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Community assembly

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https://www.readbyqxmd.com/read/28340301/ten-years-of-barcoding-at-the-african-centre-for-dna-barcoding
#1
Simeon Bezeng Bezeng, T Jonathan Davies, Barnabas H Daru, Ronny Mukala Kabongo, Olivier Maurin, Kowiyou Yessoufou, Herman van der Bank, Michelle Van der Bank
The African Centre for DNA Barcoding (ACDB) was established in 2005 as part of a global initiative to accurately and rapidly survey biodiversity using short DNA sequences. The mitochondrial cytochrome c oxidase 1 gene (CO1) was rapidly adopted as the de facto barcode for animals. Following the evaluation of several candidate loci for plants, the Plant Working Group of the Consortium for the Barcoding of Life in 2009 recommended that the two plastid genes, rbcLa and matK, be adopted as core DNA barcodes for terrestrial plants...
March 24, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28334205/tetrahymena-phagocytic-vesicles-as-ecological-micro-niches-of-phage-transfer
#2
Iqbal Aijaz, Gerald B Koudelka
The microbial communities in natural environments such as soil, pond water, or animal rumens are comprised of a diverse mixture of bacteria and protozoa including ciliates or flagellates. In such microbiomes, a major source of bacterial mortality is grazing by phagocytic protists. Many protists are omnivorous heterotrophs, feeding on a range of different bacterial species. Due to this indiscriminate feeding, different bacterial species can assemble together in the same phagocytic vesicles where can they potentially exchange genetic material...
March 3, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28334139/environmental-filtering-drives-the-shape-and-breadth-of-the-seed-germination-niche-in-coastal-plant-communities
#3
Eduardo Fernández-Pascual, Adrián Pérez-Arcoiza, José Alberto Prieto, Tomás E Díaz
Background and Aims: 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...
February 27, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28334050/improving-transcriptome-de-novo-assembly-by-using-a-reference-genome-of-a-related-species-translational-genomics-from-oil-palm-to-coconut
#4
Alix Armero, Luc Baudouin, Stéphanie Bocs, Dominique This
The palms are a family of tropical origin and one of the main constituents of the ecosystems of these regions around the world. The two main species of palm represent different challenges: coconut (Cocos nucifera L.) is a source of multiple goods and services in tropical communities, while oil palm (Elaeis guineensis Jacq) is the main protagonist of the oil market. In this study, we present a workflow that exploits the comparative genomics between a target species (coconut) and a reference species (oil palm) to improve the transcriptomic data, providing a proteome useful to answer functional or evolutionary questions...
2017: PloS One
https://www.readbyqxmd.com/read/28332847/phase-behavior-and-physical-properties-of-new-biobased-ionic-liquid-crystals
#5
Ariel Antonio Campos Toledo Hijo, Guilherme José Maximo, Mariana Conceição Costa, Rosiane Lopes Cunha, Jorge Fernando Brandão Pereira, Kiki Adi Kurnia, Eduardo A Caldas Batista, Antonio J A Meirelles
Protic ionic liquids (PILs) have emerged as promising compounds and attracted the interest of the industry and the academy community, due to their easy preparation and unique properties. In the context of green chemistry, the use of biocompounds, such as fatty acids for their synthesis could disclose a possible alternative way to produce ILs with low or non-toxic effect and consequently, expanding their applicability in bio-based processes or in the development of bioproducts. This work addressed efforts to a better comprehension of the complex Solid-Liquid-Crystal-Liquid thermodynamic equilibrium of twenty new PILs synthesized by using fatty acids commonly found in vegetable oils, as well as their rheological profile and self-assembling ability...
March 23, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28331595/context-dependent-functional-dispersion-across-similar-ranges-of-trait-space-covered-by-intertidal-rocky-shore-communities
#6
Nelson Valdivia, Viviana Segovia-Rivera, Eliseo Fica, César C Bonta, Moisés A Aguilera, Bernardo R Broitman
Functional diversity is intimately linked with community assembly processes, but its large-scale patterns of variation are often not well understood. Here, we investigated the spatiotemporal changes in multiple trait dimensions ("trait space") along vertical intertidal environmental stress gradients and across a landscape scale. We predicted that the range of the trait space covered by local assemblages (i.e., functional richness) and the dispersion in trait abundances (i.e., functional dispersion) should increase from high- to low-intertidal elevations, due to the decreasing influence of environmental filtering...
March 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28331178/habitat-filtering-and-exclusion-of-weak-competitors-jointly-explain-fern-species-assemblage-along-a-light-and-water-gradient
#7
Hui Zhang, Shidan Zhu, Robert John, Ronghua Li, Hui Liu, Qing Ye
Fern species are an important component of the diversity of forest plant communities, but very little is known about how fern communities assemble in different environments. In this study, we use multiple trait-based tests to examine the relationships between several key eco-physiological traits which are direct indicators of shade and drought tolerance, and the abundance of fern species in pine forest (PF), pine and mixed broad leaf forest (PMBF) and matured broad leaf forest (MBF) in southern China. These forests are characterized by decreasing light but increasing water availability during succession, and the fern communities correspondingly differ in species composition...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327913/the-use-of-oxford-nanopore-native-barcoding-for-complete-genome-assembly
#8
Sion C Bayliss, Vicky L Hunt, Maho Yokoyama, Harry A Thorpe, Edward J Feil
Background: The Oxford Nanopore Technologies MinION(TM) is a mobile DNA sequencer that can produce long read sequences with a short turn-around time. Here we report the first demonstration of single contig genome assembly using Oxford Nanopore native barcoding when applied to a multiplexed library of 12 samples and combined with existing Illumina short-read data. This paves the way for the closure of multiple bacterial genomes from a single MinION(TM) sequencing run, given the availability of existing short-read data...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28325890/environmental-filtering-triggers-community-assembly-of-forest-understorey-plants-in-central-european-pine-stands
#9
Werner Ulrich, Piotr Sewerniak, Radosław Puchałka, Marcin Piwczyński
Habitat filtering models predict ecologically similar plant species to jointly colonize sites due to comparable environmental characteristics leading to an aggregated pattern of species spatial occurrence. Models focused on interspecific competition expect species with similar ecological requirements to be spatially segregated. While both models are corroborated by field work, few empirical studies have tried to infer under which habitat conditions these patterns of co-occurrence prevail. Here we use an exceptional data set on central European pine forest understorey plant communities to assess the change in community structure along gradients of soil productivity and heterogeneity...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28323280/defining-the-functional-traits-that-drive-bacterial-decomposer-community-productivity
#10
Rachael Evans, Anna M Alessi, Susannah Bird, Simon J McQueen-Mason, Neil C Bruce, Michael A Brockhurst
Microbial communities are essential to a wide range of ecologically and industrially important processes. To control or predict how these communities function, we require a better understanding of the factors which influence microbial community productivity. Here, we combine functional resource use assays with a biodiversity-ecosystem functioning (BEF) experiment to determine whether the functional traits of constituent species can be used to predict community productivity. We quantified the abilities of 12 bacterial species to metabolise components of lignocellulose and then assembled these species into communities of varying diversity and composition to measure their productivity growing on lignocellulose, a complex natural substrate...
March 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28321234/a-review-of-bioinformatics-tools-for-bio-prospecting-from-metagenomic-sequence-data
#11
REVIEW
Despoina D Roumpeka, R John Wallace, Frank Escalettes, Ian Fotheringham, Mick Watson
The microbiome can be defined as the community of microorganisms that live in a particular environment. Metagenomics is the practice of sequencing DNA from the genomes of all organisms present in a particular sample, and has become a common method for the study of microbiome population structure and function. Increasingly, researchers are finding novel genes encoded within metagenomes, many of which may be of interest to the biotechnology and pharmaceutical industries. However, such "bioprospecting" requires a suite of sophisticated bioinformatics tools to make sense of the data...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28319885/bacterioplankton-assembly-and-interspecies-interaction-indicating-increasing-coastal-eutrophication
#12
Wenfang Dai, Jinjie Zhang, Qichao Tu, Ye Deng, Qiongfen Qiu, Jinbo Xiong
Anthropogenic perturbations impose negative effects on coastal ecosystems, such as increasing levels of eutrophication. Given the biogeochemical significance of microorganisms, understanding the processes and mechanisms underlying their spatial distribution under changing environmental conditions is critical. To address this question, we examined how coastal bacterioplankton communities respond to increasing eutrophication levels created by anthropogenic perturbations. The results showed that the magnitude of changes in the bacterioplankton community compositions (BCCs) and the importance of deterministic processes that constrained bacterial assembly were closely associated with eutrophication levels...
March 9, 2017: Chemosphere
https://www.readbyqxmd.com/read/28319716/multiple-stressors-in-sediments-impact-adjacent-hard-substrate-habitats-and-across-biological-domains
#13
Jasmin C Lawes, Katherine A Dafforn, Graeme F Clark, Mark V Brown, Emma L Johnston
Coastal systems are increasingly impacted by human activities. While the direct effects of individual contaminants have been investigated, the potential for multiple contaminants to impact adjacent hard substrate habitats is poorly understood. Sediment-bound contaminants pose a risk to water column organisms through resuspension and the fluxing of dissolved nutrients and metals. This study experimentally manipulated contaminated coastal sediments in mesocosms with additions of a common fertiliser to investigate the impact on both bacterial biofilms and macrofouling communities on nearby hard substrates...
March 16, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28317296/how-to-make-more-out-of-community-data-a-conceptual-framework-and-its-implementation-as-models-and-software
#14
Otso Ovaskainen, Gleb Tikhonov, Anna Norberg, F Guillaume Blanchet, Leo Duan, David Dunson, Tomas Roslin, Nerea Abrego
Community ecology aims to understand what factors determine the assembly and dynamics of species assemblages at different spatiotemporal scales. To facilitate the integration between conceptual and statistical approaches in community ecology, we propose Hierarchical Modelling of Species Communities (HMSC) as a general, flexible framework for modern analysis of community data. While non-manipulative data allow for only correlative and not causal inference, this framework facilitates the formulation of data-driven hypotheses regarding the processes that structure communities...
March 20, 2017: Ecology Letters
https://www.readbyqxmd.com/read/28317103/outside-the-envelope-rare-events-disrupt-the-relationship-between-climate-factors-and-species-interactions
#15
Katharine L Stuble, Emily Zefferman, Kristina Wolf, Kurt J Vaughn, Truman P Young
The order in which species arrive during community assembly can be an important driver of community composition and function. However, the strength of these priority effects can be variable, in part because of strong site and year effects. To understand how priority effects vary in importance with abiotic conditions, we initiated identical community assembly experiments in which we varied the timing of arrival of native and exotic grass species in each of four years across three grassland sites in northern California...
March 19, 2017: Ecology
https://www.readbyqxmd.com/read/28304369/the-role-of-adaptive-immunity-as-an-ecological-filter-on-the-gut-microbiota-in-zebrafish
#16
Keaton Stagaman, Adam R Burns, Karen Guillemin, Brendan Jm Bohannan
All animals live in intimate association with communities of microbes, collectively referred to as their microbiota. Certain host traits can influence which microbial taxa comprise the microbiota. One potentially important trait in vertebrate animals is the adaptive immune system, which has been hypothesized to act as an ecological filter, promoting the presence of some microbial taxa over others. Here we surveyed the intestinal microbiota of 68 wild-type zebrafish, with functional adaptive immunity, and 61 rag1(-) zebrafish, lacking functional B- and T-cell receptors, to test the role of adaptive immunity as an ecological filter on the intestinal microbiota...
March 17, 2017: ISME Journal
https://www.readbyqxmd.com/read/28303197/heterogeneous-tempo-and-mode-of-evolutionary-diversification-of-compounds-in-lizard-chemical-signals
#17
Roberto García-Roa, Manuel Jara, Pilar López, José Martín, Daniel Pincheira-Donoso
Important part of the multivariate selection shaping social and interspecific interactions among and within animal species emerges from communication. Therefore, understanding the diversification of signals for animal communication is a central endeavor in evolutionary biology. Over the last decade, the rapid development of phylogenetic approaches has promoted a stream of studies investigating evolution of communication signals. However, comparative research has primarily focused on visual and acoustic signals, while the evolution of chemical signals remains largely unstudied...
February 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28303177/community-assembly-in-lake-tanganyika-cichlid-fish-quantifying-the-contributions-of-both-niche-based-and-neutral-processes
#18
Thijs Janzen, Adriana Alzate, Moritz Muschick, Martine E Maan, Fons van der Plas, Rampal S Etienne
The cichlid family features some of the most spectacular examples of adaptive radiation. Evolutionary studies have highlighted the importance of both trophic adaptation and sexual selection in cichlid speciation. However, it is poorly understood what processes drive the composition and diversity of local cichlid species assemblages on relatively short, ecological timescales. Here, we investigate the relative importance of niche-based and neutral processes in determining the composition and diversity of cichlid communities inhabiting various environmental conditions in the littoral zone of Lake Tanganyika, Zambia...
February 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28297714/root-microbiota-drive-direct-integration-of-phosphate-stress-and-immunity
#19
Gabriel Castrillo, Paulo José Pereira Lima Teixeira, Sur Herrera Paredes, Theresa F Law, Laura de Lorenzo, Meghan E Feltcher, Omri M Finkel, Natalie W Breakfield, Piotr Mieczkowski, Corbin D Jones, Javier Paz-Ares, Jeffery L Dangl
Plants live in biogeochemically diverse soils with diverse microbiota. Plant organs associate intimately with a subset of these microbes, and the structure of the microbial community can be altered by soil nutrient content. Plant-associated microbes can compete with the plant and with each other for nutrients, but may also carry traits that increase the productivity of the plant. It is unknown how the plant immune system coordinates microbial recognition with nutritional cues during microbiome assembly. Here we establish that a genetic network controlling the phosphate stress response influences the structure of the root microbiome community, even under non-stress phosphate conditions...
March 23, 2017: Nature
https://www.readbyqxmd.com/read/28295937/integrating-phylogenetic-and-ecological-distances-reveals-new-insights-into-parasite-host-specificity
#20
Nicholas J Clark, Sonya M Clegg
The range of hosts a pathogen infects (host specificity) is a key element of disease risk that may be influenced by both shared phylogenetic history and shared ecological attributes of prospective hosts. Phylospecificity indices quantify host specificity in terms of host relatedness, but can fail to capture ecological attributes that increase susceptibility. For instance, similarity in habitat niche may expose phylogenetically unrelated host species to similar pathogen assemblages. Using a recently proposed method that integrates multiple distances, we develop a new index to assess the relative contributions of host phylogenetic and functional distances to pathogen host specificity (functional-phylogenetic host specificity)...
March 13, 2017: Molecular Ecology
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