors of niche studies. Relevant items for niche measurement were determined based on the results of a literature search and recommendations of a focus group. Two online questionnaires were sent to the expert panel and one group meeting was organized. Consensus was predefined as a consensus rate of at least 70%. In total 15 experts participated in this study. Consensus was reached for a total of 42 items on niche evaluation, including definitions, relevance, method of measurement and tips for visualization of the niche. All experts agreed on the proposed guideline for niche evaluation in non-pregnant women as presented in this paper. Consensus between niche experts was achieved on all items regarding ultrasonographic niche measurement. This article is protected by copyright. All rights reserved.

  5. Morphology and ultrastructure of epilithic versus cryptic, microbial growth in lower Cambrian phosphorites from the Montagne Noire, France.

    Science.gov (United States)

    Alvaro, J J; Clausen, S

    2010-03-01

    The lower Cambrian grainy phosphorites of the northern Montagne Noire occur interbedded with grey to black, laminated to massive shales and limestones deposited along the edge of a continental shelf, associated with slope-related facies and unstable substrates. The concentration of phosphate took place by repeated alternations of low sedimentation rates and condensation (hardgrounds), in situ early-diagenetic precipitation of fluorapatite, winnowing and polyphase reworking of previously phosphatized skeletons and hardground-derived clasts. The succession of repeated cycles of sedimentation, phosphate concentration, and reworking led to multi-event phosphate deposits rich in allochthonous particles. Phosphogenesis was primarily mediated by microbial activity, which is evidenced by the abundance of phosphatized putative microbial remains. These occur as smooth and segmented filaments, sheaths, and ovoid-shaped coccoids. These simple morphologies commonly form composite frameworks as a result of their aggregation and entanglement, leading to the record of biofilms, microbial mats, and complex networks. These infested the calcitic skeletonized microfossils that littered the substrate. Microbial activity evidences epilithic (anisotropic coatings on skeletons), euendolithic (perforating skeletal walls), and cryptoendolithic (lining inter- and intraparticulate pores) strategies, the latter dominated by bundles of filaments and globular clusters that grew along the cavities of helcionellids and hyoliths. According to their epilithic versus cryptic strategies, microbial populations that penetrated and dwelled inside hard skeletal substrates show different network and colonial morphologies. These early Cambrian shell concentrations were the loci of a stepwise colonization made by saprophytic to mutualistic, cyanobacterial-fungal consortia. Their euendolithic and cryptoendolithic ecological niches provided microbial refugia to manage the grazing impact mainly led by metazoans.

  6. A Comparative Pan-Genome Perspective of Niche-Adaptable Cell-Surface Protein Phenotypes in Lactobacillus rhamnosus

    Science.gov (United States)

    Kant, Ravi; Sigvart-Mattila, Pia; Paulin, Lars; Mecklin, Jukka-Pekka; Saarela, Maria; Palva, Airi; von Ossowski, Ingemar

    2014-01-01

    Lactobacillus rhamnosus is a ubiquitously adaptable Gram-positive bacterium and as a typical commensal can be recovered from various microbe-accessible bodily orifices and cavities. Then again, other isolates are food-borne, with some of these having been long associated with naturally fermented cheeses and yogurts. Additionally, because of perceived health benefits to humans and animals, numerous L. rhamnosus strains have been selected for use as so-called probiotics and are often taken in the form of dietary supplements and functional foods. At the genome level, it is anticipated that certain genetic variances will have provided the niche-related phenotypes that augment the flexible adaptiveness of this species, thus enabling its strains to grow and survive in their respective host environments. For this present study, we considered it functionally informative to examine and catalogue the genotype-phenotype variation existing at the cell surface between different L. rhamnosus strains, with the presumption that this might be relatable to habitat preferences and ecological adaptability. Here, we conducted a pan-genomic study involving 13 genomes from L. rhamnosus isolates with various origins. In using a benchmark strain (gut-adapted L. rhamnosus GG) for our pan-genome comparison, we had focused our efforts on a detailed examination and description of gene products for certain functionally relevant surface-exposed proteins, each of which in effect might also play a part in niche adaptability among the other strains. Perhaps most significantly of the surface protein loci we had analyzed, it would appear that the spaCBA operon (known to encode SpaCBA-called pili having a mucoadhesive phenotype) is a genomic rarity and an uncommon occurrence in L. rhamnosus. However, for any of the so-piliated L. rhamnosus strains, they will likely possess an increased niche-specific fitness, which functionally might presumably be manifested by a protracted transient colonization of

  7. Co-niche construction between hosts and symbionts

    Indian Academy of Sciences (India)

    Symbiosis is a process that can generate evolutionary novelties and can extend the phenotypic niche space of organisms. Symbionts can act together with their hosts to co-construct host organs, within which symbionts are housed. Once established within hosts, symbionts can also influence various aspects of host ...

  8. Tracking niche variation over millennial timescales in sympatric killer whale lineages.

    Science.gov (United States)

    Foote, Andrew D; Newton, Jason; Ávila-Arcos, María C; Kampmann, Marie-Louise; Samaniego, Jose A; Post, Klaas; Rosing-Asvid, Aqqalu; Sinding, Mikkel-Holger S; Gilbert, M Thomas P

    2013-10-07

    Niche variation owing to individual differences in ecology has been hypothesized to be an early stage of sympatric speciation. Yet to date, no study has tracked niche width over more than a few generations. In this study, we show the presence of isotopic niche variation over millennial timescales and investigate the evolutionary outcomes. Isotopic ratios were measured from tissue samples of sympatric killer whale Orcinus orca lineages from the North Sea, spanning over 10 000 years. Isotopic ratios spanned a range similar to the difference in isotopic values of two known prey items, herring Clupea harengus and harbour seal Phoca vitulina. Two proxies of the stage of speciation, lineage sorting of mitogenomes and genotypic clustering, were both weak to intermediate indicating that speciation has made little progress. Thus, our study confirms that even with the necessary ecological conditions, i.e. among-individual variation in ecology, it is difficult for sympatric speciation to progress in the face of gene flow. In contrast to some theoretical models, our empirical results suggest that sympatric speciation driven by among-individual differences in ecological niche is a slow process and may not reach completion. We argue that sympatric speciation is constrained in this system owing to the plastic nature of the behavioural traits under selection when hunting either mammals or fish.

  9. Trophic niche shifts driven by phytoplankton in sandy beach ecosystems

    Science.gov (United States)

    Bergamino, Leandro; Martínez, Ana; Han, Eunah; Lercari, Diego; Defeo, Omar

    2016-10-01

    Stable isotopes (δ13C and δ15N) together with chlorophyll a and densities of surf diatoms were used to analyze changes in trophic niches of species in two sandy beaches of Uruguay with contrasting morphodynamics (i.e. dissipative vs. reflective). Consumers and food sources were collected over four seasons, including sediment organic matter (SOM), suspended particulate organic matter (POM) and the surf zone diatom Asterionellopsis guyunusae. Circular statistics and a Bayesian isotope mixing model were used to quantify food web differences between beaches. Consumers changed their trophic niche between beaches in the same direction of the food web space towards higher reliance on surf diatoms in the dissipative beach. Mixing models indicated that A. guyunusae was the primary nutrition source for suspension feeders in the dissipative beach, explaining their change in dietary niche compared to the reflective beach where the proportional contribution of surf diatoms was low. The high C/N ratios in A. guyunusae indicated its high nutritional value and N content, and may help to explain the high assimilation by suspension feeders at the dissipative beach. Furthermore, density of A. guyunusae was higher in the dissipative than in the reflective beach, and cell density was positively correlated with chlorophyll a only in the dissipative beach. Therefore, surf diatoms are important drivers in the dynamics of sandy beach food webs, determining the trophic niche space and productivity. Our study provides valuable insights on shifting foraging behavior by beach fauna in response to changes in resource availability.

  10. Niche as a determinant of word fate in online groups.

    Directory of Open Access Journals (Sweden)

    Eduardo G Altmann

    2011-05-01

    Full Text Available Patterns of word use both reflect and influence a myriad of human activities and interactions. Like other entities that are reproduced and evolve, words rise or decline depending upon a complex interplay between their intrinsic properties and the environments in which they function. Using Internet discussion communities as model systems, we define the concept of a word niche as the relationship between the word and the characteristic features of the environments in which it is used. We develop a method to quantify two important aspects of the size of the word niche: the range of individuals using the word and the range of topics it is used to discuss. Controlling for word frequency, we show that these aspects of the word niche are strong determinants of changes in word frequency. Previous studies have already indicated that word frequency itself is a correlate of word success at historical time scales. Our analysis of changes in word frequencies over time reveals that the relative sizes of word niches are far more important than word frequencies in the dynamics of the entire vocabulary at shorter time scales, as the language adapts to new concepts and social groupings. We also distinguish endogenous versus exogenous factors as additional contributors to the fates of words, and demonstrate the force of this distinction in the rise of novel words. Our results indicate that short-term nonstationarity in word statistics is strongly driven by individual proclivities, including inclinations to provide novel information and to project a distinctive social identity.

  11. Towards Defining the Ecological Niches of Novel Coastal Gulf of Mexico Bacterial Isolates

    Science.gov (United States)

    Henson, M. W.; Thrash, C.; Nall, E.

    2016-02-01

    The study of microbial contributions to biogeochemistry is critical to understanding the cycles of fundamental compounds and gain predictive capabilities in a changing environment. Such study requires observation of microbial communities and genetics in nature, coupled with experimental testing of hypotheses both in situ and in laboratory settings. This study combines dilution-to-extinction based high-throughput culturing (HTC) with cultivation-independent and geochemical measurements to define potential ecological niches of novel bacterial isolates from the coastal northern Gulf of Mexico (cnGOM). Here we report findings from the first of a three-year project. In total, 43 cultures from seven HTC experiments were capable of being repeatedly transferred. Sanger sequencing of the 16S rRNA gene identified these isolates as belonging to the phyla Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, and Betaproteobacteria. Eight are being genome sequenced, with two selected for further physiological characterization due to their phylogenic novelty and potential ecological significance. Strain LSUCC101 likely represents a novel family of Gammaproteobacteria (best blast hit to a cultured representative showed 91% sequence identity) and strain LSUCC96 belongs to the OM252 clade, with the Hawaiian isolate HIMB30 as its closest relative. Both are small (0.3-0.5 µm) cocci. The environmental importance of both LSUCC101 and LSUCC96 was illustrated by their presence within the top 30 OTU0.03 of cnGOM 16S rRNA gene datasets as well as within clone libraries from coastal regions around the world. Ongoing work is determining growth efficiencies, substrate utilization profiles, and metabolic potential to elucidate the roles of these organisms in the cnGOM. Comparative genomics will examine the evolutionary divergence of these organisms from their closest neighbors, and metagenomic recruitment to genomes will help identify strain-based variation from different coastal regions.

  12. The Microbial Resource Research Infrastructure MIRRI: Strength through Coordination

    Directory of Open Access Journals (Sweden)

    Erko Stackebrandt

    2015-11-01

    Full Text Available Microbial resources have been recognized as essential raw materials for the advancement of health and later for biotechnology, agriculture, food technology and for research in the life sciences, as their enormous abundance and diversity offer an unparalleled source of unexplored solutions. Microbial domain biological resource centres (mBRC provide live cultures and associated data to foster and support the development of basic and applied science in countries worldwide and especially in Europe, where the density of highly advanced mBRCs is high. The not-for-profit and distributed project MIRRI (Microbial Resource Research Infrastructure aims to coordinate access to hitherto individually managed resources by developing a pan-European platform which takes the interoperability and accessibility of resources and data to a higher level. Providing a wealth of additional information and linking to datasets such as literature, environmental data, sequences and chemistry will enable researchers to select organisms suitable for their research and enable innovative solutions to be developed. The current independent policies and managed processes will be adapted by partner mBRCs to harmonize holdings, services, training, and accession policy and to share expertise. The infrastructure will improve access to enhanced quality microorganisms in an appropriate legal framework and to resource-associated data in a more interoperable way.

  13. Bifurcation into functional niches in adaptation.

    Science.gov (United States)

    White, Justin S; Adami, Christoph

    2004-01-01

    One of the central questions in evolutionary biology concerns the dynamics of adaptation and diversification. This issue can be addressed experimentally if replicate populations adapting to identical environments can be investigated in detail. We have studied 501 such replicas using digital organisms adapting to at least two fundamentally different functional niches (survival strategies) present in the same environment: one in which fast replication is the way to live, and another where exploitation of the environment's complexity leads to complex organisms with longer life spans and smaller replication rates. While these two modes of survival are closely analogous to those expected to emerge in so-called r and K selection scenarios respectively, the bifurcation of evolutionary histories according to these functional niches occurs in identical environments, under identical selective pressures. We find that the branching occurs early, and leads to drastic phenotypic differences (in fitness, sequence length, and gestation time) that are permanent and irreversible. This study confirms an earlier experimental effort using microorganisms, in that diversification can be understood at least in part in terms of bifurcations on saddle points leading to peak shifts, as in the picture drawn by Sewall Wright.

  14. The exploitation of the niche market through innovation and marketing : the case of Japanese small businesses

    OpenAIRE

    Sato, Yoshio

    1992-01-01

    Japan's economic growth brought many business oportunities and niche markets for small business, where new entrepreneurs entered. Competition and self-revolutionalizing efforts made the level of their technology and management highly specialized. Various examples of niche marketing strategies in Japan by several types of smaller businesses are followed. Recent new ventures' strategies, typical "venture businesses" activities, niche marketing by diversification strategies and self revolutional...

  15. The human socio-cognitive niche and its evolutionary origins

    Science.gov (United States)

    Whiten, Andrew; Erdal, David

    2012-01-01

    Hominin evolution took a remarkable pathway, as the foraging strategy extended to large mammalian prey already hunted by a guild of specialist carnivores. How was this possible for a moderately sized ape lacking the formidable anatomical adaptations of these competing ‘professional hunters’? The long-standing answer that this was achieved through the elaboration of a new ‘cognitive niche’ reliant on intelligence and technology is compelling, yet insufficient. Here we present evidence from a diversity of sources supporting the hypothesis that a fuller answer lies in the evolution of a new socio-cognitive niche, the principal components of which include forms of cooperation, egalitarianism, mindreading (also known as ‘theory of mind’), language and cultural transmission, that go far beyond the most comparable phenomena in other primates. This cognitive and behavioural complex allows a human hunter–gatherer band to function as a unique and highly competitive predatory organism. Each of these core components of the socio-cognitive niche is distinctive to humans, but primate research has increasingly identified related capacities that permit inferences about significant ancestral cognitive foundations to the five pillars of the human social cognitive niche listed earlier. The principal focus of the present study was to review and integrate this range of recent comparative discoveries. PMID:22734055

  16. The inverse niche model for food webs with parasites

    Science.gov (United States)

    Warren, Christopher P.; Pascual, Mercedes; Lafferty, Kevin D.; Kuris, Armand M.

    2010-01-01

    Although parasites represent an important component of ecosystems, few field and theoretical studies have addressed the structure of parasites in food webs. We evaluate the structure of parasitic links in an extensive salt marsh food web, with a new model distinguishing parasitic links from non-parasitic links among free-living species. The proposed model is an extension of the niche model for food web structure, motivated by the potential role of size (and related metabolic rates) in structuring food webs. The proposed extension captures several properties observed in the data, including patterns of clustering and nestedness, better than does a random model. By relaxing specific assumptions, we demonstrate that two essential elements of the proposed model are the similarity of a parasite's hosts and the increasing degree of parasite specialization, along a one-dimensional niche axis. Thus, inverting one of the basic rules of the original model, the one determining consumers' generality appears critical. Our results support the role of size as one of the organizing principles underlying niche space and food web topology. They also strengthen the evidence for the non-random structure of parasitic links in food webs and open the door to addressing questions concerning the consequences and origins of this structure.

  17. Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach.

    Directory of Open Access Journals (Sweden)

    Erin A Gontang

    Full Text Available Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach's food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans.

  18. Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach.

    Science.gov (United States)

    Gontang, Erin A; Aylward, Frank O; Carlos, Camila; Glavina Del Rio, Tijana; Chovatia, Mansi; Fern, Alison; Lo, Chien-Chi; Malfatti, Stephanie A; Tringe, Susannah G; Currie, Cameron R; Kolter, Roberto

    2017-01-01

    Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach's food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans.

  19. Enabling the synthesis of medium chain alkanes and 1-alkenes in yeast

    DEFF Research Database (Denmark)

    Zhu, Zhiwei; Zhou, Yongjin J.; Kang, Min Kyoung

    2017-01-01

    Microbial synthesis of medium chain aliphatic hydrocarbons, attractive drop-in molecules to gasoline and jet fuels, is a promising way to reduce our reliance on petroleum-based fuels. In this study, we enabled the synthesis of straight chain hydrocarbons (C7–C13) by yeast Saccharomyces cerevisiae...

  20. Interactive microbial distribution analysis using BioAtlas

    DEFF Research Database (Denmark)

    Lund, Jesper; List, Markus; Baumbach, Jan

    2017-01-01

    body maps and (iii) user-defined maps. It further allows for (iv) uploading of own sample data, which can be placed on existing maps to (v) browse the distribution of the associated taxonomies. Finally, BioAtlas enables users to (vi) contribute custom maps (e.g. for plants or animals) and to map...... to analyze microbial distribution in a location-specific context. BioAtlas is an interactive web application that closes this gap between sequence databases, taxonomy profiling and geo/body-location information. It enables users to browse taxonomically annotated sequences across (i) the world map, (ii) human...

  1. Wnt ligand presentation and reception: from the stem cell niche to tissue engineering.

    Science.gov (United States)

    Mills, Kate M; Szczerkowski, James L A; Habib, Shukry J

    2017-08-01

    Stem cells reside in niches where spatially restricted signals maintain a delicate balance between stem cell self-renewal and differentiation. Wnt family proteins are particularly suited for this role as they are modified by lipids, which constrain and spatially regulate their signalling range. In recent years, Wnt/β-catenin signalling has been shown to be essential for the self-renewal of a variety of mammalian stem cells. In this review, we discuss Wnt-responsive stem cells in their niche, and mechanisms by which Wnt ligands are presented to responsive cells. We also highlight recent progress in molecular visualization that has allowed for the monitoring of Wnt signalling within the stem cell compartment and new approaches to recapitulate this niche signalling in vitro Indeed, new technologies that present Wnt in a localized manner and mimic the three-dimensional microenvironment of stem cells will advance our understanding of Wnt signalling in the stem cell niche. These advances will expand current horizons to exploit Wnt ligands in the rapidly evolving fields of tissue engineering and regenerative medicine. © 2017 The Authors.

  2. Climatic niche evolution is faster in sympatric than allopatric lineages of the butterfly genus Pyrgus.

    Science.gov (United States)

    Pitteloud, Camille; Arrigo, Nils; Suchan, Tomasz; Mastretta-Yanes, Alicia; Vila, Roger; Dincă, Vlad; Hernández-Roldán, Juan; Brockmann, Ernst; Chittaro, Yannick; Kleckova, Irena; Fumagalli, Luca; Buerki, Sven; Pellissier, Loïc; Alvarez, Nadir

    2017-04-12

    Understanding how speciation relates to ecological divergence has long fascinated biologists. It is assumed that ecological divergence is essential to sympatric speciation, as a mechanism to avoid competition and eventually lead to reproductive isolation, while divergence in allopatry is not necessarily associated with niche differentiation. The impact of the spatial context of divergence on the evolutionary rates of abiotic dimensions of the ecological niche has rarely been explored for an entire clade. Here, we compare the magnitude of climatic niche shifts between sympatric versus allopatric divergence of lineages in butterflies. By combining next-generation sequencing, parametric biogeography and ecological niche analyses applied to a genus-wide phylogeny of Palaearctic Pyrgus butterflies, we compare evolutionary rates along eight climatic dimensions across sister lineages that diverged in large-scale sympatry versus allopatry. In order to examine the possible effects of the spatial scale at which sympatry is defined, we considered three sets of biogeographic assignments, ranging from narrow to broad definition. Our findings suggest higher rates of niche evolution along all climatic dimensions for sister lineages that diverge in sympatry, when using a narrow delineation of biogeographic areas. This result contrasts with significantly lower rates of climatic niche evolution found in cases of allopatric speciation, despite the biogeographic regions defined here being characterized by significantly different climates. Higher rates in allopatry are retrieved when biogeographic areas are too widely defined-in such a case allopatric events may be recorded as sympatric. Our results reveal the macro-evolutionary significance of abiotic niche differentiation involved in speciation processes within biogeographic regions, and illustrate the importance of the spatial scale chosen to define areas when applying parametric biogeographic analyses. © 2017 The Author(s).

  3. Quantitative analysis of microbial biomass yield in aerobic bioreactor.

    Science.gov (United States)

    Watanabe, Osamu; Isoda, Satoru

    2013-12-01

    We have studied the integrated model of reaction rate equations with thermal energy balance in aerobic bioreactor for food waste decomposition and showed that the integrated model has the capability both of monitoring microbial activity in real time and of analyzing biodegradation kinetics and thermal-hydrodynamic properties. On the other hand, concerning microbial metabolism, it was known that balancing catabolic reactions with anabolic reactions in terms of energy and electron flow provides stoichiometric metabolic reactions and enables the estimation of microbial biomass yield (stoichiometric reaction model). We have studied a method for estimating real-time microbial biomass yield in the bioreactor during food waste decomposition by combining the integrated model with the stoichiometric reaction model. As a result, it was found that the time course of microbial biomass yield in the bioreactor during decomposition can be evaluated using the operational data of the bioreactor (weight of input food waste and bed temperature) by the combined model. The combined model can be applied to manage a food waste decomposition not only for controlling system operation to keep microbial activity stable, but also for producing value-added products such as compost on optimum condition. Copyright © 2013 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

  4. Adopting Strategic Niche Management to Evaluate EV Demonstration Projects in China

    Directory of Open Access Journals (Sweden)

    Yixi Xue

    2016-02-01

    Full Text Available Electric Vehicles (EVs are considered to be a potential viable technology to address the persistent unsustainable problems in transport sector. In this paper, we focus on analyzing the transition processes of EVs in China because the sustainability of developing countries is essential for the worldwide sustainability. The two-round demonstration programs of EVs in China were analyzed by adopting the strategic niche management (SNM approach so as to find out what niche protection has been provided and which obstacles hamper the further development of EVs. The results show that the financial subsidy is the most important protective measure. However, the diffusion results of EVs in different pilot cities are greatly different. The main reason lies in the uneven geographical landscape. In addition, some obstacles were exposed during the niche internal processes including low quality of expectations and poor alignment within the network. Based on the analysis results, we develop a list of suggestions that are important to consider when developing EVs.

  5. Green Power Marketing - from Niches to Mass Markets

    International Nuclear Information System (INIS)

    Wuestenhagen, Rolf

    2000-01-01

    In the process of liberalization of the electricity market the customers are now in a position to participate in the decision on how their electricity is produced. In particular, many consumers have a preference for renewable energies. For the producers, marketing of 'eco-power' is an opportunity to achieve sustainable competitive advantage. However, the market share of these products is still quite small today, and 'eco-power' is usually marketed as an expensive niche product. From the perspective of sustainable development these niches are a necessary but not sufficient step. In this book, ways are discussed which could lead to a mass-market penetration of eco-power products. A theoretical analysis is combined with empirical evidence derived from the eco-power market in Germany, Switzerland, Great Britain and the U.S. as well as with a comparison with other market segments [de

  6. Role of the Stem Cell Niche in Hormone-induced Tumorigenesis in Fetal Mouse Mammary Epithelium

    National Research Council Canada - National Science Library

    Chepko, Gloria; Hilakivi-Clarke, Leena

    2006-01-01

    Develop an immunohistochemical method for identifying stem cells and stem cell niches, and to use this to determine if in utero estrogenic overstimulation causes changes in the number of stem cells or their niches...

  7. Threatened corals provide underexplored microbial habitats.

    Directory of Open Access Journals (Sweden)

    Shinichi Sunagawa

    2010-03-01

    Full Text Available Contemporary in-depth sequencing of environmental samples has provided novel insights into microbial community structures, revealing that their diversity had been previously underestimated. Communities in marine environments are commonly composed of a few dominant taxa and a high number of taxonomically diverse, low-abundance organisms. However, studying the roles and genomic information of these "rare" organisms remains challenging, because little is known about their ecological niches and the environmental conditions to which they respond. Given the current threat to coral reef ecosystems, we investigated the potential of corals to provide highly specialized habitats for bacterial taxa including those that are rarely detected or absent in surrounding reef waters. The analysis of more than 350,000 small subunit ribosomal RNA (16S rRNA sequence tags and almost 2,000 nearly full-length 16S rRNA gene sequences revealed that rare seawater biosphere members are highly abundant or even dominant in diverse Caribbean corals. Closely related corals (in the same genus/family harbored similar bacterial communities. At higher taxonomic levels, however, the similarities of these communities did not correlate with the phylogenetic relationships among corals, opening novel questions about the evolutionary stability of coral-microbial associations. Large proportions of OTUs (28.7-49.1% were unique to the coral species of origin. Analysis of the most dominant ribotypes suggests that many uncovered bacterial taxa exist in coral habitats and await future exploration. Our results indicate that coral species, and by extension other animal hosts, act as specialized habitats of otherwise rare microbes in marine ecosystems. Here, deep sequencing provided insights into coral microbiota at an unparalleled resolution and revealed that corals harbor many bacterial taxa previously not known. Given that two of the coral species investigated are listed as threatened under

  8. A Global Stem Cell Niche – Need of the Hour

    Directory of Open Access Journals (Sweden)

    Editorial

    2014-11-01

    Full Text Available A Global Stem Cell Niche – Need of the Hour The time, this issue is online, most of us would be aware of the world’s first induced pluripotent stem (iPS cell based clinical trial for age-related macular degeneration which is underway in Japan. The first patient in the trial has been transplanted with the cell sheets of retinal pigment epithelium derived from the patient's own iPS cells in September 2014 [1] and is under follow-up. As we are overwhelmed with this scientific feat, an analysis of the trends of stem cell based clinical trials globally [2] makes us realize that there is a wide variation in the clinical trials between the nations, with differences being observed in diseases that are given priority, cell sources that are being chosen, principles of ethics, regulatory frameworks etc,. A realization dawns that the scientific communities in each group or country have their own niche of cell based research leading to the above mentioned variations. While in Japan, a hi-tech iPS trial has started, Mazini et al from Morocco, describe the hurdles in creating a public cord blood bank in their country with a background of the regulatory guidelines existing there while Lee et al's work from the United States of America (USA focuses on microencapsulation of adipose derived stem cells. While each of the above subject are equally important, a global consortium is the need of the hour, where interactions among all the stake holders of cell based therapies can be established for enabling exchange of information, technology, solutions and products, thereby avoiding repetition of the same work, while gaining the insight of different viewpoints into solving an issue which could be of significance either to a local community or the entire global society. References: Reardon S, Cyranoski D. Japan stem-cell trial stirs envy. Nature. 2014 ;513(7518:287-8. Li MD, Atkins H, Bubela T. The global landscape of stem cell clinical trials. Regen Med. 2014;9(1:27-39.

  9. Molecular and Microbial Mechanisms Increasing Soil C Storage Under Future Rates of Anthropogenic N Deposition

    Energy Technology Data Exchange (ETDEWEB)

    Zak, Donald R. [Univ. of Michigan, Ann Arbor, MI (United States)

    2017-11-17

    A growing body of evidence reveals that anthropogenic N deposition can reduce the microbial decay of plant detritus and increase soil C storage across a wide range of terrestrial ecosystems. This aspect of global change has the potential to constrain the accumulation of anthropogenic CO2 in the Earth’s atmosphere, and hence slow the pace of climate warming. The molecular and microbial mechanisms underlying this biogeochemical response are not understood, and they are not a component of any coupled climate-biogeochemical model estimating ecosystem C storage, and hence, the future climate of an N-enriched Earth. Here, we report the use of genomic-enabled approaches to identify the molecular underpinnings of the microbial mechanisms leading to greater soil C storage in response to anthropogenic N deposition, thereby enabling us to better anticipate changes in soil C storage.

  10. Phylogeny and niche conservatism in North and Central American triatomine bugs (Hemiptera: Reduviidae: Triatominae), vectors of Chagas' disease.

    Science.gov (United States)

    Ibarra-Cerdeña, Carlos N; Zaldívar-Riverón, Alejandro; Peterson, A Townsend; Sánchez-Cordero, Víctor; Ramsey, Janine M

    2014-10-01

    The niche conservatism hypothesis states that related species diverge in niche characteristics at lower rates than expected, given their lineage divergence. Here we analyze whether niche conservatism is a common pattern among vector species (Hemiptera: Reduviidae: Triatominae) of Trypanosoma cruzi that inhabit North and Central America, a highly heterogeneous landmass in terms of environmental gradients. Mitochondrial and nuclear loci were used in a multi-locus phylogenetic framework to reconstruct phylogenetic relationships among species and estimate time of divergence of selected clades to draw biogeographic inferences. Then, we estimated similarity between the ecological niche of sister species and tested the niche conservatism hypothesis using our best estimate of phylogeny. Triatoma is not monophyletic. A primary clade with all North and Central American (NCA) triatomine species from the genera Triatoma, Dipetalogaster, and Panstrongylus, was consistently recovered. Nearctic species within the NCA clade (T. p. protracta, T. r. rubida) diverged during the Pliocene, whereas the Neotropical species (T. phyllosoma, T. longipennis, T. dimidiata complex) are estimated to have diverged more recently, during the Pleistocene. The hypothesis of niche conservatism could not be rejected for any of six sister species pairs. Niche similarity between sister species best fits a retention model. While this framework is used here to infer niche evolution, it has a direct impact on spatial vector dynamics driven by human population movements, expansion of transportation networks and climate change scenarios.

  11. Ecology: a niche for cyanobacteria containing chlorophyll d

    DEFF Research Database (Denmark)

    Kühl, Michael; Chen, Min; Ralph, Peter J

    2005-01-01

    we demonstrate photosynthetic activity in Acaryochloris-like phototrophs that live underneath minute coral-reef invertebrates (didemnid ascidians) in a shaded niche enriched in near-infrared light. This discovery clarifies how these cyanobacteria are able to thrive as free-living organisms...

  12. Average niche breadths of species in lake macrophyte communities respond to ecological gradients variably in four regions on two continents.

    Science.gov (United States)

    Alahuhta, Janne; Virtala, Antti; Hjort, Jan; Ecke, Frauke; Johnson, Lucinda B; Sass, Laura; Heino, Jani

    2017-05-01

    Different species' niche breadths in relation to ecological gradients are infrequently examined within the same study and, moreover, species niche breadths have rarely been averaged to account for variation in entire ecological communities. We investigated how average environmental niche breadths (climate, water quality and climate-water quality niches) in aquatic macrophyte communities are related to ecological gradients (latitude, longitude, altitude, species richness and lake area) among four distinct regions (Finland, Sweden and US states of Minnesota and Wisconsin) on two continents. We found that correlations between the three different measures of average niche breadths and ecological gradients varied considerably among the study regions, with average climate and average water quality niche breadth models often showing opposite trends. However, consistent patterns were also found, such as widening of average climate niche breadths and narrowing of average water quality niche breadths of aquatic macrophytes along increasing latitudinal and altitudinal gradients. This result suggests that macrophyte species are generalists in relation to temperature variations at higher latitudes and altitudes, whereas species in southern, lowland lakes are more specialised. In contrast, aquatic macrophytes growing in more southern nutrient-rich lakes were generalists in relation to water quality, while specialist species are adapted to low-productivity conditions and are found in highland lakes. Our results emphasise that species niche breadths should not be studied using only coarse-scale data of species distributions and corresponding environmental conditions, but that investigations on different kinds of niche breadths (e.g., climate vs. local niches) also require finer resolution data at broad spatial extents.

  13. Microbial Community Response to Carbon Substrate Amendment in Mercury Impacted Sediments: Implications on Microbial Methylation of Mercury.

    Science.gov (United States)

    Elias, D. A.; Somenahally, A. C.; Moberly, J. G.; Hurt, R. A., Jr.; Brown, S. D.; Podar, M.; Palumbo, A. V.; Gilmour, C. C.

    2015-12-01

    Methylmercury (MeHg) is a neurotoxic and bio-accumulative product of the microbial methylation of inorganic mercury (Hg(II)). Methylating organisms are now known to exist in almost all anaerobic niches including fermentation, Fe(III)- and sulfate- reduction as well as methanogenesis. The study objective was to determine the effect of different carbon sources on the microbial community and methylating populations in particular along a Hg contaminated creek. Sediment cores from upstream and downstream at the Hg contaminated East Fork Poplar Creek (EFPC), Oak Ridge TN, and a background site were sectioned by depth, and Hg-methylation potential (HgMP) assays were performed using stable isotope spikes. Sediments from the lowest depth possessed the highest in-situ activity. Replicate samples were amended with different carbon substrates (cellulose, acetate, propionate, lactate, ethanol and methanol), spiked with stable isotopes for HgMP assays and incubated for 24hrs. Sequencing of the 16S rRNA gene was performed to determine alterations in Bacterial and Archaeal population dynamics. Additionally, bioinformatics and our new qualitative and quantitative hgcAB primers were utilized to determine microbial community structure alterations and correlate organism and gene abundance with altered MeHg generation. HgMP was significantly reduced in cellulose amended sediments while acetate and propionate slightly decreased HgMP in both sites. Methanol, ethanol and lactate increased the HgMP in EFPC downstream while cellulose amendment significantly decreased the Proteobacteria, and the Firmicutes increased but none are currently known to produce MeHg. Geobacter bemidjiensis in particular significantly decreased in cellulose amended sediments in all three sites from being predominant in-situ. This suggests that in EFPC downstream and background sites, the prevalent Hg-methyaltors might be Deltaprotebacteria, since upstream, cellulose amendment did not reduce HgMP even though

  14. Foxl1-Expressing Mesenchymal Cells Constitute the Intestinal Stem Cell NicheSummary

    Directory of Open Access Journals (Sweden)

    Reina Aoki

    2016-03-01

    Full Text Available Background & Aims: Intestinal epithelial stem cells that express leucine-rich repeat-containing G-protein coupled receptor 5 (Lgr5 and/or B cell specific Moloney murine leukemia virus integration site 1 (Bmi1 continuously replicate and generate differentiated cells throughout life. Previously, Paneth cells were suggested to constitute an epithelium-intrinsic niche that regulates the behavior of these stem cells. However, ablating Paneth cells has no effect on the maintenance of functional stem cells. Here, we show definitively that a small subset of mesenchymal subepithelial cells expressing the winged-helix transcription factor forkhead box l1 (Foxl1 are a critical component of the intestinal stem cell niche. Methods: We genetically ablated Foxl1+ mesenchymal cells in adult mice using 2 separate models by expressing either the human or simian diphtheria toxin receptor under Foxl1 promoter control. Conclusions: Killing Foxl1+ cells by diphtheria toxin administration led to an abrupt cessation of proliferation of both epithelial stem- and transit-amplifying progenitor cell populations that was associated with a loss of active Wnt signaling to the intestinal epithelium. Therefore, Foxl1-expressing mesenchymal cells constitute the fundamental niche for intestinal stem cells. Keywords: Intestinal Stem Cell Niche, Wnt, Mesenchyme

  15. Affordances and Landscapes: Overcoming the Nature-Culture Dichotomy through Niche Construction Theory.

    Science.gov (United States)

    Heras-Escribano, Manuel; De Pinedo-García, Manuel

    2017-01-01

    In this paper we reject the nature-culture dichotomy by means of the idea of affordance or possibility for action, which has important implications for landscape theory. Our hypothesis is that, just as the idea of affordance can serve to overcome the subjective-objective dichotomy, the ideas of landscape and ecological niche, properly defined, would allow us to also transcend the nature-culture dichotomy. First, we introduce an overview of landscape theory, emphasizing processual landscape theory as the most suitable approach for satisfying both cultural and naturalist approaches. After that, we introduce the idea of affordance and we analyze a tension between sociocultural and transcultural affordances (affordances that depend on cultural conventions and affordances that depend on lawful information and bodily aspects of agents). This tension has various implications for landscape theory and ecological niches. Our proposal is that sociocultural and transcultural aspects of affordances could be systematically accommodated if we apply niche construction theory (the theory that explains the process by which organisms modify their selective environments) as a methodological framework for explaining the emergence of ecological niches. This approach will lead us to an integrative account of landscapes as the products of the interaction between human and environmental elements, making it a clear example of a concept that transcends the nature-culture dichotomy.

  16. Cellular players of hematopoietic stem cell mobilization in the bone marrow niche.

    Science.gov (United States)

    Tay, Joshua; Levesque, Jean-Pierre; Winkler, Ingrid G

    2017-02-01

    Hematopoietic stem cells (HSC) reside in perivascular regions of the bone marrow (BM) embedded within a complex regulatory unit called the niche. Cellular components of HSC niches include vascular endothelial cells, mesenchymal stromal progenitor cells and a variety of mature hematopoietic cells such as macrophages, neutrophils, and megakaryocytes-further regulated by sympathetic nerves and complement components as described in this review. Three decades ago the discovery that cytokines induce a large number of HSC to mobilize from the BM into the blood where they are easily harvested, revolutionised the field of HSC transplantation-curative for immune-deficiencies and some malignancies. However, despite now routine use of granulocyte-colony stimulating factor (G-CSF) to mobilise HSC for transplant, only in last 15 years has research on the mechanisms behind why and how HSC can be induced to move into the blood began. These studies have revealed the complexity of the niche that retains HSC in the BM. This review describes how BM niches and HSC themselves change during administration of G-CSF-or in the recovery phase of chemotherapy-to facilitate movement of HSC into the blood, and research now leading to development of novel therapeutics to further boost HSC mobilization and transplant success.

  17. Mineralogical Control on Microbial Diversity in a Weathered Granite?

    Science.gov (United States)

    Gleeson, D.; Clipson, N.; McDermott, F.

    2003-12-01

    Mineral transformation reactions and the behaviour of metals in rock and soils are affected not only by physicochemical parameters but also by biological factors, particularly by microbial activity. Microbes inhabit a wide range of niches in surface and subsurface environments, with mineral-microbe interactions being generally poorly understood. The focus of this study is to elucidate the role of microbial activity in the weathering of common silicate minerals in granitic rocks. A site in the Wicklow Mountains (Ireland) has been identified that consists of an outcrop surface of Caledonian (ca. 400 million years old) pegmatitic granite from which large intact crystals of variably weathered muscovite, plagioclase, K-feldspar and quartz were sampled, together with whole-rock granite. Culture-based microbial approaches have been widely used to profile microbial communities, particularly from copiotrophic environments, but it is now well established that for oligotrophic environments such as those that would be expected on weathering faces, perhaps less than 1% of microbial diversity can be profiled by cultural means. A number of culture-independent molecular based approaches have been developed to profile microbial diversity and community structure. These rely on successfully isolating environmental DNA from a given environment, followed by the use of the polymerase chain reaction (PCR) to amplify the typically small quantities of extracted DNA. Amplified DNA can then be analysed using cloning based approaches as well as community fingerprinting systems such as denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP) and ribosomal intergenic spacer analysis (RISA). Community DNA was extracted and the intergenic spacer region (ITS) between small (16S) and large (23S) bacterial subunit rRNA genes was amplified. RISA fragments were then electrophoresed on a non-denaturing polyacrylamide gel. Banding patterns suggest that

  18. Prediction of the niche effect for single flat panels with or without attached sound absorbing materials.

    Science.gov (United States)

    Sgard, Franck; Atalla, Noureddine; Nélisse, Hugues

    2015-01-01

    The sound transmission loss (STL) of a test sample measured in sound transmission facilities is affected by the opening in which it is located. This is called the niche effect. This paper uses a modal approach to study the STL of a rectangular plate with or without an attached porous material located inside a box-shaped niche. The porous material is modeled as a limp equivalent fluid. The proposed model is validated by comparison with finite element/boundary element computations. Using a condensation of the pressure fields in the niche, the niche effect is interpreted in terms of a modification of the modal blocked pressure fields acting on the panel induced by the front cavity and by a modification of the radiation efficiency of the panel modes due to the presence of the back cavity. The modal approach is then used to investigate the impact of (1) the presence of a porous material attached to the panel on the niche effect and (2) the niche effect on the assessment of the porous material insertion loss. A simplified model for the porous material based on a transfer matrix approach is also proposed to predict the STL of the system and its validity is discussed.

  19. Multifaceted Roles of Connexin 43 in Stem Cell Niches.

    Science.gov (United States)

    Genet, Nafiisha; Bhatt, Neha; Bourdieu, Antonin; Hirschi, Karen K

    2018-01-01

    Considerable progress has been made in the field of stem cell research; nonetheless, the use of stem cells for regenerative medicine therapies, for either endogenous tissue repair or cellular grafts post injury, remains a challenge. To better understand how to maintain stem cell potential in vivo and promote differentiation ex vivo, it is fundamentally important to elucidate the interactions between stem cells and their surrounding partners within their distinct niches. Among the vast array of proteins depicted as mediators for cell-to-cell interactions, connexin-comprised gap junctions play pivotal roles in the regulation of stem cell fate both in vivo and in vitro. This review summarizes and illustrates the current knowledge regarding the multifaceted roles of Cx43, specifically, in various stem cell niches.

  20. Transcriptional Activities of the Microbial Consortium Living with the Marine Nitrogen-Fixing Cyanobacterium Trichodesmium Reveal Potential Roles in Community-Level Nitrogen Cycling.

    Science.gov (United States)

    Lee, Michael D; Webb, Eric A; Walworth, Nathan G; Fu, Fei-Xue; Held, Noelle A; Saito, Mak A; Hutchins, David A

    2018-01-01

    Trichodesmium is a globally distributed cyanobacterium whose nitrogen-fixing capability fuels primary production in warm oligotrophic oceans. Like many photoautotrophs, Trichodesmium serves as a host to various other microorganisms, yet little is known about how this associated community modulates fluxes of environmentally relevant chemical species into and out of the supraorganismal structure. Here, we utilized metatranscriptomics to examine gene expression activities of microbial communities associated with Trichodesmium erythraeum (strain IMS101) using laboratory-maintained enrichment cultures that have previously been shown to harbor microbial communities similar to those of natural populations. In enrichments maintained under two distinct CO 2 concentrations for ∼8 years, the community transcriptional profiles were found to be specific to the treatment, demonstrating a restructuring of overall gene expression had occurred. Some of this restructuring involved significant increases in community respiration-related transcripts under elevated CO 2 , potentially facilitating the corresponding measured increases in host nitrogen fixation rates. Particularly of note, in both treatments, community transcripts involved in the reduction of nitrate, nitrite, and nitrous oxide were detected, suggesting the associated organisms may play a role in colony-level nitrogen cycling. Lastly, a taxon-specific analysis revealed distinct ecological niches of consistently cooccurring major taxa that may enable, or even encourage, the stable cohabitation of a diverse community within Trichodesmium consortia. IMPORTANCE Trichodesmium is a genus of globally distributed, nitrogen-fixing marine cyanobacteria. As a source of new nitrogen in otherwise nitrogen-deficient systems, these organisms help fuel carbon fixation carried out by other more abundant photoautotrophs and thereby have significant roles in global nitrogen and carbon cycling. Members of the Trichodesmium genus tend to

  1. Ontogenetic niche shifts in three Vaccinium species on a sub-alpine mountain side

    DEFF Research Database (Denmark)

    Auffret, Alistair G.; Meineri, Eric; Bruun, Hans Henrik

    2010-01-01

    Background: Climate warming in arctic and alpine regions is expected to result in the altitudinal migration of plant species, but current predictions neglect differences between species' regeneration niche and established niche. Aims: To examine potential recruitment of Vaccinium myrtillus, V. ul...

  2. UNTANGLING THE FUNGAL NICHE: A TRAIT-BASED APPROACH

    Directory of Open Access Journals (Sweden)

    Thomas W Crowther

    2014-10-01

    Full Text Available Fungi are prominent components of most terrestrial ecosystems, both in terms of biomass and ecosystem functioning, but the hyper-diverse nature of most communities has obscured the search for unifying principles governing community organization. In particular, unlike plants and animals, observational studies provide little evidence for the existence of niche processes in structuring fungal communities at broad spatial scales. This limits our capacity to predict how communities, and their functioning, vary across landscapes. We outline how a shift in focus, from taxonomy towards functional traits, might prove to be valuable in the search for general patterns in fungal ecology. We build on theoretical advances in plant and animal ecology to provide an empirical framework for a trait-based approach in fungal community ecology. Drawing upon specific characteristics of the fungal system, we highlight the significance of drought stress and combat in structuring free-living fungal communities. We propose a conceptual model to formalize how trade-offs between stress-tolerance and combative dominance are likely to organize communities across environmental gradients. Given that the survival of a fungus in a given environment is contingent on its ability to tolerate antagonistic competitors, measuring variation in combat trait expression along environmental gradients provides a means of elucidating realized, from fundamental niche spaces. We conclude that, using a trait-based understanding of how niche processes structure fungal communities across time and space, we can ultimately link communities with ecosystem functioning. Our trait-based framework highlights fundamental uncertainties that require testing in the fungal system, given their potential to uncover general mechanisms in fungal ecology.

  3. Foraging niche segregation in Malaysian babblers (Family: Timaliidae.

    Directory of Open Access Journals (Sweden)

    Mohammad Saiful Mansor

    Full Text Available Tropical rainforests are considered as hotspots for bird diversity, yet little is known about the system that upholds the coexistence of species. Differences in body size that are associated with foraging strategies and spatial distribution are believed to promote the coexistence of closely related species by reducing competition. However, the fact that many babbler species do not differ significantly in their morphology has challenged this view. We studied the foraging ecology of nine sympatric babbler species (i.e., Pellorneum capistratum, P. bicolor, P. malaccense, Malacopteron cinereum, M. magnum, Stachyris nigriceps, S. nigricollis, S. maculata, and Cyanoderma erythropterum in the Krau Wildlife Reserve in Peninsular Malaysia. We investigated; i how these babblers forage in the wild and use vegetation to obtain food, and ii how these trophically similar species differ in spatial distribution and foraging tactics. Results indicated that most babblers foraged predominantly on aerial leaf litter and used gleaning manoeuvre in intermediate-density foliage but exhibited wide ranges of vertical strata usage, thus reducing interspecific competition. The principal component analysis indicated that two components, i.e., foraging height and substrate are important as mechanisms to allow the coexistence of sympatric babblers. The present findings revealed that these bird species have unique foraging niches that are distinct from each other, and this may apply to other insectivorous birds inhabiting tropical forests. This suggests that niche separation does occur among coexisting birds, thus following Gause' law of competitive exclusion, which states two species occupying the same niche will not stably coexist.

  4. Foraging niche segregation in Malaysian babblers (Family: Timaliidae).

    Science.gov (United States)

    Mansor, Mohammad Saiful; Ramli, Rosli

    2017-01-01

    Tropical rainforests are considered as hotspots for bird diversity, yet little is known about the system that upholds the coexistence of species. Differences in body size that are associated with foraging strategies and spatial distribution are believed to promote the coexistence of closely related species by reducing competition. However, the fact that many babbler species do not differ significantly in their morphology has challenged this view. We studied the foraging ecology of nine sympatric babbler species (i.e., Pellorneum capistratum, P. bicolor, P. malaccense, Malacopteron cinereum, M. magnum, Stachyris nigriceps, S. nigricollis, S. maculata, and Cyanoderma erythropterum) in the Krau Wildlife Reserve in Peninsular Malaysia. We investigated; i) how these babblers forage in the wild and use vegetation to obtain food, and ii) how these trophically similar species differ in spatial distribution and foraging tactics. Results indicated that most babblers foraged predominantly on aerial leaf litter and used gleaning manoeuvre in intermediate-density foliage but exhibited wide ranges of vertical strata usage, thus reducing interspecific competition. The principal component analysis indicated that two components, i.e., foraging height and substrate are important as mechanisms to allow the coexistence of sympatric babblers. The present findings revealed that these bird species have unique foraging niches that are distinct from each other, and this may apply to other insectivorous birds inhabiting tropical forests. This suggests that niche separation does occur among coexisting birds, thus following Gause' law of competitive exclusion, which states two species occupying the same niche will not stably coexist.

  5. Spermatogonial stem cell markers and niche in equids.

    Directory of Open Access Journals (Sweden)

    Guilherme M J Costa

    Full Text Available Spermatogonial stem cells (SSCs are the foundation of spermatogenesis and are located in a highly dynamic microenvironment called "niche" that influences all aspects of stem cell function, including homing, self-renewal and differentiation. Several studies have recently identified specific proteins that regulate the fate of SSCs. These studies also aimed at identifying surface markers that would facilitate the isolation of these cells in different vertebrate species. The present study is the first to investigate SSC physiology and niche in stallions and to offer a comparative evaluation of undifferentiated type A spermatogonia (Aund markers (GFRA1, PLZF and CSF1R in three different domestic equid species (stallions, donkeys, and mules. Aund were first characterized according to their morphology and expression of the GFRA1 receptor. Our findings strongly suggest that in stallions these cells were preferentially located in the areas facing the interstitium, particularly those nearby blood vessels. This distribution is similar to what has been observed in other vertebrate species. In addition, all three Aund markers were expressed in the equid species evaluated in this study. These markers have been well characterized in other mammalian species, which suggests that the molecular mechanisms that maintain the niche and Aund/SSCs physiology are conserved among mammals. We hope that our findings will help future studies needing isolation and cryopreservation of equids SSCs. In addition, our data will be very useful for studies that aim at preserving the germplasm of valuable animals, and involve germ cell transplantation or xenografts of equids testis fragments/germ cells suspensions.

  6. Foraging niche segregation in Malaysian babblers (Family: Timaliidae)

    Science.gov (United States)

    Mansor, Mohammad Saiful; Ramli, Rosli

    2017-01-01

    Tropical rainforests are considered as hotspots for bird diversity, yet little is known about the system that upholds the coexistence of species. Differences in body size that are associated with foraging strategies and spatial distribution are believed to promote the coexistence of closely related species by reducing competition. However, the fact that many babbler species do not differ significantly in their morphology has challenged this view. We studied the foraging ecology of nine sympatric babbler species (i.e., Pellorneum capistratum, P. bicolor, P. malaccense, Malacopteron cinereum, M. magnum, Stachyris nigriceps, S. nigricollis, S. maculata, and Cyanoderma erythropterum) in the Krau Wildlife Reserve in Peninsular Malaysia. We investigated; i) how these babblers forage in the wild and use vegetation to obtain food, and ii) how these trophically similar species differ in spatial distribution and foraging tactics. Results indicated that most babblers foraged predominantly on aerial leaf litter and used gleaning manoeuvre in intermediate-density foliage but exhibited wide ranges of vertical strata usage, thus reducing interspecific competition. The principal component analysis indicated that two components, i.e., foraging height and substrate are important as mechanisms to allow the coexistence of sympatric babblers. The present findings revealed that these bird species have unique foraging niches that are distinct from each other, and this may apply to other insectivorous birds inhabiting tropical forests. This suggests that niche separation does occur among coexisting birds, thus following Gause’ law of competitive exclusion, which states two species occupying the same niche will not stably coexist. PMID:28253284

  7. Division within the North American boreal forest: Ecological niche divergence between the Bicknell's Thrush (Catharus bicknelli) and Gray-cheeked Thrush (C. minimus).

    Science.gov (United States)

    FitzGerald, Alyssa M

    2017-07-01

    Sister species that diverged in allopatry in similar environments are expected to exhibit niche conservatism. Using ecological niche modeling and a multivariate analysis of climate and habitat data, I test the hypothesis that the Bicknell's Thrush ( Catharus bicknelli ) and Gray-cheeked Thrush ( C. mimimus ), sister species that breed in the North American boreal forest, show niche conservatism. Three tree species that are important components of breeding territories of both thrush species were combined with climatic variables to create niche models consisting of abiotic and biotic components. Abiotic-only, abiotic+biotic, and biotic-only models were evaluated using the area under the curve (AUC) criterion. Abiotic+biotic models had higher AUC scores and did not over-project thrush distributions compared to abiotic-only or biotic-only models. From the abiotic+biotic models, I tested for niche conservatism or divergence by accounting for the differences in the availability of niche components by calculating (1) niche overlap from ecological niche models and (2) mean niche differences of environmental values at occurrence points. Niche background similarity tests revealed significant niche divergence in 10 of 12 comparisons, and multivariate tests revealed niche divergence along 2 of 3 niche axes. The Bicknell's Thrush breeds in warmer and wetter regions with a high abundance of balsam fir ( Abies balsamea ), whereas Gray-cheeked Thrush often co-occurs with black spruce ( Picea mariana ). Niche divergence, rather than conservatism, was the predominant pattern for these species, suggesting that ecological divergence has played a role in the speciation of the Bicknell's Thrush and Gray-cheeked Thrush. Furthermore, because niche models were improved by the incorporation of biotic variables, this study validates the inclusion of relevant biotic factors in ecological niche modeling to increase model accuracy.

  8. Microbial ecology and genomics: A crossroads of opportunity

    Energy Technology Data Exchange (ETDEWEB)

    Stahl, David A. [University of Washington; Tiedje, James M. [Michigan State University

    2002-08-30

    Microbes have dominated life on Earth for most of its 4.5 billionyear history. They are the foundation of the biosphere, controlling the biogeochemical cycles and affecting geology, hydrology, and local and global climates. All life is completely dependent upon them. Humans cannot survive without the rich diversity of microbes, but most microbial species can survive without humans. Extraordinary advances in molecular technology have fostered an explosion of information in microbial biology. It is now known that microbial species in culture poorly represent their natural diversity—which dwarfs conventions established for the visible world. This was revealed over the last decade using newer molecular tools to explore environmental diversity and has sparked an explosive growth in microbial ecology and technologies that may profit from the bounty of natural biochemical diversity. Several colloquia and meetings have helped formulate policy recommendations to enable sustained research programs in these areas. One such colloquium organized by the American Academy of Microbiology (“The Microbial World: Foundation of the Biosphere,” 1997) made two key recommendations: (1) develop a more complete inventory of living organisms and the interagency cooperation needed to accomplish this goal, and (2) develop strategies to harvest this remarkable biological diversity for the benefit of science, technology, and society. Complete genome sequence information was identified as an essential part of strategy development, and the recommendation was made to sequence the genome of at least one species of each of the major divisions of microbial life.

  9. ECRB ALCOVE AND NICHE GROUND SUPPORT ANALYSIS

    International Nuclear Information System (INIS)

    J.W. Keifer

    1999-01-01

    The purpose of the analysis is to provide design bases for Enhanced Characterization of the Repository Block (ECRB) alcove and niche ground support drawings. The objective is to evaluate the ESF Alcove Ground Support Analysis (Ref 5.1) to determine if the calculations technically bound the ECRB alcoves and to address specific differences in the conditions and constraints

  10. Targeting Unknowns Just Underfoot: Microbial Ecology and Community Genomics of C Cycling in Soil Informed and Enabled with DNA-SIP

    Science.gov (United States)

    Pepe-Ranney, C. P.; Campbell, A.; Buckley, D. H.

    2015-12-01

    Microorganisms drive biogeochemical cycles and because soil is a large global carbon (C) reservoir (soil contains more C than plants and the atmosphere combined), soil microorganisms are important players in the global C-cycle. Frustratingly, however, many soil microorganisms resist cultivation and soil communities are astoundingly complex. This makes soil microbiology difficult to study and without a solid understanding of soil microbial ecology, models of soil C feedbacks to climate change are under-informed. Stable isotope probing (SIP) is a useful approach for establishing identity-function connections in microbial communities but has been challenging to employ in soil due to the inadequate resolution of microbial community fingerprinting techniques. High throughput DNA sequencing improves SIP resolving power transforming it into a powerful tool for studying the soil C cycle. We conducted a DNA-SIP experiment to track flow of xylose-C, a labile component of plant biomass, and cellulose-C, the most abundant global biopolymer, through a soil microbial community. We could track 13C into microbial DNA even when added 13C amounted to less than 5% of native C and found Spartobacteria, Chloroflexi, and Planctomycetes taxa were among those that assimilated 13C cellulose. These lineages are cosmopolitan in soil but little is known of their ecophysiology. By profiling SSU rRNA genes across entire DNA-SIP density gradients, we assessed relative DNA atom % 13C per taxon in 13C treatments and found cellulose degraders exhibited signal consistent with a specialist lifestyle with respect to C preference. Further, DNA-SIP enriches DNA of targeted microorganisms (Verrucomicrobia cellulose degraders were enriched by nearly two orders of magnitude) and this enriched DNA can serve as template for community genomics. We produced draft genomes from soil cellulose degraders including microorganisms belonging to Verrucomicrobia, Chloroflexi, and Planctomycetes from SIP enriched DNA

  11. INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.

    Science.gov (United States)

    Alam, Intikhab; Antunes, André; Kamau, Allan Anthony; Ba Alawi, Wail; Kalkatawi, Manal; Stingl, Ulrich; Bajic, Vladimir B

    2013-01-01

    The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes. We developed a data warehouse system (INDIGO) that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea. We provide examples of utilizing the system to gain new insights into specific aspects on the unique lifestyle and adaptations of these organisms to extreme environments. We developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial genomes. It will be regularly updated and extended with new genomes. It is aimed to serve as a resource dedicated to the Red Sea microbes. In addition, through INDIGO, we provide our Automatic Annotation of Microbial Genomes (AAMG) pipeline. The INDIGO web server is freely available at http://www.cbrc.kaust.edu.sa/indigo.

  12. Isotopic niche partitioning between two apex predators over time.

    Science.gov (United States)

    Drago, Massimiliano; Cardona, Luis; Franco-Trecu, Valentina; Crespo, Enrique A; Vales, Damián G; Borella, Florencia; Zenteno, Lisette; Gonzáles, Enrique M; Inchausti, Pablo

    2017-07-01

    Stable isotope analyses have become an important tool in reconstructing diets, analysing resource use patterns, elucidating trophic relations among predators and understanding the structure of food webs. Here, we use stable carbon and nitrogen isotope ratios in bone collagen to reconstruct and compare the isotopic niches of adult South American fur seals (Arctocephalus australis; n = 86) and sea lions (Otaria flavescens; n = 49) - two otariid species with marked morphological differences - in the Río de la Plata estuary (Argentina - Uruguay) and the adjacent Atlantic Ocean during the second half of the 20th century and the beginning of the 21st century. Samples from the middle Holocene (n = 7 fur seals and n = 5 sea lions) are also included in order to provide a reference point for characterizing resource partitioning before major anthropogenic modifications of the environment. We found that the South American fur seals and South American sea lions had distinct isotopic niches during the middle Holocene. Isotopic niche segregation was similar at the beginning of the second half of the 20th century, but has diminished over time. The progressive convergence of the isotopic niches of these two otariids during the second half of the 20th century and the beginning of the 21st century is most likely due to the increased reliance of South American fur seals on demersal prey. This recent dietary change in South American fur seals can be explained by at least two non-mutually exclusive mechanisms: (i) the decrease in the abundance of sympatric South American sea lions as a consequence of small colony size and high pup mortality resulting from commercial sealing; and (ii) the decrease in the average size of demersal fishes due to intense fishing of the larger class sizes, which may have increased their accessibility to those eared seals with a smaller mouth gape, that is, South American fur seals of both sexes and female South American sea lions. © 2017 The Authors

  13. Microbial gut diversity of Africanized and European honey bee larval instars.

    Directory of Open Access Journals (Sweden)

    Svjetlana Vojvodic

    Full Text Available The first step in understanding gut microbial ecology is determining the presence and potential niche breadth of associated microbes. While the core gut bacteria of adult honey bees is becoming increasingly apparent, there is very little and inconsistent information concerning symbiotic bacterial communities in honey bee larvae. The larval gut is the target of highly pathogenic bacteria and fungi, highlighting the need to understand interactions between typical larval gut flora, nutrition and disease progression. Here we show that the larval gut is colonized by a handful of bacterial groups previously described from guts of adult honey bees or other pollinators. First and second larval instars contained almost exclusively Alpha 2.2, a core Acetobacteraceae, while later instars were dominated by one of two very different Lactobacillus spp., depending on the sampled site. Royal jelly inhibition assays revealed that of seven bacteria occurring in larvae, only one Neisseriaceae and one Lactobacillus sp. were inhibited. We found both core and environmentally vectored bacteria with putatively beneficial functions. Our results suggest that early inoculation by Acetobacteraceae may be important for microbial succession in larvae. This assay is a starting point for more sophisticated in vitro models of nutrition and disease resistance in honey bee larvae.

  14. Combgap Promotes Ovarian Niche Development and Chromatin Association of EcR-Binding Regions in BR-C.

    Science.gov (United States)

    Hitrik, Anna; Popliker, Malka; Gancz, Dana; Mukamel, Zohar; Lifshitz, Aviezer; Schwartzman, Omer; Tanay, Amos; Gilboa, Lilach

    2016-11-01

    The development of niches for tissue-specific stem cells is an important aspect of stem cell biology. Determination of niche size and niche numbers during organogenesis involves precise control of gene expression. How this is achieved in the context of a complex chromatin landscape is largely unknown. Here we show that the nuclear protein Combgap (Cg) supports correct ovarian niche formation in Drosophila by controlling ecdysone-Receptor (EcR)- mediated transcription and long-range chromatin contacts in the broad locus (BR-C). Both cg and BR-C promote ovarian growth and the development of niches for germ line stem cells. BR-C levels were lower when Combgap was either reduced or over-expressed, indicating an intricate regulation of the BR-C locus by Combgap. Polytene chromosome stains showed that Cg co-localizes with EcR, the major regulator of BR-C, at the BR-C locus and that EcR binding to chromatin was sensitive to changes in Cg levels. Proximity ligation assay indicated that the two proteins could reside in the same complex. Finally, chromatin conformation analysis revealed that EcR-bound regions within BR-C, which span ~30 KBs, contacted each other. Significantly, these contacts were stabilized in an ecdysone- and Combgap-dependent manner. Together, these results highlight Combgap as a novel regulator of chromatin structure that promotes transcription of ecdysone target genes and ovarian niche formation.

  15. Replacement of harmful animal use in life science education: the approach and activities of InterNICHE.

    Science.gov (United States)

    Jukes, Nick

    2004-06-01

    Harmful animal use in undergraduate education is increasingly being replaced by alternatives, such as computer software, manikins and simulators, ethically sourced animal cadavers, apprentice work with animal patients, and student self-experimentation. Combinations of such alternatives can better meet teaching objectives, reduce costs and avoid the negative pedagogical and social impact of animal experimentation. Since 1988, the International Network for Humane Education (InterNICHE, formerly EuroNICHE) has been working with teachers to replace harmful animal use and has been supporting students' right to conscientious objection. This paper presents the approach, history and current activities of InterNICHE. With a vision of 100% replacement, the network aims for empowerment by networking information and providing support. It works with the belief that most teachers want investment in the best quality and most humane education possible. The forthcoming second edition of the InterNICHE book, from Guinea Pig to Computer Mouse,1 includes practical details of progressive teaching aids and approaches, as well as case studies from teachers who employ such alternatives. In 1999, InterNICHE produced the film Alternatives in Education, now available in 20 languages. Such resources are complemented by outreach trips and conferences and an Alternatives Loan System, which offers products for familiarisation and assessment. The InterNICHE website (www.interniche.org) was launched in 2001.

  16. Climatic niche conservatism and biogeographical non-equilibrium in Eschscholzia californica (Papaveraceae), an invasive plant in the Chilean Mediterranean region.

    Science.gov (United States)

    Peña-Gómez, Francisco T; Guerrero, Pablo C; Bizama, Gustavo; Duarte, Milén; Bustamante, Ramiro O

    2014-01-01

    Species climate requirements are useful for predicting their geographic distribution. It is often assumed that the niche requirements for invasive plants are conserved during invasion, especially when the invaded regions share similar climate conditions. California and central Chile have a remarkable degree of convergence in their vegetation structure, and a similar Mediterranean climate. Such similarities make these geographic areas an interesting natural experiment for testing climatic niche dynamics and the equilibrium of invasive species in a new environment. We tested to see if the climatic niche of Eschscholzia californica is conserved in the invaded range (central Chile), and we assessed whether the invasion process has reached a biogeographical equilibrium, i.e., occupy all the suitable geographic locations that have suitable conditions under native niche requirements. We compared the climatic niche in the native and invaded ranges as well as the projected potential geographic distribution in the invaded range. In order to compare climatic niches, we conducted a Principal Component Analysis (PCA) and Species Distribution Models (SDMs), to estimate E. californica's potential geographic distribution. We also used SDMs to predict altitudinal distribution limits in central Chile. Our results indicated that the climatic niche occupied by E. californica in the invaded range is firmly conserved, occupying a subset of the native climatic niche but leaving a substantial fraction of it unfilled. Comparisons of projected SDMs for central Chile indicate a similarity, yet the projection from native range predicted a larger geographic distribution in central Chile compared to the prediction of the model constructed for central Chile. The projected niche occupancy profile from California predicted a higher mean elevation than that projected from central Chile. We concluded that the invasion process of E. californica in central Chile is consistent with climatic niche

  17. Alternative natural seasoning to improve the microbial stability of low-salt beef patties.

    Science.gov (United States)

    García-Lomillo, Javier; González-SanJosé, M A Luisa; Del Pino-García, Raquel; Rivero-Pérez, M A Dolores; Muñiz-Rodríguez, Pilar

    2017-07-15

    The meat industry is seeking new strategies to reduce the sodium content of meat products without shortening their shelf-life. Natural seasonings as salt alternatives are more appreciated than chemical preservatives and also enable the incorporation of interesting nutrients. The present work studies the potential of a new red wine pomace seasoning (RWPS), derived from wine pomace, to inhibit spoilage growth in beef patties with different salt levels (2%, 1.5% and 1%) held in storage at 4°C. The use of RWPS (2% w/w) improved the microbial stability of the patties, delaying total aerobic mesophilic, and lactic acid bacteria growth, especially in samples with low salt levels. Satisfactory results were obtained in modified-atmosphere and air-packaged patties. RWPS also enabled the incorporation of fiber and phenolic compounds, and increased potassium and calcium levels. In summary, RWPS presented an interesting potential as a seasoning in meat products, enabling salt reduction without compromising their microbial stability. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Affordances and Landscapes: Overcoming the Nature–Culture Dichotomy through Niche Construction Theory

    Science.gov (United States)

    Heras-Escribano, Manuel; De Pinedo-García, Manuel

    2018-01-01

    In this paper we reject the nature–culture dichotomy by means of the idea of affordance or possibility for action, which has important implications for landscape theory. Our hypothesis is that, just as the idea of affordance can serve to overcome the subjective–objective dichotomy, the ideas of landscape and ecological niche, properly defined, would allow us to also transcend the nature–culture dichotomy. First, we introduce an overview of landscape theory, emphasizing processual landscape theory as the most suitable approach for satisfying both cultural and naturalist approaches. After that, we introduce the idea of affordance and we analyze a tension between sociocultural and transcultural affordances (affordances that depend on cultural conventions and affordances that depend on lawful information and bodily aspects of agents). This tension has various implications for landscape theory and ecological niches. Our proposal is that sociocultural and transcultural aspects of affordances could be systematically accommodated if we apply niche construction theory (the theory that explains the process by which organisms modify their selective environments) as a methodological framework for explaining the emergence of ecological niches. This approach will lead us to an integrative account of landscapes as the products of the interaction between human and environmental elements, making it a clear example of a concept that transcends the nature–culture dichotomy. PMID:29375426

  19. The role of macrobiota in structuring microbial communities along rocky shores

    Directory of Open Access Journals (Sweden)

    Catherine A. Pfister

    2014-10-01

    Full Text Available Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of the gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota.

  20. Weak Evidence of Regeneration Habitat but Strong Evidence of Regeneration Niche for a Leguminous Shrub

    Science.gov (United States)

    Delerue, Florian; Gonzalez, Maya; Michalet, Richard; Pellerin, Sylvain; Augusto, Laurent

    2015-01-01

    The identification of an ecological niche specific to the regeneration phase has mobilised significant attention. However, the importance of the regeneration niche concept remains unclear. Our main objective was to study the existence of such a regeneration niche for a leguminous shrub, Ulex europaeus. This study was carried out in southwest France in the context of water and nutrient stresses (mainly phosphorus limitation) due to the presence of nutrient-poor sandy soils. We analysed the regeneration of the species from the germination of seeds and emergence of new seedlings until the seedlings reached young shrub size. Our design included a P fertilisation treatment. We also investigated microsite characteristics (micro-topography and vegetation development) as they can interact with meteorological conditions and determine water availability for seeds and seedlings. We found that P availability controlled seedling growth and the time necessary to reach young shrub size. Water availability appeared to impact the species germination and seedlings survival. We also found that P and water availability depended on the interactions between microsite characteristics and climatic variations. Finally we found evidence that P and water availability are important ecological factors shaping the regeneration niche of the species, but we found weak evidence that any microsite would be appropriate for the regeneration of the species in the long term. Future studies regarding regeneration niches need to distinguish more clearly the ecological factors important for regeneration (the regeneration niche per se) and the physical world where the seedlings appear and develop (the regeneration habitat). PMID:26098877

  1. Weak Evidence of Regeneration Habitat but Strong Evidence of Regeneration Niche for a Leguminous Shrub.

    Directory of Open Access Journals (Sweden)

    Florian Delerue

    Full Text Available The identification of an ecological niche specific to the regeneration phase has mobilised significant attention. However, the importance of the regeneration niche concept remains unclear. Our main objective was to study the existence of such a regeneration niche for a leguminous shrub, Ulex europaeus. This study was carried out in southwest France in the context of water and nutrient stresses (mainly phosphorus limitation due to the presence of nutrient-poor sandy soils. We analysed the regeneration of the species from the germination of seeds and emergence of new seedlings until the seedlings reached young shrub size. Our design included a P fertilisation treatment. We also investigated microsite characteristics (micro-topography and vegetation development as they can interact with meteorological conditions and determine water availability for seeds and seedlings. We found that P availability controlled seedling growth and the time necessary to reach young shrub size. Water availability appeared to impact the species germination and seedlings survival. We also found that P and water availability depended on the interactions between microsite characteristics and climatic variations. Finally we found evidence that P and water availability are important ecological factors shaping the regeneration niche of the species, but we found weak evidence that any microsite would be appropriate for the regeneration of the species in the long term. Future studies regarding regeneration niches need to distinguish more clearly the ecological factors important for regeneration (the regeneration niche per se and the physical world where the seedlings appear and develop (the regeneration habitat.

  2. Single-cell genomics reveal metabolic strategies for microbial growth and survival in an oligotrophic aquifer

    Energy Technology Data Exchange (ETDEWEB)

    Wilkins, Michael J.; Kennedy, David W.; Castelle, Cindy; Field, Erin; Stepanauskas, Ramunas; Fredrickson, Jim K.; Konopka, Allan

    2014-02-09

    Bacteria from the genus Pedobacter are a major component of microbial assemblages at Hanford Site and have been shown to significantly change in abundance in response to the subsurface intrusion of Columbia River water. Here we employed single cell genomics techniques to shed light on the physiological niche of these microorganisms. Analysis of four Pedobacter single amplified genomes (SAGs) from Hanford Site sediments revealed a chemoheterotrophic lifestyle, with the potential to exist under both aerobic and microaerophilic conditions via expression of both aa3­-type and cbb3-type cytochrome c oxidases. These SAGs encoded a wide-range of both intra-and extra­-cellular carbohydrate-active enzymes, potentially enabling the degradation of recalcitrant substrates such as xylan and chitin, and the utilization of more labile sugars such as mannose and fucose. Coupled to these enzymes, a diversity of transporters and sugar-binding molecules were involved in the uptake of carbon from the extracellular local environment. The SAGs were enriched in TonB-dependent receptors (TBDRs), which play a key role in uptake of substrates resulting from degradation of recalcitrant carbon. CRISPR-Cas mechanisms for resisting viral infections were identified in all SAGs. These data demonstrate the potential mechanisms utilized for persistence by heterotrophic microorganisms in a carbon-limited aquifer, and hint at potential linkages between observed Pedobacter abundance shifts within the 300 Area subsurface and biogeochemical shifts associated with Columbia River water intrusion.

  3. Pleiotrophin Regulates the Retention and Self-Renewal of Hematopoietic Stem Cells in the Bone Marrow Vascular Niche

    Directory of Open Access Journals (Sweden)

    Heather A. Himburg

    2012-10-01

    Full Text Available The mechanisms through which the bone marrow (BM microenvironment regulates hematopoietic stem cell (HSC fate remain incompletely understood. We examined the role of the heparin-binding growth factor pleiotrophin (PTN in regulating HSC function in the niche. PTN−/− mice displayed significantly decreased BM HSC content and impaired hematopoietic regeneration following myelosuppression. Conversely, mice lacking protein tyrosine phosphatase receptor zeta, which is inactivated by PTN, displayed significantly increased BM HSC content. Transplant studies revealed that PTN action was not HSC autonomous, but rather was mediated by the BM microenvironment. Interestingly, PTN was differentially expressed and secreted by BM sinusoidal endothelial cells within the vascular niche. Furthermore, systemic administration of anti-PTN antibody in mice substantially impaired both the homing of hematopoietic progenitor cells to the niche and the retention of BM HSCs in the niche. PTN is a secreted component of the BM vascular niche that regulates HSC self-renewal and retention in vivo.

  4. Microbial syntrophy: interaction for the common good.

    Science.gov (United States)

    Morris, Brandon E L; Henneberger, Ruth; Huber, Harald; Moissl-Eichinger, Christine

    2013-05-01

    Classical definitions of syntrophy focus on a process, performed through metabolic interaction between dependent microbial partners, such as the degradation of complex organic compounds under anoxic conditions. However, examples from past and current scientific discoveries suggest that a new, simple but wider definition is necessary to cover all aspects of microbial syntrophy. We suggest the term 'obligately mutualistic metabolism', which still focuses on microbial metabolic cooperation but also includes an ecological aspect: the benefit for both partners. By the combined metabolic activity of microorganisms, endergonic reactions can become exergonic through the efficient removal of products and therefore enable a microbial community to survive with minimal energy resources. Here, we explain the principles of classical and non-classical syntrophy and illustrate the concepts with various examples. We present biochemical fundamentals that allow microorganism to survive under a range of environmental conditions and to drive important biogeochemical processes. Novel technologies have contributed to the understanding of syntrophic relationships in cultured and uncultured systems. Recent research highlights that obligately mutualistic metabolism is not limited to certain metabolic pathways nor to certain environments or microorganisms. This beneficial microbial interaction is not restricted to the transfer of reducing agents such as hydrogen or formate, but can also involve the exchange of organic, sulfurous- and nitrogenous compounds or the removal of toxic compounds. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  5. Microbial diversity and metabolic networks in acid mine drainage habitats

    Directory of Open Access Journals (Sweden)

    Celia eMendez-Garcia

    2015-05-01

    Full Text Available Acid mine drainage (AMD emplacements are low-complexity natural systems. Low-pH conditions appear to be the main factor underlying the limited diversity of the microbial populations thriving in these environments, although temperature, ionic composition, total organic carbon and dissolved oxygen are also considered to significantly influence their microbial life. This natural reduction in diversity driven by extreme conditions was reflected in several studies on the microbial populations inhabiting the various micro-environments present in such ecosystems. Early studies based on the physiology of the autochthonous microbiota and the growing success of omics technologies have enabled a better understanding of microbial ecology and function in low-pH mine outflows; however, complementary omics-derived data should be included to completely describe their microbial ecology. Furthermore, recent updates on the distribution of eukaryotes and ultra-micro-archaea demand their inclusion in the microbial characterisation of AMD systems. In this review, we present a complete overview of the bacterial, archaeal (including ultra-micro-archaeal and eukaryotic diversity in these ecosystems and include a thorough depiction of the metabolism and element cycling in AMD habitats. We also review different metabolic network structures at the organismal level, which is necessary to disentangle the role of each member of the AMD communities described thus far.

  6. Microbial healing of cracks in concrete: a review.

    Science.gov (United States)

    Joshi, Sumit; Goyal, Shweta; Mukherjee, Abhijit; Reddy, M Sudhakara

    2017-11-01

    Concrete is the most widely used construction material of the world and maintaining concrete structures from premature deterioration is proving to be a great challenge. Early age formation of micro-cracking in concrete structure severely affects the serviceability leading to high cost of maintenance. Apart from conventional methods of repairing cracks with sealants or treating the concrete with adhesive chemicals to prevent the cracks from widening, a microbial crack-healing approach has shown promising results. The unique feature of the microbial system is that it enables self-healing of concrete. The effectiveness of microbially induced calcium carbonate precipitation (MICCP) in improving durability of cementitious building materials, restoration of stone monuments and soil bioclogging is discussed. Main emphasis has been laid on the potential of bacteria-based crack repair in concrete structure and the applications of different bacterial treatments to self-healing cracks. Furthermore, recommendations to employ the MICCP technology at commercial scale and reduction in the cost of application are provided in this review.

  7. Biofuel alternatives to ethanol: pumping the microbial well

    Energy Technology Data Exchange (ETDEWEB)

    Fortman, J.L.; Chhabra, Swapnil; Mukhopadhyay, Aindrila; Chou, Howard; Lee, Taek Soon; Steen, Eric; Keasling, Jay D.

    2009-08-19

    Engineered microorganisms are currently used for the production of food products, pharmaceuticals, ethanol fuel and more. Even so, the enormous potential of this technology has yet to be fully exploited. The need for sustainable sources of transportation fuels has generated a tremendous interest in technologies that enable biofuel production. Decades of work have produced a considerable knowledge-base for the physiology and pathway engineering of microbes, making microbial engineering an ideal strategy for producing biofuel. Although ethanol currently dominates the biofuel market, some of its inherent physical properties make it a less than ideal product. To highlight additional options, we review advances in microbial engineering for the production of other potential fuel molecules, using a variety of biosynthetic pathways.

  8. Multi-user cognitive radio network resource allocation based on the adaptive niche immune genetic algorithm

    International Nuclear Information System (INIS)

    Zu Yun-Xiao; Zhou Jie

    2012-01-01

    Multi-user cognitive radio network resource allocation based on the adaptive niche immune genetic algorithm is proposed, and a fitness function is provided. Simulations are conducted using the adaptive niche immune genetic algorithm, the simulated annealing algorithm, the quantum genetic algorithm and the simple genetic algorithm, respectively. The results show that the adaptive niche immune genetic algorithm performs better than the other three algorithms in terms of the multi-user cognitive radio network resource allocation, and has quick convergence speed and strong global searching capability, which effectively reduces the system power consumption and bit error rate. (geophysics, astronomy, and astrophysics)

  9. Climatic niche conservatism and ecological opportunity in the explosive radiation of arvicoline rodents (Arvicolinae, Cricetidae).

    Science.gov (United States)

    Lv, Xue; Xia, Lin; Ge, Deyan; Wu, Yongjie; Yang, Qisen

    2016-05-01

    Climatic niche conservatism shapes patterns of diversity in many taxonomic groups, while ecological opportunity (EO) can trigger rapid speciation that is less constrained by the amount of time a lineage has occupied a given habitat. These two processes are well studied, but limited research has considered their joint and relative roles in shaping diversity patterns. We characterized climatic and biogeographic variables for 102 species of arvicoline rodents (Arvicolinae, Cricetidae), testing the effects of climatic niche conservatism and EO on arvicoline diversification as lineages transitioned between biogeographic regions. We found that the amount of time a lineage has occupied a precipitation niche is positively correlated with diversity along a precipitation gradient, suggesting climatic niche conservatism. In contrast, shift in diversification rate explained diversity patterns along a temperature gradient. Our results suggest that an indirect relationship exists between temperature and diversification that is associated with EO as arvicoline rodents colonized warm Palearctic environments. Climatic niche conservatism alone did not fully explain diversity patterns under density-dependence, highlighting the additional importance of EO-related processes in promoting the explosive radiation in arvicoline rodents and shaping diversity pattern among biogeographic regions and along climatic gradients. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  10. The vasculature as a neural stem cell niche.

    Science.gov (United States)

    Otsuki, Leo; Brand, Andrea H

    2017-11-01

    Neural stem cells (NSCs) are multipotent, self-renewing progenitors that generate progeny that differentiate into neurons and glia. NSCs in the adult mammalian brain are generally quiescent. Environmental stimuli such as learning or exercise can activate quiescent NSCs, inducing them to proliferate and produce new neurons and glia. How are these behaviours coordinated? The neurovasculature, the circulatory system of the brain, is a key component of the NSC microenvironment, or 'niche'. Instructive signals from the neurovasculature direct NSC quiescence, proliferation, self-renewal and differentiation. During ageing, a breakdown in the niche accompanies NSC dysfunction and cognitive decline. There is much interest in reversing these changes and enhancing NSC activity by targeting the neurovasculature therapeutically. Here we discuss principles of neurovasculature-NSC crosstalk, and the implications for the design of NSC-based therapies. We also consider the emerging contributions to this field of the model organism Drosophila melanogaster. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. Towards evolution-guided microbial engineering - tools development and applications

    DEFF Research Database (Denmark)

    Genee, Hans Jasper

    is thedevelopment of highly robust biosensor-based synthetic selection systemsthat enable high-throughput functional interrogation of complexphenotypic libraries. Using the model organism Escherichia coli as a host, Ideploy these systems to i) perform metagenome wide sequenceindependentidentification of novel...... for microbial engineering anddemonstrates direct applications to gene discovery, protein engineering andcell factory development....

  12. Prospects for Jatropha biofuels in Tanzania: An analysis with Strategic Niche Management

    International Nuclear Information System (INIS)

    Eijck, Janske van; Romijn, Henny

    2008-01-01

    The paper reports on research in Tanzania about the scope for developing biofuels from an oil-seed bearing plant called Jatropha curcas Linnaeus. The plant is widely seen to have potential to help combat the greenhouse effect, help to stop local soil erosion, create additional income for the rural poor, and provide a major source of energy both locally and internationally. The principal analytic tool is Strategic Niche Management (SNM), an approach rooted in evolutionary innovation theory. We analyse how the scope for an energy transition is influenced by factors at three societal levels: the overarching 'landscape'; the sectoral setting or 'regime'; and the 'niche' level where the innovation develops and diffuses. Valuable niche processes were found in a few areas, especially in cultivation, but we conclude that there are still many obstacles in Tanzania's prevailing energy regime. The development of Jatropha biofuels is still in an early phase. We list policy recommendations and discuss some methodological issues arising from the use of SNM

  13. Proximity-based differential single cell analysis of the niche to identify stem/progenitor cell regulators

    Science.gov (United States)

    Silberstein, Lev; Goncalves, Kevin A; Kharchenko, Peter V; Turcotte, Raphael; Kfoury, Youmna; Mercier, Francois; Baryawno, Ninib; Severe, Nicolas; Bachand, Jacqueline; Spencer, Joel; Papazian, Ani; Lee, Dongjun; Chitteti, Brahmananda Reddy; Srour, Edward F; Hoggatt, Jonathan; Tate, Tiffany; Celso, Cristina Lo; Ono, Noriaki; Nutt, Stephen; Heino, Jyrki; Sipilä, Kalle; Shioda, Toshihiro; Osawa, Masatake; Lin, Charles P; Hu, Guo-fu; Scadden, David T

    2016-01-01

    SUMMARY Physiological stem cell function is regulated by secreted factors produced by niche cells. In this study, we describe an unbiased approach based on differential single-cell gene expression analysis of mesenchymal osteolineage cells close to and further removed from hematopoietic stem/progenitor cells to identify candidate niche factors. Mesenchymal cells displayed distinct molecular profiles based on their relative location. Amongst the genes which were preferentially expressed in proximal cells, we functionally examined three secreted or cell surface molecules not previously connected to HSPC biology: the secreted RNase Angiogenin, the cytokine IL18 and the adhesion molecule Embigin and discovered that all of these factors are HSPC quiescence regulators. Our proximity-based differential single cell approach therefore reveals molecular heterogeneity within niche cells and can be used to identify novel extrinsic stem/progenitor cell regulators. Similar approaches could also be applied to other stem cell/niche pairs to advance understanding of microenvironmental regulation of stem cell function. PMID:27524439

  14. The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project.

    Science.gov (United States)

    Weston, David J; Turetsky, Merritt R; Johnson, Matthew G; Granath, Gustaf; Lindo, Zoë; Belyea, Lisa R; Rice, Steven K; Hanson, David T; Engelhardt, Katharina A M; Schmutz, Jeremy; Dorrepaal, Ellen; Euskirchen, Eugénie S; Stenøien, Hans K; Szövényi, Péter; Jackson, Michelle; Piatkowski, Bryan T; Muchero, Wellington; Norby, Richard J; Kostka, Joel E; Glass, Jennifer B; Rydin, Håkan; Limpens, Juul; Tuittila, Eeva-Stiina; Ullrich, Kristian K; Carrell, Alyssa; Benscoter, Brian W; Chen, Jin-Gui; Oke, Tobi A; Nilsson, Mats B; Ranjan, Priya; Jacobson, Daniel; Lilleskov, Erik A; Clymo, R S; Shaw, A Jonathan

    2018-01-01

    Considerable progress has been made in ecological and evolutionary genetics with studies demonstrating how genes underlying plant and microbial traits can influence adaptation and even 'extend' to influence community structure and ecosystem level processes. Progress in this area is limited to model systems with deep genetic and genomic resources that often have negligible ecological impact or interest. Thus, important linkages between genetic adaptations and their consequences at organismal and ecological scales are often lacking. Here we introduce the Sphagnome Project, which incorporates genomics into a long-running history of Sphagnum research that has documented unparalleled contributions to peatland ecology, carbon sequestration, biogeochemistry, microbiome research, niche construction, and ecosystem engineering. The Sphagnome Project encompasses a genus-level sequencing effort that represents a new type of model system driven not only by genetic tractability, but by ecologically relevant questions and hypotheses. © 2017 UT-Battelle New Phytologist © 2017 New Phytologist Trust.

  15. Keeping stem cells under control: new insights into the mechanisms that limit niche-stem cell signaling within the reproductive system

    OpenAIRE

    Inaba, Mayu; Yamashita, Yukiko M.; Buszczak, Michael

    2016-01-01

    Adult stem cells reside in specialized microenvironments called niches that maintain stem cells in an undifferentiated and self-renewing state. Despite extensive studies on the signaling pathways that operate within stem cells and their niches, the mechanisms that restrict niche signal exclusively to stem cells remained elusive: such a mechanism is crucially important to ensure that stem cells undergo self-renewal while their progeny, often located just one cell diameter away from the niche, ...

  16. Adaptation and niche construction in human prehistory: a case study from the southern Scandinavian Late Glacial.

    Science.gov (United States)

    Riede, Felix

    2011-03-27

    The niche construction model postulates that human bio-social evolution is composed of three inheritance domains, genetic, cultural and ecological, linked by feedback selection. This paper argues that many kinds of archaeological data can serve as proxies for human niche construction processes, and presents a method for investigating specific niche construction hypotheses. To illustrate this method, the repeated emergence of specialized reindeer (Rangifer tarandus) hunting/herding economies during the Late Palaeolithic (ca 14.7-11.5 kyr BP) in southern Scandinavia is analysed from a niche construction/triple-inheritance perspective. This economic relationship resulted in the eventual domestication of Rangifer. The hypothesis of whether domestication was achieved as early as the Late Palaeolithic, and whether this required the use of domesticated dogs (Canis familiaris) as hunting, herding or transport aids, is tested via a comparative analysis using material culture-based phylogenies and ecological datasets in relation to demographic/genetic proxies. Only weak evidence for sustained niche construction behaviours by prehistoric hunter-gatherer in southern Scandinavia is found, but this study nonetheless provides interesting insights into the likely processes of dog and reindeer domestication, and into processes of adaptation in Late Glacial foragers.

  17. Novel therapeutic strategies to target leukemic cells that hijack compartmentalized continuous hematopoietic stem cell niches

    NARCIS (Netherlands)

    Hira, Vashendriya V. V.; van Noorden, Cornelis J. F.; Carraway, Hetty E.; Maciejewski, Jaroslaw P.; Molenaar, Remco J.

    2017-01-01

    Acute myeloid leukemia and acute lymphoblastic leukemia cells hijack hematopoietic stem cell (HSC) niches in the bone marrow and become leukemic stem cells (LSCs) at the expense of normal HSCs. LSCs are quiescent and resistant to chemotherapy and can cause relapse of the disease. HSCs in niches are

  18. Ovarian Stem Cell Niche and Follicular Renewal in Mammals

    Czech Academy of Sciences Publication Activity Database

    Bukovský, Antonín

    2011-01-01

    Roč. 294, č. 8 (2011), s. 1284-1306 ISSN 1932-8486 Institutional research plan: CEZ:AV0Z50520701 Keywords : ovary * stem cell niche * neo-oogenesis Subject RIV: EA - Cell Biology Impact factor: 1.473, year: 2011

  19. Branding Prince Edward County as a Gastronomic Niche Tourism Destination: A Case Study

    OpenAIRE

    Geneviève Brisson; Rocci Luppicini

    2015-01-01

    Increasingly, gastronomy is playing a role in people's motivation for travel, and destinations are making food and beverages their main attraction. This study explored the growing field of gastronomic tourism, a type of niche tourism, through the theoretical framework of destination branding theory. Using a qualitative case study research design, this research examined the branding of the emergent region of Prince Edward County, Ontario, Canada as a gastronomic niche tourism destination from ...

  20. INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.

    Directory of Open Access Journals (Sweden)

    Intikhab Alam

    Full Text Available The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes.We developed a data warehouse system (INDIGO that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea. We provide examples of utilizing the system to gain new insights into specific aspects on the unique lifestyle and adaptations of these organisms to extreme environments.We developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial genomes. It will be regularly updated and extended with new genomes. It is aimed to serve as a resource dedicated to the Red Sea microbes. In addition, through INDIGO, we provide our Automatic Annotation of Microbial Genomes (AAMG pipeline. The INDIGO web server is freely available at http://www.cbrc.kaust.edu.sa/indigo.

  1. Enabling fast electron transfer through both bacterial outer-membrane redox centers and endogenous electron mediators by polyaniline hybridized large-mesoporous carbon anode for high-performance microbial fuel cells

    International Nuclear Information System (INIS)

    Zou, Long; Qiao, Yan; Zhong, Canyu; Li, Chang Ming

    2017-01-01

    Both physical structure and chemical property of an electrode play critical roles in extracellular electron transfer from microbes to electrodes in microbial fuel cells (MFCs). Herein a novel polyaniline hybridized large mesoporous carbon (PANI-LMC) anode is fabricated from natural biomass by nanostructured CaCO 3 template-assisted carbonization followed by in situ chemical polymerizing PANI to enable fast extracellular electron transfer, in which the LMC with rich disorder-interconnected large mesopores (∼20−50 nm) and large surface area facilitates a fast mediated electron transfer through electron mediators, while the decorated PANI on LMC surface enables the direct electron transfer via bacterial outer-membrane redox centers. Owing to the unique synergistic effect from both excellent electron transfer paths, the PANI-LMC hybrid anode harvests high power electricity with a maximum output power density of 1280 mW m −2 in Shewanella putrefaciens CN32 MFCs, 10-fold higher than that of conventional carbon cloth. The findings from this work suggest a new insight on design of high-efficient anode according to the multiple and flexible electrochemical process for practical MFC applications.

  2. The neural crest is a source of mesenchymal stem cells with specialized hematopoietic stem cell niche function.

    Science.gov (United States)

    Isern, Joan; García-García, Andrés; Martín, Ana M; Arranz, Lorena; Martín-Pérez, Daniel; Torroja, Carlos; Sánchez-Cabo, Fátima; Méndez-Ferrer, Simón

    2014-09-25

    Mesenchymal stem cells (MSCs) and osteolineage cells contribute to the hematopoietic stem cell (HSC) niche in the bone marrow of long bones. However, their developmental relationships remain unclear. In this study, we demonstrate that different MSC populations in the developing marrow of long bones have distinct functions. Proliferative mesoderm-derived nestin(-) MSCs participate in fetal skeletogenesis and lose MSC activity soon after birth. In contrast, quiescent neural crest-derived nestin(+) cells preserve MSC activity, but do not generate fetal chondrocytes. Instead, they differentiate into HSC niche-forming MSCs, helping to establish the HSC niche by secreting Cxcl12. Perineural migration of these cells to the bone marrow requires the ErbB3 receptor. The neonatal Nestin-GFP(+) Pdgfrα(-) cell population also contains Schwann cell precursors, but does not comprise mature Schwann cells. Thus, in the developing bone marrow HSC niche-forming MSCs share a common origin with sympathetic peripheral neurons and glial cells, and ontogenically distinct MSCs have non-overlapping functions in endochondrogenesis and HSC niche formation.

  3. Microbial community structure of relict niter-beds previously used for saltpeter production.

    Directory of Open Access Journals (Sweden)

    Takashi Narihiro

    Full Text Available From the 16th to the 18th centuries in Japan, saltpeter was produced using a biological niter-bed process and was formed under the floor of gassho-style houses in the historic villages of Shirakawa-go and Gokayama, which are classified as United Nations Educational, Scientific and Cultural Organization (UNESCO World Heritage Sites. The relict niter-beds are now conserved in the underfloor space of gassho-style houses, where they are isolated from destabilizing environmental factors and retain the ability to produce nitrate. However, little is known about the nitrifying microbes in such relict niter-bed ecosystems. In this study, the microbial community structures within nine relict niter-bed soils were investigated using 454 pyrotag analysis targeting the 16S rRNA gene and the bacterial and archaeal ammonia monooxygenase gene (amoA. The 16S rRNA gene pyrotag analysis showed that members of the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, and Planctomycetes were major microbial constituents, and principal coordinate analysis showed that the NO3-, Cl-, K+, and Na+ contents were potential determinants of the structures of entire microbial communities in relict niter-bed soils. The bacterial and archaeal amoA libraries indicated that members of the Nitrosospira-type ammonia-oxidizing bacteria (AOB and "Ca. Nitrososphaera"-type ammonia-oxidizing archaea (AOA, respectively, predominated in relict niter-bed soils. In addition, soil pH and organic carbon content were important factors for the ecological niche of AOB and AOA in relict niter-bed soil ecosystems.

  4. Plant diversification promotes biocontrol services in peach orchards by shaping the ecological niches of insect herbivores and their natural enemies

    DEFF Research Database (Denmark)

    Wan, Nian Feng; Ji, Xiang Yun; Deng, Jian Yu

    2018-01-01

    Ecological niche indicators have been scarcely adopted to assess the biological control of insect herbivores by their natural enemies. We hypothesize that plant diversification promotes the biocontrol services by narrowing the niches of herbivores and broadening the niches of natural enemies....... Our study reveals that plant diversification promotes the biocontrol services by shaping the niche of herbivores and natural enemies, and provides a new assessment method to understand the biodiversity-niche-ecosystem management interactions........ In a large-scale experiment, we found that the abundance of natural enemies was increased by 38.1%, and the abundance of insect herbivores was decreased by 16.9% in peach orchards with plant diversification (treatment) compared to ones with monoculture (control). Stratified sampling indicated...

  5. PTEN Signaling in the Postnatal Perivascular Progenitor Niche Drives Medulloblastoma Formation.

    Science.gov (United States)

    Zhu, Guo; Rankin, Sherri L; Larson, Jon D; Zhu, Xiaoyan; Chow, Lionel M L; Qu, Chunxu; Zhang, Jinghui; Ellison, David W; Baker, Suzanne J

    2017-01-01

    Loss of the tumor suppressor gene PTEN exerts diverse outcomes on cancer in different developmental contexts. To gain insight into the effect of its loss on outcomes in the brain, we conditionally inactivated the murine Pten gene in neonatal neural stem/progenitor cells. Pten inactivation created an abnormal perivascular proliferative niche in the cerebellum that persisted in adult animals but did not progress to malignancy. Proliferating cells showed undifferentiated morphology and expressed the progenitor marker Nestin but not Math1, a marker of committed granule neuron progenitors. Codeletion of Pten and Trp53 resulted in fully penetrant medulloblastoma originating from the perivascular niche, which exhibited abnormal blood vessel networks and advanced neuronal differentiation of tumor cells. EdU pulse-chase experiments demonstrated a perivascular cancer stem cell population in Pten/Trp53 double mutant medulloblastomas. Genetic analyses revealed recurrent somatic inactivations of the tumor suppressor gene Ptch1 and a recapitulation of the sonic hedgehog subgroup of human medulloblastomas. Overall, our results showed that PTEN acts to prevent the proliferation of a progenitor niche in postnatal cerebellum predisposed to oncogenic induction of medulloblastoma. Cancer Res; 77(1); 123-33. ©2016 AACR. ©2016 American Association for Cancer Research.

  6. Bone marrow macrophages maintain hematopoietic stem cell (HSC) niches and their depletion mobilizes HSCs.

    Science.gov (United States)

    Winkler, Ingrid G; Sims, Natalie A; Pettit, Allison R; Barbier, Valérie; Nowlan, Bianca; Helwani, Falak; Poulton, Ingrid J; van Rooijen, Nico; Alexander, Kylie A; Raggatt, Liza J; Lévesque, Jean-Pierre

    2010-12-02

    In the bone marrow, hematopoietic stem cells (HSCs) reside in specific niches near osteoblast-lineage cells at the endosteum. To investigate the regulation of these endosteal niches, we studied the mobilization of HSCs into the bloodstream in response to granulocyte colony-stimulating factor (G-CSF). We report that G-CSF mobilization rapidly depletes endosteal osteoblasts, leading to suppressed endosteal bone formation and decreased expression of factors required for HSC retention and self-renewal. Importantly, G-CSF administration also depleted a population of trophic endosteal macrophages (osteomacs) that support osteoblast function. Osteomac loss, osteoblast suppression, and HSC mobilization occurred concomitantly, suggesting that osteomac loss could disrupt endosteal niches. Indeed, in vivo depletion of macrophages, in either macrophage Fas-induced apoptosis (Mafia) transgenic mice or by administration of clodronate-loaded liposomes to wild-type mice, recapitulated the: (1) loss of endosteal osteoblasts and (2) marked reduction of HSC-trophic cytokines at the endosteum, with (3) HSC mobilization into the blood, as observed during G-CSF administration. Together, these results establish that bone marrow macrophages are pivotal to maintain the endosteal HSC niche and that the loss of such macrophages leads to the egress of HSCs into the blood.

  7. Manipulation of signaling thresholds in "engineered stem cell niches" identifies design criteria for pluripotent stem cell screens.

    Directory of Open Access Journals (Sweden)

    Raheem Peerani

    Full Text Available In vivo, stem cell fate is regulated by local microenvironmental parameters. Governing parameters in this stem cell niche include soluble factors, extra-cellular matrix, and cell-cell interactions. The complexity of this in vivo niche limits analyses into how individual niche parameters regulate stem cell fate. Herein we use mouse embryonic stem cells (mESC and micro-contact printing (microCP to investigate how niche size controls endogenous signaling thresholds. microCP is used to restrict colony diameter, separation, and degree of clustering. We show, for the first time, spatial control over the activation of the Janus kinase/signal transducer and activator of transcription pathway (Jak-Stat. The functional consequences of this niche-size-dependent signaling control are confirmed by demonstrating that direct and indirect transcriptional targets of Stat3, including members of the Jak-Stat pathway and pluripotency-associated genes, are regulated by colony size. Modeling results and empirical observations demonstrate that colonies less than 100 microm in diameter are too small to maximize endogenous Stat3 activation and that colonies separated by more than 400 microm can be considered independent from each other. These results define parameter boundaries for the use of ESCs in screening studies, demonstrate the importance of context in stem cell responsiveness to exogenous cues, and suggest that niche size is an important parameter in stem cell fate control.

  8. Feeding niches of four large herbivores in the Hluhluwe Game ...

    African Journals Online (AJOL)

    Feeding niches of four large herbivores in the Hluhluwe Game Reserve, Natal. ... equus burchelli burchelli; feeding; grass; grasses; habitat; herbivores; hluhluwe game reserve; kwazulu-natal; large herbivores; ... AJOL African Journals Online.

  9. Supply Chain Development: Insights from Strategic Niche Management

    Science.gov (United States)

    Caniels, Marjolein C. J.; Romijn, Henny A.

    2008-01-01

    Purpose: The purpose of this paper is to contribute to the study of supply chain design from the perspective of complex dynamic systems. Unlike extant studies that use formal simulation modelling and associated methodologies rooted in the physical sciences, it adopts a framework rooted in the social sciences, strategic niche management, which…

  10. Environmental niche divergence among three dune shrub sister species with parapatric distributions.

    Science.gov (United States)

    Chozas, Sergio; Chefaoui, Rosa M; Correia, Otília; Bonal, Raúl; Hortal, Joaquín

    2017-05-01

    The geographical distributions of species are constrained by their ecological requirements. The aim of this work was to analyse the effects of environmental conditions, historical events and biogeographical constraints on the diversification of the three species of the western Mediterranean shrub genus Stauracanthus , which have a parapatric distribution in the Iberian Peninsula. Ecological niche factor analysis and generalized linear models were used to measure the response of all Stauracanthus species to the environmental gradients and map their potential distributions in the Iberian Peninsula. The bioclimatic niche overlap between the three species was determined by using Schoener's index. The genetic differentiation of the Iberian and northern African populations of Stauracanthus species was characterized with GenalEx. The effects on genetic distances of the most important environmental drivers were assessed through Mantel tests and non-metric multidimensional scaling. The three Stauracanthus species show remarkably similar responses to climatic conditions. This supports the idea that all members of this recently diversified clade retain common adaptations to climate and consequently high levels of climatic niche overlap. This contrasts with the diverse edaphic requirements of Stauracanthus species. The populations of the S. genistoides-spectabilis clade grow on Miocene and Pliocene fine-textured sedimentary soils, whereas S. boivinii , the more genetically distant species, occurs on older and more coarse-textured sedimentary substrates. These patterns of diversification are largely consistent with a stochastic process of geographical range expansion and fragmentation coupled with niche evolution in the context of spatially complex environmental fluctuations. : The combined analysis of the distribution, realized environmental niche and phylogeographical relationships of parapatric species proposed in this work allows integration of the biogeographical

  11. Rates of change in climatic niches in plant and animal populations are much slower than projected climate change

    Science.gov (United States)

    Jezkova, Tereza

    2016-01-01

    Climate change may soon threaten much of global biodiversity. A critical question is: can species undergo niche shifts of sufficient speed and magnitude to persist within their current geographic ranges? Here, we analyse niche shifts among populations within 56 plant and animal species using time-calibrated trees from phylogeographic studies. Across 266 phylogeographic groups analysed, rates of niche change were much slower than rates of projected climate change (mean difference > 200 000-fold for temperature variables). Furthermore, the absolute niche divergence among populations was typically lower than the magnitude of projected climate change over the next approximately 55 years for relevant variables, suggesting the amount of change needed to persist may often be too great, even if these niche shifts were instantaneous. Rates were broadly similar between plants and animals, but especially rapid in some arthropods, birds and mammals. Rates for temperature variables were lower at lower latitudes, further suggesting that tropical species may be especially vulnerable to climate change. PMID:27881748

  12. The microbiome at the pulmonary alveolar niche and its role in Mycobacterium tuberculosis infection.

    Science.gov (United States)

    Adami, Alexander J; Cervantes, Jorge L

    2015-12-01

    Advances in next generation sequencing (NGS) technology have provided the tools to comprehensively and accurately characterize the microbial community in the respiratory tract in health and disease. The presence of commensal and pathogenic bacteria has been found to have important effects on the lung immune system. Until relatively recently, the lung has received less attention compared to other body sites in terms of microbiome characterization, and its study carries special technological difficulties related to obtaining reliable samples as compared to other body niches. Additionally, the complexity of the alveolar immune system, and its interactions with the lung microbiome, are only just beginning to be understood. Amidst this complexity sits Mycobacterium tuberculosis (Mtb), one of humanity's oldest nemeses and a significant public health concern, with millions of individuals infected with Mtb worldwide. The intricate interactions between Mtb, the lung microbiome, and the alveolar immune system are beginning to be understood, and it is increasingly apparent that improved treatment of Mtb will only come through deep understanding of the interplay between these three forces. In this review, we summarize our current understanding of the lung microbiome, alveolar immunity, and the interaction of each with Mtb. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Shifts in the ecological niche of Lutzomyia peruensis under climate change scenarios in Peru.

    Science.gov (United States)

    Moo-Llanes, D A; Arque-Chunga, W; Carmona-Castro, O; Yañez-Arenas, C; Yañez-Trujillano, H H; Cheverría-Pacheco, L; Baak-Baak, C M; Cáceres, A G

    2017-06-01

    The Peruvian Andes presents a climate suitable for many species of sandfly that are known vectors of leishmaniasis or bartonellosis, including Lutzomyia peruensis (Diptera: Psychodidae), among others. In the present study, occurrences data for Lu. peruensis were compiled from several items in the scientific literature from Peru published between 1927 and 2015. Based on these data, ecological niche models were constructed to predict spatial distributions using three algorithms [Support vector machine (SVM), the Genetic Algorithm for Rule-set Prediction (GARP) and Maximum Entropy (MaxEnt)]. In addition, the environmental requirements of Lu. peruensis and three niche characteristics were modelled in the context of future climate change scenarios: (a) potential changes in niche breadth; (b) shifts in the direction and magnitude of niche centroids, and (c) shifts in elevation range. The model identified areas that included environments suitable for Lu. peruensis in most regions of Peru (45.77%) and an average altitude of 3289 m a.s.l. Under climate change scenarios, a decrease in the distribution areas of Lu. peruensis was observed for all representative concentration pathways. However, the centroid of the species' ecological niche showed a northwest direction in all climate change scenarios. The information generated in this study may help health authorities responsible for the supervision of strategies to control leishmaniasis to coordinate, plan and implement appropriate strategies for each area of risk, taking into account the geographic distribution and potential dispersal of Lu. peruensis. © 2017 The Royal Entomological Society.

  14. Biofuel alternatives to ethanol: pumping the microbial well

    Energy Technology Data Exchange (ETDEWEB)

    Fortman, J. L.; Chhabra, Swapnil; Mukhopadhyay, Aindrila; Chou, Howard; Lee, Taek Soon; Steen, Eric; Keasling, Jay D.

    2009-12-02

    Engineered microorganisms are currently used for the production of food products, pharmaceuticals, ethanol fuel and more. Even so, the enormous potential of this technology has yet to be fully exploited. The need for sustainable sources of transportation fuels has gener-ated a tremendous interest in technologies that enable biofuel production. Decades of work have produced a considerable knowledge-base for the physiology and pathway engineering of microbes, making microbial engineering an ideal strategy for producing biofuel. Although ethanol currently dominates the biofuel mar-ket, some of its inherent physical properties make it a less than ideal product. To highlight additional options, we review advances in microbial engineering for the production of other potential fuel molecules, using a variety of biosynthetic pathways.

  15. Reproductive niche conservatism in the isolated New Zealand flora over 23 million years.

    Science.gov (United States)

    Conran, John G; Lee, William G; Lee, Daphne E; Bannister, Jennifer M; Kaulfuss, Uwe

    2014-10-01

    The temporal stability of plant reproductive features on islands has rarely been tested. Using flowers, fruits/cones and seeds from a well-dated (23 Ma) Miocene Lagerstätte in New Zealand, we show that across 23 families and 30 genera of forest angiosperms and conifers, reproductive features have remained constant for more than 20 Myr. Insect-, wind- and bird-pollinated flowers and wind- and bird-dispersed diaspores all indicate remarkable reproductive niche conservatism, despite widespread environmental and biotic change. In the past 10 Myr, declining temperatures and the absence of low-latitude refugia caused regional extinction of thermophiles, while orogenic processes steepened temperature, precipitation and nutrient gradients, limiting forest niches. Despite these changes, the palaeontological record provides empirical support for evidence from phylogeographical studies of strong niche conservatism within lineages and biomes. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  16. Umbilical cord mesenchyme stem cell local intramuscular injection for treatment of uterine niche

    Science.gov (United States)

    Fan, Dazhi; Wu, Shuzhen; Ye, Shaoxin; Wang, Wen; Guo, Xiaoling; Liu, Zhengping

    2017-01-01

    Abstract Background: Uterine niche is defined as a triangular anechoic structure at the site of the scar or a gap in the myometrium at the site of a previous caesarean section. The main clinical manifestations are postmenstrual spotting and intrauterine infection, which may seriously affect the daily life of nonpregnant women. Trials have shown an excellent safety and efficacy for the potential of mesenchymal stem cells (MSCs) as a therapeutic option for scar reconstruction. Therefore, this study is designed to investigate the safety and efficacy of using MSCs in the treatment for the uterine niche. Methods/design: This phase II clinical trial is a single-center, prospective, randomized, double-blind, placebo-controlled with 2 arms. One hundred twenty primiparous participants will be randomly (1:1 ratio) assigned to receive direct intramuscular injection of MSCs (a dose of 1∗107 cells in 1 mL of 0.9% saline) (MSCs group) or an identical-appearing 1 mL of 0.9% saline (placebo-controlled group) near the uterine incision. The primary outcome of this trial is to evaluate the proportion of participants at 6 months who is found uterine niche in the uterus by transvaginal utrasonography. Adverse events will be documented in a case report form. The study will be conducted at the Department of Obstetric of Southern Medical University Affiliated Maternal & Child Health Hospital of Foshan. Discussion: This trial is the first investigation of the potential for therapeutic use of MSCs for the management of uterine niche after cesarean delivery. Conclusion: This protocol will help to determine the efficacy and safety of MSCs treatment in uterine niche and bridge the gap with regards to the current preclinical and clinical evidence. Trial registration number: NCT02968459 (Clinical Trials.gov: http://clinicaltrials.gov/). PMID:29095305

  17. Integrating life stages into ecological niche models: a case study on tiger beetles.

    Science.gov (United States)

    Taboada, Angela; von Wehrden, Henrik; Assmann, Thorsten

    2013-01-01

    Detailed understanding of a species' natural history and environmental needs across spatial scales is a primary requisite for effective conservation planning, particularly for species with complex life cycles in which different life stages occupy different niches and respond to the environment at different scales. However, niche models applied to conservation often neglect early life stages and are mostly performed at broad spatial scales. Using the endangered heath tiger beetle (Cicindela sylvatica) as a model species, we relate presence/absence and abundance data of locally dispersing adults and sedentary larvae to abiotic and biotic variables measured in a multiscale approach within the geographic extent relevant to active conservation management. At the scale of hundreds of meters, fine-grained abiotic conditions (i.e., vegetation structure) are fundamental determinants of the occurrence of both life stages, whereas the effect of biotic factors is mostly contained in the abiotic signature. The combination of dense heath vegetation and bare ground areas is thus the first requirement for the species' preservation, provided that accessibility to the suitable habitat is ensured. At a smaller scale (centimetres), the influence of abiotic factors on larval occurrence becomes negligible, suggesting the existence of important additional variables acting within larval proximity. Sustained significant correlations between neighbouring larvae in the models provide an indication of the potential impact of neighbourhood crowding on the larval niche within a few centimetres. Since the species spends the majority of its life cycle in the larval stage, it is essential to consider the hierarchical abiotic and biotic processes affecting the larvae when designing practical conservation guidelines for the species. This underlines the necessity for a more critical evaluation of the consequences of disregarding niche variation between life stages when estimating niches and

  18. [Allelopathic effects of Artemisia sacrorum population in typical steppe based on niche theory].

    Science.gov (United States)

    Wang, Hui; Xie, Yong-Sheng; Cheng, Ji-Min; She, Xiao-Yan

    2012-03-01

    By using modified Levins niche width index and Pianka niche overlap index, this paper analyzed the ecological competition between constructive and dominant species in a typical steppe. The stem- and leaf extracts from the constructive species (Artemisia sacrorum) were utilized to study their allelopathic potential on the seed germination and plant growth of the dominant species (Stipa bungeana, Thymus mongolicus, S. grandis, and Leymus secalinus), and the ecological position of A. sacrorum in the steppe succession. In the steppe, S. bungeana had the widest niche width (0.99), followed by T. mongolicus (0.94), A. sacrorum (0.82), S. grandis (0.76), and L. secalinus (0.73). The niche overlap value between A. sacrorum and S. bungeana, S. bungeana and T. mongolicus, T. mongolicus and S. grandis, and A. sacrorum and T. mongolicus was 0.90, 0.95, 0.94, and 0.86, respectively. The allelopathic effects of A. sacrorum extracts varied with their concentration. For the seed germination, root growth, and shoot growth of the dominant species, A. sacrorum extracts showed a trend of promoting at low concentrations and inhibiting at high concentrations. The extracts of A. sacrorum had a stronger promotion effect on the root growth of S. bungeana than on that of T. mongolicus, but a stronger inhibition effect on the shoot growth of T. mongolicus than on that of S. bungeana. Methanol extracts had stronger allelopathic effects than aqueous extracts. The high niche overlap between A. sacrorum and S. bungeana, and T. mongolicus and S. grandis indicated that the steppe community would continue succession to S. bungeana, while A. sacrorum population was only an important transitional stage during the succession. The allelopathic effect of A. sacrorum played a driving role in the succession process.

  19. Within-population isotopic niche variability in savanna mammals: disparity between carnivores and herbivores

    Directory of Open Access Journals (Sweden)

    Daryl eCodron

    2016-02-01

    Full Text Available Large mammal ecosystems have relatively simple food webs, usually comprising three – and sometimes only two – trophic links. Since many syntopic species from the same trophic level therefore share resources, dietary niche partitioning features prominently within these systems. In African and other subtropical savannas, stable carbon isotopes readily distinguish between herbivore species for which foliage and other parts of dicot plants (13C-depleted C3 vegetation are the primary resource (browsers and those for which grasses (13C-enriched C4 vegetation are staples (grazers. Similarly, carbon isotopes distinguish between carnivore diets that may be richer in either browser, grazer, or intermediate-feeding prey. Here, we investigate levels of carbon and nitrogen isotopic niche variation and niche partitioning within populations (or species of carnivores and herbivores from South African savannas. We emphasize predictable differences in within-population trends across trophic levels: we expect that herbivore populations, which require more foraging effort due to higher intake requirements, are far less likely to display within-population resource partitioning than carnivore populations. Our results reveal generally narrower isotopic niche breadths in herbivore than carnivore populations, but more importantly we find lower levels of isotopic differentiation across individuals within herbivore species. While these results offer some support for our general hypothesis, the current paucity of isotopic data for African carnivores limits our ability to test the complete set of predictions arising from our hypothesis. Nevertheless, given the different ecological and ecophysiological constraints to foraging behaviour within each trophic level, comparisons across carnivores and herbivores, which are possible within such simplified foodwebs, make these systems ideal for developing a process-based understanding of conditions underlying the evolution of

  20. Role of Ergothioneine in Microbial Physiology and Pathogenesis.

    Science.gov (United States)

    Cumming, Bridgette M; Chinta, Krishna C; Reddy, Vineel P; Steyn, Adrie J C

    2018-02-20

    L-ergothioneine is synthesized in actinomycetes, cyanobacteria, methylobacteria, and some fungi. In contrast to other low-molecular-weight redox buffers, glutathione and mycothiol, ergothioneine is primarily present as a thione rather than a thiol at physiological pH, which makes it resistant to autoxidation. Ergothioneine regulates microbial physiology and enables the survival of microbes under stressful conditions encountered in their natural environments. In particular, ergothioneine enables pathogenic microbes, such as Mycobacterium tuberculosis (Mtb), to withstand hostile environments within the host to establish infection. Recent Advances: Ergothioneine has been reported to maintain bioenergetic homeostasis in Mtb and protect Mtb against oxidative stresses, thereby enhancing the virulence of Mtb in a mouse model. Furthermore, ergothioneine augments the resistance of Mtb to current frontline anti-TB drugs. Recently, an opportunistic fungus, Aspergillus fumigatus, which infects immunocompromised individuals, has been found to produce ergothioneine, which is important in conidial health and germination, and contributes to the fungal resistance against redox stresses. The molecular mechanisms of the functions of ergothioneine in microbial physiology and pathogenesis are poorly understood. It is currently not known if ergothioneine is used in detoxification or antioxidant enzymatic pathways. As ergothioneine is involved in bioenergetic and redox homeostasis and antibiotic susceptibility of Mtb, it is of utmost importance to advance our understanding of these mechanisms. A clear understanding of the role of ergothioneine in microbes will advance our knowledge of how this thione enhances microbial virulence and resistance to the host's defense mechanisms to avoid complete eradication. Antioxid. Redox Signal. 28, 431-444.

  1. Microbial Metabolic Roles in Bedrock Degradation and the Genesis of Biomineral and Biopattern Biosignatures in Caves and Mines

    Science.gov (United States)

    Boston, P. J.

    2016-12-01

    In subsurface environments like natural or anthropogenic caves (aka mines), microorganisms facilitate considerable bedrock degradation under a variety of circumstances. Mobilization of materials from these processes frequently produces distinctive biominerals, identifiable biotextures, and unique biopatterns. Microbial activities can even determine the form of speleothems (secondary mineral cave decorations), thus providing highly conspicuous macroscopic biosignatures. It is critical to understand microbial-mineral interactions, recognizing that while the lithology controls important aspects of the environment, in turn, the geochemistry is greatly affected by the biology. Microbial communities can contribute to the actual formation of cavities (speleogenesis), and subsequent enlargement of caves and vugs and the mineral deposits that enrich many subterranean spaces. A major challenge is to quantify such influences. Genetic analysis is revealing a vast but highly partitioned biodiversity in the overall rock fracture habitat of Earth's crust especially in caves and mines where the three phases of matter (solid rock, fluids, and gases) typically interact producing high niche richness. Lessons learned from the microbial/geochemical systems that we have studied include: 1) significant similarities in metabolic functions between different geochemical systems, 2) ubiquity of metal oxidation for energy, 3) ubiquity of biofilms, some highly mineralized, 4) highly interdependent, multi-species communities that can only transform materials in consortia, 5) complex ecological succession including characteristic pioneer species, 6) often very slow growth rates in culture, 7) prevalence of very small cell sizes, ( 100 - 500 nm diam.), 8) mineral reprecipitation of mobilized materials, often dependent on the presence of live microbial communities to produce initial amorphous compounds followed by gradual crystallization, and 9) resultant in situ self-fossilization. Microbial

  2. Hematopoietic stem and progenitor cells regulate the regeneration of their niche by secreting Angiopoietin-1

    Science.gov (United States)

    Zhou, Bo O; Ding, Lei; Morrison, Sean J

    2015-01-01

    Hematopoietic stem cells (HSCs) are maintained by a perivascular niche in bone marrow but it is unclear whether the niche is reciprocally regulated by HSCs. Here, we systematically assessed the expression and function of Angiopoietin-1 (Angpt1) in bone marrow. Angpt1 was not expressed by osteoblasts. Angpt1 was most highly expressed by HSCs, and at lower levels by c-kit+ hematopoietic progenitors, megakaryocytes, and Leptin Receptor+ (LepR+) stromal cells. Global conditional deletion of Angpt1, or deletion from osteoblasts, LepR+ cells, Nes-cre-expressing cells, megakaryocytes, endothelial cells or hematopoietic cells in normal mice did not affect hematopoiesis, HSC maintenance, or HSC quiescence. Deletion of Angpt1 from hematopoietic cells and LepR+ cells had little effect on vasculature or HSC frequency under steady-state conditions but accelerated vascular and hematopoietic recovery after irradiation while increasing vascular leakiness. Hematopoietic stem/progenitor cells and LepR+ stromal cells regulate niche regeneration by secreting Angpt1, reducing vascular leakiness but slowing niche recovery. DOI: http://dx.doi.org/10.7554/eLife.05521.001 PMID:25821987

  3. Proximity-Based Differential Single-Cell Analysis of the Niche to Identify Stem/Progenitor Cell Regulators.

    Science.gov (United States)

    Silberstein, Lev; Goncalves, Kevin A; Kharchenko, Peter V; Turcotte, Raphael; Kfoury, Youmna; Mercier, Francois; Baryawno, Ninib; Severe, Nicolas; Bachand, Jacqueline; Spencer, Joel A; Papazian, Ani; Lee, Dongjun; Chitteti, Brahmananda Reddy; Srour, Edward F; Hoggatt, Jonathan; Tate, Tiffany; Lo Celso, Cristina; Ono, Noriaki; Nutt, Stephen; Heino, Jyrki; Sipilä, Kalle; Shioda, Toshihiro; Osawa, Masatake; Lin, Charles P; Hu, Guo-Fu; Scadden, David T

    2016-10-06

    Physiological stem cell function is regulated by secreted factors produced by niche cells. In this study, we describe an unbiased approach based on the differential single-cell gene expression analysis of mesenchymal osteolineage cells close to, and further removed from, hematopoietic stem/progenitor cells (HSPCs) to identify candidate niche factors. Mesenchymal cells displayed distinct molecular profiles based on their relative location. We functionally examined, among the genes that were preferentially expressed in proximal cells, three secreted or cell-surface molecules not previously connected to HSPC biology-the secreted RNase angiogenin, the cytokine IL18, and the adhesion molecule Embigin-and discovered that all of these factors are HSPC quiescence regulators. Therefore, our proximity-based differential single-cell approach reveals molecular heterogeneity within niche cells and can be used to identify novel extrinsic stem/progenitor cell regulators. Similar approaches could also be applied to other stem cell/niche pairs to advance the understanding of microenvironmental regulation of stem cell function. Copyright © 2016 Elsevier Inc. All rights reserved.

  4. Predicting fundamental and realized distributions based on thermal niche: A case study of a freshwater turtle

    Science.gov (United States)

    Rodrigues, João Fabrício Mota; Coelho, Marco Túlio Pacheco; Ribeiro, Bruno R.

    2018-04-01

    Species distribution models (SDM) have been broadly used in ecology to address theoretical and practical problems. Currently, there are two main approaches to generate SDMs: (i) correlative, which is based on species occurrences and environmental predictor layers and (ii) process-based models, which are constructed based on species' functional traits and physiological tolerances. The distributions estimated by each approach are based on different components of species niche. Predictions of correlative models approach species realized niches, while predictions of process-based are more akin to species fundamental niche. Here, we integrated the predictions of fundamental and realized distributions of the freshwater turtle Trachemys dorbigni. Fundamental distribution was estimated using data of T. dorbigni's egg incubation temperature, and realized distribution was estimated using species occurrence records. Both types of distributions were estimated using the same regression approaches (logistic regression and support vector machines), both considering macroclimatic and microclimatic temperatures. The realized distribution of T. dorbigni was generally nested in its fundamental distribution reinforcing theoretical assumptions that the species' realized niche is a subset of its fundamental niche. Both modelling algorithms produced similar results but microtemperature generated better results than macrotemperature for the incubation model. Finally, our results reinforce the conclusion that species realized distributions are constrained by other factors other than just thermal tolerances.

  5. When do plant radiations influence community assembly? The importance of historical contingency in the race for niche space.

    Science.gov (United States)

    Tanentzap, Andrew J; Brandt, Angela J; Smissen, Rob D; Heenan, Peter B; Fukami, Tadashi; Lee, William G

    2015-07-01

    Plant radiations are widespread but their influence on community assembly has rarely been investigated. Theory and some evidence suggest that radiations can allow lineages to monopolize niche space when founding species arrive early into new bioclimatic regions and exploit ecological opportunities. These early radiations may subsequently reduce niche availability and dampen diversification of later arrivals. We tested this hypothesis of time-dependent lineage diversification and community dominance using the alpine flora of New Zealand. We estimated ages of 16 genera from published phylogenies and determined their relative occurrence across climatic and physical gradients in the alpine zone. We used these data to reconstruct occupancy of environmental space through time, integrating palaeoclimatic and palaeogeological changes. Our analysis suggested that earlier-colonizing lineages encountered a greater availability of environmental space, which promoted greater species diversity and occupancy of niche space. Genera that occupied broader niches were subsequently more dominant in local communities. An earlier time of arrival also contributed to greater diversity independently of its influence in accessing niche space. We suggest that plant radiations influence community assembly when they arise early in the occupancy of environmental space, allowing them to exclude later-arriving colonists from ecological communities by niche preemption. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  6. Effects of microbial inhibitors on anaerobic degradation of DDT

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Y.S.; Chiu, T.C.; Yen, J.H. [National Taiwan Univ., Taipei (Taiwan)

    2004-09-15

    Chlorinated insecticide DDT [1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane] was extensively used for controlling pests in the agricultural field and human-being living environments in the past several decades. Due to the chemical stability, DDT was extremely persistent and recalcitrant in soils and sediments and it was banned by nations. Microorganisms usually play important roles in reducing organochlorine compounds in the environments. Under low-oxygen conditions, microbial dechlorination is thought as the onset of highly chlorinated compounds. Methanogenic and sulfate-reducing bacteria participate in microbial dechlorination under anaerobic condition has been reported. In this study, a mixed anaerobic culture enabling to dechlorinate DDT was obtained from river sediment in Taiwan. In order to understand the effect of these microorganisms on DDT dechlorination, microbial inhibitors BESA (2-bromoethanesulfonate) and molybdate, for inhibiting methanogenic and sulfate-reducing bacteria, respectively, were chosen to investigate the interaction between specific microbial communities and their degradation activities. Besides, a molecular technique, denaturing gradient gel electrophoresis (DGGE), based on analyzing the 16S rDNA of bacteria, was used for monitoring the bacterial community structure in this study.

  7. To predict the niche, model colonization and extinction

    Science.gov (United States)

    Charles B. Yackulic; James D. Nichols; Janice Reid; Ricky Der

    2015-01-01

    Ecologists frequently try to predict the future geographic distributions of species. Most studies assume that the current distribution of a species reflects its environmental requirements (i.e., the species’ niche). However, the current distributions of many species are unlikely to be at equilibrium with the current distribution of environmental conditions, both...

  8. Stem Cell Niches in Glioblastoma: A Neuropathological View

    Directory of Open Access Journals (Sweden)

    Davide Schiffer

    2014-01-01

    Full Text Available Glioblastoma (GBM stem cells (GSCs, responsible for tumor growth, recurrence, and resistance to therapies, are considered the real therapeutic target, if they had no molecular mechanisms of resistance, in comparison with the mass of more differentiated cells which are insensitive to therapies just because of being differentiated and nonproliferating. GSCs occur in tumor niches where both stemness status and angiogenesis are conditioned by the microenvironment. In both perivascular and perinecrotic niches, hypoxia plays a fundamental role. Fifteen glioblastomas have been studied by immunohistochemistry and immunofluorescence for stemness and differentiation antigens. It has been found that circumscribed necroses develop inside hyperproliferating areas that are characterized by high expression of stemness antigens. Necrosis developed inside them because of the imbalance between the proliferation of tumor cells and endothelial cells; it reduces the number of GSCs to a thin ring around the former hyperproliferating area. The perinecrotic GSCs are nothing else that the survivors remnants of those populating hyperproliferating areas. In the tumor, GSCs coincide with malignant areas so that the need to detect where they are located is not so urgent.

  9. Satellite Cells and the Muscle Stem Cell Niche

    Science.gov (United States)

    Yin, Hang; Price, Feodor

    2013-01-01

    Adult skeletal muscle in mammals is a stable tissue under normal circumstances but has remarkable ability to repair after injury. Skeletal muscle regeneration is a highly orchestrated process involving the activation of various cellular and molecular responses. As skeletal muscle stem cells, satellite cells play an indispensible role in this process. The self-renewing proliferation of satellite cells not only maintains the stem cell population but also provides numerous myogenic cells, which proliferate, differentiate, fuse, and lead to new myofiber formation and reconstitution of a functional contractile apparatus. The complex behavior of satellite cells during skeletal muscle regeneration is tightly regulated through the dynamic interplay between intrinsic factors within satellite cells and extrinsic factors constituting the muscle stem cell niche/microenvironment. For the last half century, the advance of molecular biology, cell biology, and genetics has greatly improved our understanding of skeletal muscle biology. Here, we review some recent advances, with focuses on functions of satellite cells and their niche during the process of skeletal muscle regeneration. PMID:23303905

  10. Microbial competition among anammox bacteria in nitrite-limited bioreactors

    KAUST Repository

    Zhang, Lei

    2017-08-26

    Phylogenetically diverse anammox bacteria have been detected in most of anoxic natural and engineered ecosystems and thus regarded as key players in the global nitrogen cycle. However, ecological niche differentiation of anammox bacteria remains unresolved despite its ecological and practical importance. In this study, the microbial competitions for a common substrate (nitrite) among three anammox species (i.e. “Candidatus Brocadia sinica”, “Candidatus Jettenia caeni” and “Candidatus Kuenenia stuttgartiensis”) were systematically investigated in nitrite-limited gel-immobilized column reactors (GICR) and membrane bioreactors (MBRs) under different nitrogen loading rates (NLRs). 16 S rRNA gene-based population dynamics revealed that “Ca. J. caeni” could proliferate only at low NLRs, whereas “Ca. B. sinica” outcompeted other two species at higher NLRs in both types of reactors. Furthermore, FISH analysis revealed that “Ca. J. caeni” was mainly present as spherical microclusters at the inner part (low NO2− environment), whereas “Ca. B. sinica” was present throughout the gel beads and granules. This spatial distribution supports the outcomes of the competition experiments. However, the successful competition of “Ca. J. caeni” at low NLR could not be explained with the Monod model probably due to inaccuracy of kinetic parameters such as half saturation constant (Ks) for nitrite and a difference in the maintenance rate (m). In addition, the growth of “Ca. K. stuttgartiensis” could not be observed in any experimental conditions, suggesting possible unknown factor(s) is missing. Taken together, NLR was one of factors determining ecological niche differentiation of “Ca. B. sinica” and “Ca. J. caeni”.

  11. Microbial competition among anammox bacteria in nitrite-limited bioreactors

    KAUST Repository

    Zhang, Lei; Narita, Yuko; Gao, Lin; Ali, Muhammad; Oshiki, Mamoru; Ishii, Satoshi; Okabe, Satoshi

    2017-01-01

    Phylogenetically diverse anammox bacteria have been detected in most of anoxic natural and engineered ecosystems and thus regarded as key players in the global nitrogen cycle. However, ecological niche differentiation of anammox bacteria remains unresolved despite its ecological and practical importance. In this study, the microbial competitions for a common substrate (nitrite) among three anammox species (i.e. “Candidatus Brocadia sinica”, “Candidatus Jettenia caeni” and “Candidatus Kuenenia stuttgartiensis”) were systematically investigated in nitrite-limited gel-immobilized column reactors (GICR) and membrane bioreactors (MBRs) under different nitrogen loading rates (NLRs). 16 S rRNA gene-based population dynamics revealed that “Ca. J. caeni” could proliferate only at low NLRs, whereas “Ca. B. sinica” outcompeted other two species at higher NLRs in both types of reactors. Furthermore, FISH analysis revealed that “Ca. J. caeni” was mainly present as spherical microclusters at the inner part (low NO2− environment), whereas “Ca. B. sinica” was present throughout the gel beads and granules. This spatial distribution supports the outcomes of the competition experiments. However, the successful competition of “Ca. J. caeni” at low NLR could not be explained with the Monod model probably due to inaccuracy of kinetic parameters such as half saturation constant (Ks) for nitrite and a difference in the maintenance rate (m). In addition, the growth of “Ca. K. stuttgartiensis” could not be observed in any experimental conditions, suggesting possible unknown factor(s) is missing. Taken together, NLR was one of factors determining ecological niche differentiation of “Ca. B. sinica” and “Ca. J. caeni”.

  12. Polymer Separators for High-Power, High-Efficiency Microbial Fuel Cells

    KAUST Repository

    Chen, Guang

    2012-12-26

    Microbial fuel cells (MFCs) with hydrophilic poly(vinyl alcohol) (PVA) separators showed higher Coulombic efficiencies (94%) and power densities (1220 mW m-2) than cells with porous glass fiber separators or reactors without a separator after 32 days of operation. These remarkable increases in both the coublomic efficiency and the power production of the microbial fuel cells were made possible by the separator\\'s unique characteristics of fouling mitigation of the air cathode without a large increase in ionic resistance in the cell. This new type of polymer gel-like separator design will be useful for improving MFC reactor performance by enabling compact cell designs. © 2012 American Chemical Society.

  13. Niche partitioning of feeding microhabitats produces a unique function for herbivorous rabbitfishes (Perciformes, Siganidae) on coral reefs

    Science.gov (United States)

    Fox, R. J.; Bellwood, D. R.

    2013-03-01

    Niche theory predicts that coexisting species minimise competition by evolving morphological or behavioural specialisations that allow them to spread out along resource axes such as space, diet and temporal activity. These specialisations define how a species interacts with its environment and, by extension, determine its functional role. Here, we examine the feeding niche of three species of coral reef-dwelling rabbitfishes (Siganidae, Siganus). By comparing aspects of their feeding behaviour (bite location, bite rate, foraging distance) with that of representative species from two other abundant herbivorous fish families, the parrotfishes (Labridae, Scarus) and surgeonfishes (Acanthuridae, Acanthurus), we examine whether rabbitfishes have a feeding niche distinct from other members of the herbivore guild. Measurements of the penetration of the fishes' snouts and bodies into reef concavities when feeding revealed that rabbitfish fed to a greater degree from reef crevices and interstices than other herbivores. There was just a 40 % overlap in the penetration-depth niche between rabbitfish and surgeonfish and a 45 % overlap between rabbitfish and parrotfish, compared with the almost complete niche overlap (95 %) recorded for parrotfish and surgeonfish along this spatial niche axis. Aspects of the morphology of rabbitfish which may contribute to this niche segregation include a comparatively longer, narrower snout and narrower head. Our results suggest that sympatric coexistence of rabbitfish and other reef herbivores is facilitated by segregation along a spatial (and potentially dietary) axis. This segregation results in a unique functional role for rabbitfishes among roving herbivores that of "crevice-browser": a group that specifically feeds on crevice-dwelling algal or benthic organisms. This functional trait may have implications for reef ecosystem processes in terms of controlling the successional development of crevice-based algal communities, reducing their

  14. Microbial ecology of deep-sea hypersaline anoxic basins

    KAUST Repository

    Merlino, Giuseppe

    2018-05-09

    Deep hypersaline anoxic basins (DHABs) are unique water bodies occurring within fractures at the bottom of the sea, where the dissolution of anciently buried evaporites created dense anoxic brines that are separated by a chemocline/pycnocline from the overlying oxygenated deep-seawater column. DHABs have been described in the Gulf of Mexico, the Mediterranean Sea, the Black Sea and the Red Sea. They are characterized by prolonged historical separation of the brines from the upper water column due to lack of mixing and by extreme conditions of salinity, anoxia, and relatively high hydrostatic pressure and temperatures. Due to these combined selection factors, unique microbial assemblages thrive in these polyextreme ecosystems. The topological localization of the different taxa in the brine-seawater transition zone coupled with the metabolic interactions and niche adaptations determine the metabolic functioning and biogeochemistry of DHABs. In particular, inherent metabolic strategies accompanied by genetic adaptations have provided insights on how prokaryotic communities can adapt to salt-saturated condition. Here, we review the current knowledge on the diversity, genomics, metabolisms and ecology of prokaryotes in DHABs.

  15. Malaria in Africa: vector species' niche models and relative risk maps.

    Directory of Open Access Journals (Sweden)

    Alexander Moffett

    2007-09-01

    Full Text Available A central theoretical goal of epidemiology is the construction of spatial models of disease prevalence and risk, including maps for the potential spread of infectious disease. We provide three continent-wide maps representing the relative risk of malaria in Africa based on ecological niche models of vector species and risk analysis at a spatial resolution of 1 arc-minute (9 185 275 cells of approximately 4 sq km. Using a maximum entropy method we construct niche models for 10 malaria vector species based on species occurrence records since 1980, 19 climatic variables, altitude, and land cover data (in 14 classes. For seven vectors (Anopheles coustani, A. funestus, A. melas, A. merus, A. moucheti, A. nili, and A. paludis these are the first published niche models. We predict that Central Africa has poor habitat for both A. arabiensis and A. gambiae, and that A. quadriannulatus and A. arabiensis have restricted habitats in Southern Africa as claimed by field experts in criticism of previous models. The results of the niche models are incorporated into three relative risk models which assume different ecological interactions between vector species. The "additive" model assumes no interaction; the "minimax" model assumes maximum relative risk due to any vector in a cell; and the "competitive exclusion" model assumes the relative risk that arises from the most suitable vector for a cell. All models include variable anthrophilicity of vectors and spatial variation in human population density. Relative risk maps are produced from these models. All models predict that human population density is the critical factor determining malaria risk. Our method of constructing relative risk maps is equally general. We discuss the limits of the relative risk maps reported here, and the additional data that are required for their improvement. The protocol developed here can be used for any other vector-borne disease.

  16. Integrated Approach to Reconstruction of Microbial Regulatory Networks

    Energy Technology Data Exchange (ETDEWEB)

    Rodionov, Dmitry A [Sanford-Burnham Medical Research Institute; Novichkov, Pavel S [Lawrence Berkeley National Laboratory

    2013-11-04

    This project had the goal(s) of development of integrated bioinformatics platform for genome-scale inference and visualization of transcriptional regulatory networks (TRNs) in bacterial genomes. The work was done in Sanford-Burnham Medical Research Institute (SBMRI, P.I. D.A. Rodionov) and Lawrence Berkeley National Laboratory (LBNL, co-P.I. P.S. Novichkov). The developed computational resources include: (1) RegPredict web-platform for TRN inference and regulon reconstruction in microbial genomes, and (2) RegPrecise database for collection, visualization and comparative analysis of transcriptional regulons reconstructed by comparative genomics. These analytical resources were selected as key components in the DOE Systems Biology KnowledgeBase (SBKB). The high-quality data accumulated in RegPrecise will provide essential datasets of reference regulons in diverse microbes to enable automatic reconstruction of draft TRNs in newly sequenced genomes. We outline our progress toward the three aims of this grant proposal, which were: Develop integrated platform for genome-scale regulon reconstruction; Infer regulatory annotations in several groups of bacteria and building of reference collections of microbial regulons; and Develop KnowledgeBase on microbial transcriptional regulation.

  17. An Automatic K-Means Clustering Algorithm of GPS Data Combining a Novel Niche Genetic Algorithm with Noise and Density

    Directory of Open Access Journals (Sweden)

    Xiangbing Zhou

    2017-12-01

    Full Text Available Rapidly growing Global Positioning System (GPS data plays an important role in trajectory and their applications (e.g., GPS-enabled smart devices. In order to employ K-means to mine the better origins and destinations (OD behind the GPS data and overcome its shortcomings including slowness of convergence, sensitivity to initial seeds selection, and getting stuck in a local optimum, this paper proposes and focuses on a novel niche genetic algorithm (NGA with density and noise for K-means clustering (NoiseClust. In NoiseClust, an improved noise method and K-means++ are proposed to produce the initial population and capture higher quality seeds that can automatically determine the proper number of clusters, and also handle the different sizes and shapes of genes. A density-based method is presented to divide the number of niches, with its aim to maintain population diversity. Adaptive probabilities of crossover and mutation are also employed to prevent the convergence to a local optimum. Finally, the centers (the best chromosome are obtained and then fed into the K-means as initial seeds to generate even higher quality clustering results by allowing the initial seeds to readjust as needed. Experimental results based on taxi GPS data sets demonstrate that NoiseClust has high performance and effectiveness, and easily mine the city’s situations in four taxi GPS data sets.

  18. Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures.

    Science.gov (United States)

    Schloss, Patrick D; Handelsman, Jo

    2006-10-01

    The recent advent of tools enabling statistical inferences to be drawn from comparisons of microbial communities has enabled the focus of microbial ecology to move from characterizing biodiversity to describing the distribution of that biodiversity. Although statistical tools have been developed to compare community structures across a phylogenetic tree, we lack tools to compare the memberships and structures of two communities at a particular operational taxonomic unit (OTU) definition. Furthermore, current tests of community structure do not indicate the similarity of the communities but only report the probability of a statistical hypothesis. Here we present a computer program, SONS, which implements nonparametric estimators for the fraction and richness of OTUs shared between two communities.

  19. Inter-specific and seasonal comparison of the niches occupied by small cetaceans off north-west Iberia

    DEFF Research Database (Denmark)

    Fernandez Garcia, Rut; MacLeod, C. D.; Pierce, G. J.

    2013-01-01

    Knowledge of species' ecological niches can be used to assess ecological interactions between different taxa. Sixteen species of cetaceans have been recorded in Galician waters and niche partitioning is expected to occur among these species in order to allow them to co-exist. In this study, the n...

  20. Different Motile Behaviors of Human Hematopoietic Stem versus Progenitor Cells at the Osteoblastic Niche

    Directory of Open Access Journals (Sweden)

    Katie Foster

    2015-11-01

    Full Text Available Despite advances in our understanding of interactions between mouse hematopoietic stem cells (HSCs and their niche, little is known about communication between human HSCs and the microenvironment. Using a xenotransplantation model and intravital imaging, we demonstrate that human HSCs display distinct motile behaviors to their hematopoietic progenitor cell (HPC counterparts, and the same pattern can be found between mouse HSCs and HPCs. HSCs become significantly less motile after transplantation, while progenitor cells remain motile. We show that human HSCs take longer to find their niche than previously expected and suggest that the niche be defined as the position where HSCs stop moving. Intravital imaging is the only technique to determine where in the bone marrow stem cells stop moving, and future analyses should focus on the environment surrounding the HSC at this point.

  1. Co-niche construction between hosts and symbionts: ideas and ...

    Indian Academy of Sciences (India)

    RENEE M. BORGES

    2017-07-05

    Jul 5, 2017 ... Centre for Ecological Sciences, Indian Institute of Science, Bengaluru 560 012, India ... Symbiosis is a process that can generate evolutionary novelties and can extend the phenotypic niche ..... order to facilitate interactions with ants, plants provide ... of mutualistic pollinators develops within the pollinated ...

  2. Cell organisation in the colonic crypt: a theoretical comparison of the pedigree and niche concepts.

    Directory of Open Access Journals (Sweden)

    Richard C van der Wath

    Full Text Available The intestinal mucosa is a monolayer of rapidly self-renewing epithelial cells which is not only responsible for absorption of water and nutrients into the bloodstream but also acts as a protective barrier against harmful microbes entering the body. New functional epithelial cells are produced from stem cells, and their proliferating progeny. These stem cells are found within millions of crypts (tubular pits spaced along the intestinal tract. The entire intestinal epithelium is replaced every 2-3 days in mice (3-5 days in humans and hence cell production, differentiation, migration and turnover need to be tightly regulated. Malfunctions in this regulation are strongly linked to inflammatory bowel diseases and to the formation of adenomas and ultimately cancerous tumours. Despite a great deal of biological experimentation and observation, precisely how colonic crypts are regulated to produce mature colonocytes remains unclear. To assist in understanding how cell organisation in crypts is achieved, two very different conceptual models of cell behaviour are developed here, referred to as the 'pedigree' and the 'niche' models. The pedigree model proposes that crypt cells are largely preprogrammed and receive minimal prompting from the environment as they move through a routine of cell differentiation and proliferation to become mature colonocytes. The niche model proposes that crypt cells are primarily influenced by the local microenvironments along the crypt, and that predetermined cell behaviour plays a negligible role in their development. In this paper we present a computational model of colonic crypts in the mouse, which enables a comparison of the quality and controllability of mature coloncyte production by crypts operating under these two contrasting conceptual models of crypt regulation.

  3. Unveiling current Guanaco distribution in chile based upon niche structure of phylogeographic lineages: Andean puna to subpolar forests.

    Science.gov (United States)

    González, Benito A; Samaniego, Horacio; Marín, Juan Carlos; Estades, Cristián F

    2013-01-01

    Niche description and differentiation at broad geographic scales have been recent major topics in ecology and evolution. Describing the environmental niche structure of sister taxa with known evolutionary trajectories stands out as a useful exercise in understanding niche requirements. Here we model the environmental niche structure and distribution of the recently resolved phylogeography of guanaco (Lama guanicoe) lineages on the western slope of the southern Andes. Using a maximum entropy framework, field data, and information on climate, topography, human density, and vegetation cover, we identify differences between the two subspecies (L.g.cacsilensis, L.g.guanicoe) and their intermediate-hybrid lineage, that most likely determine the distribution of this species. While aridity seems to be a major factor influencing the distribution at the species-level (annual precipitation ecological and/or evolutionary processes are shaping the niche of guanacos in Chile, producing discrepancies when comparing range distribution at the species-level (81,756 km(2)) with lineages-level (65,321 km(2)). The subspecies-specific description of niche structure is provided here based upon detailed spatial distribution of the lineages of guanacos in Chile. Such description provides a scientific tool to further develop large scale plans for habitat conservation and preservation of intraspecific genetic variability for this far ranging South American camelid, which inhabits a diversity of ecoregion types from Andean puna to subpolar forests.

  4. Microbial metabolomics in open microscale platforms

    Science.gov (United States)

    Barkal, Layla J.; Theberge, Ashleigh B.; Guo, Chun-Jun; Spraker, Joe; Rappert, Lucas; Berthier, Jean; Brakke, Kenneth A.; Wang, Clay C. C.; Beebe, David J.; Keller, Nancy P.; Berthier, Erwin

    2016-01-01

    The microbial secondary metabolome encompasses great synthetic diversity, empowering microbes to tune their chemical responses to changing microenvironments. Traditional metabolomics methods are ill-equipped to probe a wide variety of environments or environmental dynamics. Here we introduce a class of microscale culture platforms to analyse chemical diversity of fungal and bacterial secondary metabolomes. By leveraging stable biphasic interfaces to integrate microculture with small molecule isolation via liquid–liquid extraction, we enable metabolomics-scale analysis using mass spectrometry. This platform facilitates exploration of culture microenvironments (including rare media typically inaccessible using established methods), unusual organic solvents for metabolite isolation and microbial mutants. Utilizing Aspergillus, a fungal genus known for its rich secondary metabolism, we characterize the effects of culture geometry and growth matrix on secondary metabolism, highlighting the potential use of microscale systems to unlock unknown or cryptic secondary metabolites for natural products discovery. Finally, we demonstrate the potential for this class of microfluidic systems to study interkingdom communication between fungi and bacteria. PMID:26842393

  5. Engineering chemical interactions in microbial communities.

    Science.gov (United States)

    Kenny, Douglas J; Balskus, Emily P

    2018-03-05

    Microbes living within host-associated microbial communities (microbiotas) rely on chemical communication to interact with surrounding organisms. These interactions serve many purposes, from supplying the multicellular host with nutrients to antagonizing invading pathogens, and breakdown of chemical signaling has potentially negative consequences for both the host and microbiota. Efforts to engineer microbes to take part in chemical interactions represent a promising strategy for modulating chemical signaling within these complex communities. In this review, we discuss prominent examples of chemical interactions found within host-associated microbial communities, with an emphasis on the plant-root microbiota and the intestinal microbiota of animals. We then highlight how an understanding of such interactions has guided efforts to engineer microbes to participate in chemical signaling in these habitats. We discuss engineering efforts in the context of chemical interactions that enable host colonization, promote host health, and exclude pathogens. Finally, we describe prominent challenges facing this field and propose new directions for future engineering efforts.

  6. Phylogenetic climatic niche conservatism and evolution of climatic suitability in Neotropical Angraecinae (Vandeae, Orchidaceae) and their closest African relatives.

    Science.gov (United States)

    Kolanowska, Marta; Grochocka, Elżbieta; Konowalik, Kamil

    2017-01-01

    In the present study we investigate the concept of phylogenetic niche conservatism (PNC) within the American species of angraecoid orchids ( Campylocentrum and Dendrophylax ) and their closest relatives in the Old World ( Angraecum ) using ecological niche modelling (ENM). The predicted niche occupancy profiles were matched with the outcomes of previous phylogenetic studies to reconstruct the evolution of climatic suitability within the orchid group studied and evaluate the role of niche differentiation in the speciation of Angraecinae. No correlation between preferred niches and taxonomic relationships within the orchid group studied was revealed. The climatic suitability of the majority of the species overlapped each other, either fully or partially. This pattern is also present in the species of other orchid genera. Our research confirms a significant level of PNC in Orchidaceae, even within taxa exhibiting a transatlantic disjunction. The analysis of the evolution of climatic suitability indicated that the adaptation to various climatic conditions is not a factor that has driven speciation within orchids studied.

  7. The importance of anabolism in microbial control over soil carbon storage

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Chao; Schimel, Joshua P.; Jastrow, Julie D.

    2017-07-25

    Studies of the decomposition, transformation and stabilization of soil organic matter (SOM) have dramatically increased in recent years owing to growing interest in studying the global carbon (C) cycle as it pertains to climate change. While it is readily accepted that the magnitude of the organic C reservoir in soils depends upon microbial involvement, as soil C dynamics are ultimately the consequence of microbial growth and activity, it remains largely unknown how these microorganism-mediated processes lead to soil C stabilization. Here, we define two pathways—ex vivo modification and in vivo turnover—which jointly explain soil C dynamics driven by microbial catabolism and/or anabolism. Accordingly, we use the conceptual framework of the soil ‘microbial carbon pump’ (MCP) to demonstrate how microorganisms are an active player in soil C storage. The MCP couples microbial production of a set of organic compounds to their further stabilization, which we define as the entombing effect. This integration captures the cumulative long-term legacy of microbial assimilation on SOM formation, with mechanisms (whether via physical protection or a lack of activation energy due to chemical composition) that ultimately enable the entombment of microbial-derived C in soils. We propose a need for increased efforts and seek to inspire new studies that utilize the soil MCP as a conceptual guideline for improving mechanistic understandings of the contributions of soil C dynamics to the responses of the terrestrial C cycle under global change.

  8. Niche differentiation in nitrogen metabolism among methanotrophs within an operational taxonomic unit.

    Science.gov (United States)

    Hoefman, Sven; van der Ha, David; Boon, Nico; Vandamme, Peter; De Vos, Paul; Heylen, Kim

    2014-04-04

    The currently accepted thesis on nitrogenous fertilizer additions on methane oxidation activity assumes niche partitioning among methanotrophic species, with activity responses to changes in nitrogen content being dependent on the in situ methanotrophic community structure Unfortunately, widely applied tools for microbial community assessment only have a limited phylogenetic resolution mostly restricted to genus level diversity, and not to species level as often mistakenly assumed. As a consequence, intragenus or intraspecies metabolic versatility in nitrogen metabolism was never evaluated nor considered among methanotrophic bacteria as a source of differential responses of methane oxidation to nitrogen amendments. We demonstrated that fourteen genotypically different Methylomonas strains, thus distinct below the level at which most techniques assign operational taxonomic units (OTU), show a versatile physiology in their nitrogen metabolism. Differential responses, even among strains with identical 16S rRNA or pmoA gene sequences, were observed for production of nitrite and nitrous oxide from nitrate or ammonium, nitrogen fixation and tolerance to high levels of ammonium, nitrate, and hydroxylamine. Overall, reduction of nitrate to nitrite, nitrogen fixation, higher tolerance to ammonium than nitrate and tolerance and assimilation of nitrite were general features. Differential responses among closely related methanotrophic strains to overcome inhibition and toxicity from high nitrogen loads and assimilation of various nitrogen sources yield competitive fitness advantages to individual methane-oxidizing bacteria. Our observations proved that community structure at the deepest phylogenetic resolution potentially influences in situ functioning.

  9. Phylogenetic climatic niche conservatism and evolution of climatic suitability in Neotropical Angraecinae (Vandeae, Orchidaceae) and their closest African relatives

    Czech Academy of Sciences Publication Activity Database

    Kolanowska, Marta; Grochocka, E.; Konowalik, K.

    2017-01-01

    Roč. 5, may (2017), č. článku e3328. ISSN 2167-8359 R&D Projects: GA ČR GB14-36098G Institutional support: RVO:86652079 Keywords : campylocentrum orchidaceae * molecular phylogenetics * environmental niches * costa-rica * diversity * models * speciation * ecology * pollination * divergence * Angraecinae * Ecological niche modeling * Orchidaceae * Phylogenetic niche conservatism * Angraecum * Campylocentrum * Dendrophylax Subject RIV: EH - Ecology, Behaviour OBOR OECD: Biodiversity conservation Impact factor: 2.177, year: 2016

  10. Unveiling current Guanaco distribution in chile based upon niche structure of phylogeographic lineages: Andean puna to subpolar forests.

    Directory of Open Access Journals (Sweden)

    Benito A González

    Full Text Available Niche description and differentiation at broad geographic scales have been recent major topics in ecology and evolution. Describing the environmental niche structure of sister taxa with known evolutionary trajectories stands out as a useful exercise in understanding niche requirements. Here we model the environmental niche structure and distribution of the recently resolved phylogeography of guanaco (Lama guanicoe lineages on the western slope of the southern Andes. Using a maximum entropy framework, field data, and information on climate, topography, human density, and vegetation cover, we identify differences between the two subspecies (L.g.cacsilensis, L.g.guanicoe and their intermediate-hybrid lineage, that most likely determine the distribution of this species. While aridity seems to be a major factor influencing the distribution at the species-level (annual precipitation <900 mm, we also document important differences in niche specificity for each subspecies, where distribution of Northern lineage is explained mainly by elevation (mean = 3,413 m and precipitation seasonality (mean = 161 mm, hybrid lineage by annual precipitation (mean = 139 mm, and Southern subspecies by annual precipitation (mean = 553 mm, precipitation seasonality (mean = 21 mm and grass cover (mean = 8.2%. Among lineages, we detected low levels of niche overlap: I (Similarity Index = 0.06 and D (