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Community assembly

Jacqueline Heckenhauer, Kamariah Abu Salim, Mark W Chase, Kyle G Dexter, R Toby Pennington, Sylvester Tan, Maria Ellen Kaye, Rosabelle Samuel
DNA barcoding is a fast and reliable tool to assess and monitor biodiversity and, via community phylogenetics, to investigate ecological and evolutionary processes that may be responsible for the community structure of forests. In this study, DNA barcodes for the two widely used plastid coding regions rbcL and matK are used to contribute to identification of morphologically undetermined individuals, as well as to investigate phylogenetic structure of tree communities in 70 subplots (10 × 10m) of a 25-ha forest-dynamics plot in Brunei (Borneo, Southeast Asia)...
2017: PloS One
Ainhoa Magrach, Juan P González-Varo, Mathieu Boiffier, Montserrat Vilà, Ignasi Bartomeus
During the past decades, managed honeybee stocks have increased globally. Managed honeybees are particularly used within mass-flowering crops and often spill over to adjacent natural habitats after crop blooming. Here, we uniquely show the simultaneous impact that honeybee spillover has on wild plant and animal communities in flower-rich woodlands via changes in plant-pollinator network structure that translate into a direct negative effect on the reproductive success of a dominant wild plant. Honeybee spillover leads to a re-assembly of plant-pollinator interactions through increased competition with other pollinator species...
September 2017: Nature ecology & evolution
Hiromi Yasuda, Tomohiro Tachi, Mia Lee, Jinkyu Yang
Origami has recently received significant interest from the scientific community as a method for designing building blocks to construct metamaterials. However, the primary focus has been placed on their kinematic applications by leveraging the compactness and auxeticity of planar origami platforms. Here, we present volumetric origami cells-specifically triangulated cylindrical origami (TCO)-with tunable stability and stiffness, and demonstrate their feasibility as non-volatile mechanical memory storage devices...
October 17, 2017: Nature Communications
Silvia Bertagnolio, Rachel L Beanland, Michael R Jordan, Meg Doherty, And Gottfried Hirnschall
The global community, including the World Health Organization (WHO), has committed to ending the AIDS epidemic and to ensuring that 90% of people living with human immunodeficiency virus (HIV) are diagnosed, 90% start treatment, and 90% achieve and maintain virological suppression. The emergence of HIV drug resistance (HIVDR) as antiretroviral treatment programs expand could preclude the 90-90-90 targets adopted by the United Nations General Assembly at the High-Level Meeting on Ending AIDS from being achieved...
October 13, 2017: Journal of Infectious Diseases
Pierre Pericard, Yoann Dufresne, Loïc Couderc, Samuel Blanquart, Hélène Touzet
Motivation: Advances in the sequencing of uncultured environmental samples, dubbed metagenomics, raise a growing need for accurate taxonomic assignment. Accurate identification of organisms present within a community is essential to understanding even the most elementary ecosystems. However, current high-throughput sequencing technologies generate short reads which partially cover full-length marker genes and this poses difficult bioinformatic challenges for taxonomy identification at high resolution...
October 11, 2017: Bioinformatics
Britt Koskella, Lindsay J Hall, C Jessica E Metcalf
The ecological and evolutionary study of community formation, diversity, and stability is rooted in general theory and reinforced by decades of system-specific empirical work. Deploying these ideas to study the assembly, complexity, and dynamics of microbial communities living in and on eukaryotes has proved seductive, but challenging. The success of this research endeavour depends on our capacity to observe and characterize the distributions, abundances, and functional traits of microbiota, representing an array of technical and analytical challenges...
October 16, 2017: Nature ecology & evolution
Xuan Guo, Zhou Li, Qiuming Yao, Ryan S Mueller, Jimmy K Eng, David L Tabb, William Judson Hervey, Chongle Pan
Motivation: Complex microbial communities can be characterized by metagenomics and metaproteomics. However, metagenome assemblies often generate enormous, and yet incomplete, protein databases, which undermines the identification of peptides and proteins in metaproteomics. This challenge calls for increased discrimination of true identifications from false identifications by database searching and filtering algorithms in metaproteomics. Results: Sipros Ensemble was developed here for metaproteomics using an ensemble approach...
September 22, 2017: Bioinformatics
Ali Ebrahimi, Dani Or
Changes in soil hydration status affect microbial community dynamics and shape key biogeochemical processes. Evidence suggests that local anoxic conditions may persist and support anaerobic microbial activity in soil aggregates (or in similar hot spots) long after the bulk soil becomes aerated. To facilitate systematic studies of interactions among environmental factors with biogeochemical emissions of CO2 , N2 O and CH4 from soil aggregates, we remolded silt soil aggregates to different sizes and incorporated carbon at different configurations (core, mixed, no addition)...
October 13, 2017: Global Change Biology
Kathrin Näpflin, Paul Schmid-Hempel
1.To what extent host-associated microbiota assembly is driven by host selection or simply by happenstance remains an open question in microbiome research. 2.Here, we take a first step towards elucidating the relative importance of host selection on the establishing gut microbial community in an ecologically relevant organism. 3.We presented germ-free bumblebee, Bombus terrestris, workers from ten colonies with a "global" microbial species pool comprised of an equal mixture of the gut microbiota of all colonies...
October 11, 2017: Journal of Animal Ecology
Jizhong Zhou, Daliang Ning
Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly in microbial ecology. Although stochastic processes are believed to play nonnegligible roles in shaping community structure, their importance relative to deterministic processes is hotly debated. The importance of ecological stochasticity in shaping microbial community structure is far less appreciated. Some of the main reasons for such heavy debates are the difficulty in defining stochasticity and the diverse methods used for delineating stochasticity...
December 2017: Microbiology and Molecular Biology Reviews: MMBR
Emlyn Resetarits, Sara Cathey, Mathew Leibold
Although the influence of regional processes on local patches is well studied, the influence of local patches and their spatial arrangement on regional processes is likely to be complex. One interesting idea is the keystone community concept (KCC); this posits that there may be some patches that have a disproportionately large effect on the metacommunity compared to other patches. We experimentally test the KCC by using replicate protist microcosm metacommunities with single-patch removals. Removing single patches had no effect on average community richness, evenness and biomass of our metacommunities, but did cause metacommunities to be assembled significantly less by local environmental conditions and more by spatial effects related to stochastic factors...
October 9, 2017: Ecology
Bruno S de O Silva, Felipe H Coutinho, Gustavo B Gregoracci, Luciana Leomil, Louisi S de Oliveira, Adriana Fróes, Diogo Tschoeke, Ana Carolina Soares, Anderson S Cabral, Nicholas D Ward, Jeffrey E Richey, Alex V Krusche, Patricia L Yager, Carlos Eduardo de Rezende, Cristiane C Thompson, Fabiano L Thompson
The Amazon River watershed and its associated plume comprise a vast continental and oceanic area. The microbial activities along this continuum contribute substantially to global carbon and nutrient cycling, and yet there is a dearth of information on the diversity, abundance, and possible roles of viruses in this globally important river. The aim of this study was to elucidate the diversity and structure of virus assemblages of the Amazon River-ocean continuum. Environmental viral DNA sequences were obtained for 12 locations along the river's lower reach (n = 5) and plume (n = 7)...
September 2017: MSphere
Anne T Tuukkanen, Alessandro Spilotros, Dmitri I Svergun
Small-angle X-ray scattering (SAXS) is an established technique that provides low-resolution structural information on macromolecular solutions. Recent decades have witnessed significant progress in both experimental facilities and in novel data-analysis approaches, making SAXS a mainstream method for structural biology. The technique is routinely applied to directly reconstruct low-resolution shapes of proteins and to generate atomistic models of macromolecular assemblies using hybrid approaches. Very importantly, SAXS is capable of yielding structural information on systems with size and conformational polydispersity, including highly flexible objects...
September 1, 2017: IUCrJ
Trevor J Krabbenhoft, Thomas F Turner
Comparative transcriptomics can now be conducted on organisms in natural settings, which has greatly enhanced understanding of genome-environment interactions. Here, we demonstrate the utility and potential pitfalls of comparative transcriptomics of wild organisms, with an example from three cyprinid fish species (Teleostei:Cypriniformes). We present extensively filtered and annotated transcriptome assemblies that provide a valuable resource for studies of genome evolution (e.g. polyploidy), ecological and morphological diversification, speciation, and shared and unique responses to environmental variation in cyprinid fishes...
September 6, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
Lisa B VanWagner, Matthew E Harinstein, James R Runo, Christopher Darling, Marina Serper, Shelley Hall, Jon A Kobashigawa, Laura L Hammel
Liver transplant (LT) candidates today are older, have greater medical severity of illness, and have more cardiovascular comorbidities than ever before. In addition, there are specific cardiovascular responses in cirrhosis that can be detrimental to the LT candidate. Cirrhotic cardiomyopathy, a condition characterized by increased cardiac output and a reduced ventricular response to stress, is present in up to 30% of patients with cirrhosis thus challenging perioperative management. Current noninvasive tests that assess for subclinical coronary and myocardial disease have low sensitivity, and altered hemodynamics during the LT surgery can unmask latent cardiovascular disease either intraoperatively or in the immediate postoperative period...
October 6, 2017: American Journal of Transplantation
Peter T Green, Kyle E Harms
The emergent properties of the collection of species in a natural community, such as diversity and the distribution of relative abundances, are influenced by both niche-based and neutral (stochastic) processes. This pluralistic view of the natural world reconciles theory with empirical observations better than does either a strictly niche- or neutrality-based perspective. Even so, rules (or rules-of-thumb) that govern the relative contributions that niche-based and stochastic processes make as communities assemble remain only vaguely formulated and incompletely tested...
October 4, 2017: Ecology
E D Beaton, Marilyne Stuart, Sim Stroes-Gascoyne, Karen J King-Sharp, Ioana Gurban, Amy Festarini, Hui Q Chen
Proposed radioactive waste repositories require long residence times within deep geological settings for which we have little knowledge of local or regional subsurface dynamics that could affect the transport of hazardous species over the period of radioactive decay. Given the role of microbial processes on element speciation and transport, knowledge and understanding of local microbial ecology within geological formations being considered as host formations can aid predictions for long term safety. In this relatively unexplored environment, sampling opportunities are few and opportunistic...
2017: Frontiers in Microbiology
Adam R Burns, Elizabeth Miller, Meghna Agarwal, Annah S Rolig, Kathryn Milligan-Myhre, Steve Seredick, Karen Guillemin, Brendan J M Bohannan
The diverse collections of microorganisms associated with humans and other animals, collectively referred to as their "microbiome," are critical for host health, but the mechanisms that govern their assembly are poorly understood. This has made it difficult to identify consistent host factors that explain variation in microbiomes across hosts, despite large-scale sampling efforts. While ecological theory predicts that the movement, or dispersal, of individuals can have profound and predictable consequences on community assembly, its role in the assembly of animal-associated microbiomes remains underexplored...
October 2, 2017: Proceedings of the National Academy of Sciences of the United States of America
Edmo Montes Rodrigues, Daniel Kumazawa Morais, Victor Satler Pylro, Marc Redmile-Gordon, Juraci Alves de Oliveira, Luiz Fernando Wurdig Roesch, Dionéia Evangelista Cesar, Marcos Rogério Tótola
The microbial diversity and functioning around oceanic islands is poorly described, despite its importance for ecosystem homeostasis. Here, we aimed to verify the occurrence of microbe-driven phenanthrene co-oxidation in the seawater surrounding the Trindade Island (Brazil). We also used Next-Generation Sequencing to evaluate the effects of aliphatic and polycyclic aromatic hydrocarbons (PAHs) on these microbial community assemblies. Microcosms containing seawater from the island enriched with either labelled (9-(14)C) or non-labelled phenanthrene together with hexadecane, weathered oil, fluoranthene or pyrene, and combinations of these compounds were incubated...
October 3, 2017: Microbial Ecology
Chen Xiao, Zhen-Ming Lu, Xiao-Juan Zhang, Song-Tao Wang, Ling Ao, Cai-Hong Shen, Jin-Song Shi, Zheng-Hong Xu
Daqu is a saccharifying and fermentative agent commonly used in the traditional solid-state fermentation industry (e.g., Baijiu and vinegar). The pattern of microbial community succession and flavor formation were highly similar among batches, yet the mechanisms promoting temporal succession in the Daqu microbial ecology remain unclear. Here, we firstly correlated temporal profiles of microbial community succession with environmental variables (temperature, moisture, and titratable acidity) in medium temperature-Daqu (MT-Daqu) through fermentation...
September 29, 2017: Applied and Environmental Microbiology
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