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Community assembly

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https://www.readbyqxmd.com/read/29452289/polypharmacy-in-people-with-dementia-associations-with-adverse-health-outcomes
#1
Christoph Mueller, Mariam Molokhia, Gayan Perera, Nicola Veronese, Brendon Stubbs, Hitesh Shetty, David Codling, Jonathan Huntley, Robert Stewart
Polypharmacy has been linked to higher risks of hospitalisation and death in community samples. It is commonly present in people with dementia but these risks have rarely been studied in this population. We aimed investigate associations between polypharmacy and emergency department attendance, any and unplanned hospitalisation, and mortality in patients with dementia. Using a large mental health care database in South London, linked to hospitalisation and mortality data, we assembled a retrospective cohort of patients diagnosed with dementia...
February 13, 2018: Experimental Gerontology
https://www.readbyqxmd.com/read/29450746/impact-of-habitat-heterogeneity-on-zooplankton-assembly-in-a-temperate-river-floodplain-system
#2
Anita Galir Balkić, Ivančica Ternjej, Irella Bogut
Dissimilar life features of Rotifera, Cladocera and Copepoda enable these organisms to respond differently to changes in the hydrological regime which influence alterations in environmental characteristics. We investigated the effect of habitat heterogeneity (e.g. eupotamal, parapotamal, palaeopotamal) on individual zooplankton group assemblages and biodiversity indices (α, β and γ diversity) during hydro regime change in floodplain waterbodies. Dissolved oxygen and organic nitrogen concentrations changed significantly among hydrological states while water depth was affected by both site and hydro regime replacement...
February 15, 2018: Environmental Monitoring and Assessment
https://www.readbyqxmd.com/read/29447212/predicting-species-emergence-in-simulated-complex-pre-biotic-networks
#3
Omer Markovitch, Natalio Krasnogor
An intriguing question in evolution is what would happen if one could "replay" life's tape. Here, we explore the following hypothesis: when replaying the tape, the details ("decorations") of the outcomes would vary but certain "invariants" might emerge across different life-tapes sharing similar initial conditions. We use large-scale simulations of an in silico model of pre-biotic evolution called GARD (Graded Autocatalysis Replication Domain) to test this hypothesis. GARD models the temporal evolution of molecular assemblies, governed by a rates matrix (i...
2018: PloS One
https://www.readbyqxmd.com/read/29445133/photoautotrophic-organisms-control-microbial-abundance-diversity-and-physiology-in-different-types-of-biological-soil-crusts
#4
Stefanie Maier, Alexandra Tamm, Dianming Wu, Jennifer Caesar, Martin Grube, Bettina Weber
Biological soil crusts (biocrusts) cover about 12% of the Earth's land masses, thereby providing ecosystem services and affecting biogeochemical fluxes on a global scale. They comprise photoautotrophic cyanobacteria, algae, lichens and mosses, which grow together with heterotrophic microorganisms, forming a model system to study facilitative interactions and assembly principles in natural communities. Biocrusts can be classified into cyanobacteria-, lichen-, and bryophyte-dominated types, which reflect stages of ecological succession...
February 14, 2018: ISME Journal
https://www.readbyqxmd.com/read/29445132/microbiome-assembly-of-avian-eggshells-and-their-potential-as-transgenerational-carriers-of-maternal-microbiota
#5
H Pieter J van Veelen, Joana Falcão Salles, B Irene Tieleman
The microbiome is essential for development, health and homeostasis throughout an animal's life. Yet, the origins and transmission processes governing animal microbiomes remain elusive for non-human vertebrates, oviparous vertebrates in particular. Eggs may function as transgenerational carriers of the maternal microbiome, warranting characterisation of egg microbiome assembly. Here, we investigated maternal and environmental contributions to avian eggshell microbiota in wild passerine birds: woodlark Lullula arborea and skylark Alauda arvensis...
February 14, 2018: ISME Journal
https://www.readbyqxmd.com/read/29443420/experimentally-altered-rainfall-regimes-and-host-root-traits-affect-grassland-arbuscular-mycorrhizal-fungal-communities
#6
Coline Deveautour, Suzanne Donn, Sally Power, Alison E Bennett, Jeff R Powell
Future climate scenarios predict changes in rainfall regimes. These changes are expected to affect plants via effects on the expression of root traits associated with water and nutrient uptake. Associated microorganisms may also respond to these new precipitation regimes, either directly in response to changes in the soil environment or indirectly in response to altered root trait expression. We characterised arbuscular mycorrhizal (AM) fungal communities in an Australian grassland exposed to experimentally altered rainfall regimes...
February 14, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29440487/generic-assembly-patterns-in-complex-ecological-communities
#7
Matthieu Barbier, Jean-François Arnoldi, Guy Bunin, Michel Loreau
The study of ecological communities often involves detailed simulations of complex networks. However, our empirical knowledge of these networks is typically incomplete and the space of simulation models and parameters is vast, leaving room for uncertainty in theoretical predictions. Here we show that a large fraction of this space of possibilities exhibits generic behaviors that are robust to modeling choices. We consider a wide array of model features, including interaction types and community structures, known to generate different dynamics for a few species...
February 13, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29436821/ph-sensitive-compounds-for-selective-inhibition-of-acid-producing-bacteria
#8
Yin Yang, Vytas Reipa, Guo Liu, Yuan Meng, Xiaohong Wang, Kenneth P Mineart, Vivek M Prabhu, Wenyuan Shi, Nancy J Lin, Xuesong He, Jirun Sun
Stimuli-responsive compounds that provide on-site, controlled antimicrobial activity promise an effective approach to prevent infections, reducing the need for systemic antibiotics. We present one novel pH-sensitive quaternary pyridinium salt (QPS) whose antibacterial activity is boosted by low pH and controlled by adjusting the pH between 4 and 8. Particularly, this compound selectively inhibits growth of acid-producing bacteria within a multispecies community. The successful antibacterial action of this QPS maintains the environmental pH above 5...
February 13, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29436230/a-metagenomic-taxonomy-guided-database-search-strategy-for-improving-metaproteomic-analysis
#9
Jinqiu Xiao, Alessandro Tanca, Ben Jia, Runqing Yang, Bo Wang, Yu Zhang, Jing Li
Metaproteomics provides a direct measure of the functional information by investigating all proteins expressed by a microbiota. However, due to the complexity and heterogeneity of microbial communities, it is very hard to construct a sequence database suitable for a metaproteomic study. Using a public database, researchers might not be able to identify proteins from poorly characterized microbial species, while a sequencing-based metagenomic database may not provide adequate coverage for all potentially expressed protein sequences...
February 13, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29435256/specific-plasmid-patterns-and-high-rates-of-bacterial-co-occurrence-within-the-coral-holobiont
#10
Deborah C A Leite, Joana F Salles, Emiliano N Calderon, Jan D van Elsas, Raquel S Peixoto
Despite the importance of coral microbiomes for holobiont persistence, the interactions among these are not well understood. In particular, knowledge of the co-occurrence and taxonomic importance of specific members of the microbial core, as well as patterns of specific mobile genetic elements (MGEs), is lacking. We used seawater and mucus samples collected from Mussismilia hispida colonies on two reefs located in Bahia, Brazil, to disentangle their associated bacterial communities, intertaxa correlations, and plasmid patterns...
February 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29435247/evolution-of-a-key-trait-greatly-affects-underground-community-assembly-process-through-habitat-adaptation-in-earthworms
#11
Hiroshi Ikeda, Kayoko Fukumori, Etsuko Shoda-Kagaya, Masamichi Takahashi, Masamichi T Ito, Yoshimi Sakai, Kazuma Matsumoto
Underground community assemblies have not been studied well compared with aboveground communities, despite their importance for our understanding of whole ecosystems. To investigate underground community assembly over evolutionary timescales, we examined terrestrial earthworm communities (Oligochaeta: Haplotaxida) in conserved mountainous primary forests in Japan as a model system. We collected 553 earthworms mostly from two dominant families, the Megascolecidae and the Lumbricidae, from 12 sites. We constructed a molecular taxonomic unit tree based on the analysis of three genes to examine the effects of a biogeographic factor (dispersal ability) and an evolutionary factor (habitat adaptation) on the earthworm community assembly process...
February 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29434300/partitioning-the-regional-and-local-drivers-of-phylogenetic-and-functional-diversity-along-temperate-elevational-gradients-on-an-east-asian-peninsula
#12
Jung-Hwa Chun, Chang-Bae Lee
Species-centric approaches to biodiversity in ecological research are limited in their ability to reflect the evolutionary history and functional diversity of community assembly. Recently, the introduction of alternative facets of biodiversity, such as phylogenetic and functional diversity, has shed light on this problem and improved our understanding of the processes underlying biodiversity patterns. Here, we investigated the phylogenetic and functional diversity patterns of α, β and γ components in woody plant assemblages along regional and local elevational gradients in South Korea...
February 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29430651/foraging-responses-of-sheep-to-plant-spatial-micro-patterns-can-cause-diverse-associational-effects-of-focal-plant-at-individual-and-population-levels
#13
Yue Huang, Ling Wang, Deli Wang, De-Hui Zeng, Yexing Li, Jun Liu, Yue Wang
1.Multiple-scale foraging decisions by large herbivores can cause associational effects of focal plant individuals neighbored with different species. Spatial micro-patterns between the focal plant and its neighboring species within patches can affect herbivore foraging selectivity at within- and between-patch scale, which may consequently lead to associational plant effects occurring at both plant individual and population levels. However, these associational effects have not been explored together in the plant-herbivore interaction studies...
February 11, 2018: Journal of Animal Ecology
https://www.readbyqxmd.com/read/29429621/rampant-host-switching-shaped-the-termite-gut-microbiome
#14
Thomas Bourguignon, Nathan Lo, Carsten Dietrich, Jan Šobotník, Sarah Sidek, Yves Roisin, Andreas Brune, Theodore A Evans
The gut microbiota of animals exert major effects on host biology [1]. Although horizontal transfer is generally considered the prevalent route for the acquisition of gut bacteria in mammals [2], some bacterial lineages have co-speciated with their hosts on timescales of several million years [3]. Termites harbor a complex gut microbiota, and their advanced social behavior provides the potential for long-term vertical symbiont transmission, and co-evolution of gut symbionts and host [4-6]. Despite clear evolutionary patterns in the gut microbiota of termites [7], a consensus on how microbial communities were assembled during termite diversification has yet to be reached...
February 2, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/29426141/biogeography-and-ecological-processes-affecting-root-associated-bacterial-communities-in-soybean-fields-across-china
#15
Baogang Zhang, Jun Zhang, Yao Liu, Yanqing Guo, Peng Shi, Gehong Wei
Root-associated bacteria have profound effects on plant health and productivity, but their biogeographic patterns across large spatial scales remain poorly understood. Here, we used high-throughput sequencing to compare the bacterial distributions in the bulk soil, rhizosphere, and endosphere across 51 soybean fields in China. Environmental variables were more important than spatial variables, and edaphic variables were more important than climatic variables, for governing bacterial community turnover in each soil-root compartment...
January 27, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29423753/granivory-from-native-rodents-and-competition-from-an-exotic-invader-strongly-and-equally-limit-the-establishment-of-native-grasses
#16
Jacob E Lucero, Ragan M Callaway
Seed predation and resource competition are fundamental biotic filters that affect the assembly of plant communities, yet empirical studies rarely assess their importance relative to one another. Here, we used rodent exclosures and experimental seed additions to compare how rodent granivory and resource competition affected the net establishment of an exotic invader (Bromus tectorum) and two native bunchgrasses (Pseudoroegneria spicata and Elymus elymoides) in the Great Basin Desert, USA. Rodent granivory limited the establishment of both native grasses, but had no significant effect on B...
February 8, 2018: Oecologia
https://www.readbyqxmd.com/read/29423344/ant-mosaics-in-bornean-primary-rain-forest-high-canopy-depend-on-spatial-scale-time-of-day-and-sampling-method
#17
Kalsum M Yusah, William A Foster, Glen Reynolds, Tom M Fayle
Background: Competitive interactions in biological communities can be thought of as giving rise to "assembly rules" that dictate the species that are able to co-exist. Ant communities in tropical canopies often display a particular pattern, an "ant mosaic", in which competition between dominant ant species results in a patchwork of mutually exclusive territories. Although ant mosaics have been well-documented in plantation landscapes, their presence in pristine tropical forests remained contentious until recently...
2018: PeerJ
https://www.readbyqxmd.com/read/29411533/habitat-filtering-of-bacterial-communities-above-polymetallic-nodule-fields-and-sediments-in-the-clarion-clipperton-zone-of-the-pacific-ocean
#18
Markus V Lindh, Brianne M Maillot, Craig R Smith, Matthew J Church
Deep-sea mining of commercially valuable polymetallic nodule fields will generate a seabed sediment plume into the water column. Yet, the response of bacterial communities, critical in regulating energy and matter fluxes in marine ecosystems, to such disturbances is unknown. Metacommunity theory, traditionally used in general ecology for macroorganisms, offers a mechanistic understanding on the relative role of spatial differences compared to local environmental conditions (habitat filtering) for community assembly...
February 6, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/29411448/host-associated-bacterial-community-succession-during-amphibian-development
#19
Tiffany L Prest, Abigail K Kimball, Jordan G Kueneman, Valerie J McKenzie
Amphibians undergo significant developmental changes during their life cycle, as they typically move from a primarily aquatic environment to a more terrestrial one. Amphibian skin is a mucosal tissue that assembles communities of symbiotic microbiota. However, it is currently not well understood as to where amphibians acquire their skin symbionts, and whether the sources of microbial symbionts change throughout development. In this study, we utilized data collected from four wild boreal toad populations (Anaxyrus boreas); specifically, we sampled the skin bacterial communities during toad development, including eggs, tadpoles, subadults, and adults as well as environmental sources of bacteria (water, aquatic sediment, and soil)...
February 7, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29410660/drivers-of-macrofungi-community-structure-differ-between-soil-and-rotten-wood-substrates-in-a-temperate-mountain-forest-in-china
#20
Yun Chen, Jens-Christian Svenning, Xueying Wang, Ruofan Cao, Zhiliang Yuan, Yongzhong Ye
The effects of environmental and dispersal processes on macrofungi community assembly remain unclear. Further, it is not well understood if community assembly differs for different functional guilds of macrofungi, e.g., soil and rotten-wood macrofungi. In this study, using 2433 macrofungi sporocarps belonging to 217 species located within a forest dynamics plot in temperate mountain forest (China), we examined the explanatory power of topography, spatial eigenvectors (representing unknown spatial processes, e...
2018: Frontiers in Microbiology
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