keyword
MENU ▼
Read by QxMD icon Read
search

Community assembly

keyword
https://www.readbyqxmd.com/read/28108759/from-microhabitat-of-floral-nectar-up-to-biogeographic-scale-novel-insights-on-neutral-and-niche-bacterial-assemblies
#1
Yana Aizenberg-Gershtein, Ido Izhaki, Malka Halpern
Microbial model systems are very useful in addressing macro-ecological questions. Two major theories exist to date, to explain the community structure of organisms: (1) the dispersal (neutral) assembly theory which predicts that community similarity decreases with increasing geographic distance, independent of any environmental variables, and (2) the niche assembly theory which predicts that the communities' compositions are more homogeneous among sites characterized by similar environmental conditions. Our study system offered a unique opportunity to investigate the relative role of environmental conditions and spatial factors in shaping community composition...
January 20, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28108758/composition-of-gut-microbiota-in-the-gibel-carp-carassius-auratus-gibelio-varies-with-host-development
#2
Xinghao Li, Li Zhou, Yuhe Yu, Jiajia Ni, Wenjie Xu, Qingyun Yan
To understand how a bacteria-free fish gut ecosystem develops microbiota as the fish ages, we performed a 1-year study on the gut microbiota of hatchling gibel carp (Carassius auratus gibelio). Our results indicate that the gut microbial diversity increases significantly as the fish develop. The gut microbial community composition showed significant shifts corresponding to host age and appeared to shift at two time points despite consistent diet and environmental conditions, suggesting that some features of the gut microbial community may be determined by the host's development...
January 20, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28107542/temporal-segregation-between-dung-inhabiting-beetle-and-fly-species
#3
Frantisek Xaver Jiri Sladecek, Simon Tristram Segar, Colin Lee, Richard Wall, Martin Konvicka
The coexistence of ecologically similar species (i.e. species utilizing the same resource) is a major topic in ecology. Communities are assembled either through the biotic interactions of ecologically similar species, e.g. competition, or by the abiotic separation of species along gradients of environmental conditions. Here, we investigated the temporal segregation, succession and seasonality of dung-inhabiting Coleoptera and Diptera that utilize an identical resource in exactly the same way. The data were collected from two temperate pastures, one in the United Kingdom and the second in the Czech Republic...
2017: PloS One
https://www.readbyqxmd.com/read/28107476/origin-and-dispersal-history-of-two-colonial-ascidian-clades-in-the-botryllus-schlosseri-species-complex
#4
Marie L Nydam, Kirsten B Giesbrecht, Emily E Stephenson
Human-induced global warming and species introductions are rapidly altering the composition and functioning of Earth's marine ecosystems. Ascidians (Phylum Chordata, Subphylum Tunicata, Class Ascidiacea) are likely to play an increasingly greater role in marine communities. The colonial ascidian B. schlosseri is a cryptic species complex comprising five genetically divergent clades (A-E). Clade A is a global species, and Clade E has so far been identified in European waters only. Using the largest mitochondrial cytochrome oxidase I datasets yet assembled, we determine the origin and dispersal history of these species...
2017: PloS One
https://www.readbyqxmd.com/read/28101635/trait-assembly-in-grasslands-depends-on-habitat-history-and-spatial-scale
#5
Liina Saar, Francesco de Bello, Meelis Pärtel, Aveliina Helm
During the past century, grasslands in Europe have undergone marked changes in land-use, leading to a decline in plant diversity both at local and regional scales, thus possibly also affecting the mechanisms of species sorting into local communities. We studied plant species assembly in grasslands with differing habitat history and hypothesised that trait divergence prevails in historical grasslands due to niche differentiation and trait convergence prevails in more dynamic grasslands due to competitive exclusion and dispersal limitation...
January 19, 2017: Oecologia
https://www.readbyqxmd.com/read/28100647/marpodb-an-open-registry-for-marchantia-polymorpha-genetic-parts
#6
Mihails Delmans, Bernardo Pollak, Jim Haseloff
Marchantia polymorpha is an extant relative of the earliest terrestrial plants and has attracted a substantial interest as a model organism for evolutionary and developmental studies. Given its relatively simple genome, compact gene families, simple morphology, ease of propagation and transformation, M. polymorpha is becoming a promising platform for plant synthetic biology. Modular genetic parts have been essential for development of synthetic biology approaches, so we sought to design an engineering oriented database for M...
January 18, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28100302/fecal-virome-of-healthy-chickens-reveals-a-large-diversity-of-the-eukaryote-viral-community-including-novel-circular-single-stranded-dna-viruses
#7
Diane Lima, Samuel Paulo Cibulski, Fabrine Finkler, Thais Teixeira, Ana Paula Varela, Cristine Cerva, Márcia Loiko, Camila Scheffer, Helton Dos Santos, Fabiana Mayer, Paulo Roehe
This study is focused on the identification of the fecal virome of healthy chickens raised in high-density, export-driven poultry farms in Brazil. Following high-throughput sequencing, a total of 7,743 de novo-assembled contigs were constructed and compared with known nucleotide/amino acid sequences from the GenBank database. Analyses with BLASTx revealed that 279 contigs (4%) were related to sequences of eukaryotic viruses. Viral genome sequences (total or partial) indicative of members of recognized viral families, including Adenoviridae, Caliciviridae, Circoviridae, Parvoviridae, Picobirnaviridae, Picornaviridae and Reoviridae, were identified, some of those representing novel genotypes...
January 18, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28100029/isolation-with-asymmetric-gene-flow-during-the-nonsynchronous-divergence-of-dry-forest-birds
#8
Jessica A Oswald, Isaac Overcast, William M Mauck, Michael J Andersen, Brian Tilston Smith
Dry forest bird communities in South America are often fragmented by intervening mountains and rainforests, generating high local endemism. The historical assembly of communities often results from dynamic processes linked to numerous population histories among co-distributed species. Nevertheless, species may diversify in the same way through time if landscape and environmental features, or species ecologies, similarly structure populations. Here we tested whether six co-distributed taxon pairs that occur in the dry forests of the Tumbes and Marañón Valley of northwestern South America show concordant patterns and modes of diversification...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28099772/exploring-the-symbiont-diversity-of-ancient-western-redcedars-arbuscular-mycorrhizal-fungi-of-long-lived-hosts
#9
Monika A Gorzelak, Brian J Pickles, Miranda M Hart
Arbuscular mycorrhizal fungi (AMF) are globally distributed, monophyletic root symbionts with ancient origins. Their contribution to carbon cycling and nutrient dynamics is ecologically important, given their obligate association with over 70% of vascular plant species. Current understanding of AMF species richness and community structure is based primarily on studies of grasses, herbs, and agricultural crops, typically in disturbed environments. Few studies have considered AMF interactions with long-lived woody perennial species in undisturbed ecosystems...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28099457/comparing-and-evaluating-metagenome-assembly-tools-from-a-microbiologist-s-perspective-not-only-size-matters
#10
John Vollmers, Sandra Wiegand, Anne-Kristin Kaster
With the constant improvement in cost-efficiency and quality of Next Generation Sequencing technologies, shotgun-sequencing approaches -such as metagenomics- have nowadays become the methods of choice for studying and classifying microorganisms from various habitats. The production of data has dramatically increased over the past years and processing and analysis steps are becoming more and more of a bottleneck. Limiting factors are partly the availability of computational resources, but mainly the bioinformatics expertise in establishing and applying appropriate processing and analysis pipelines...
2017: PloS One
https://www.readbyqxmd.com/read/28097404/complete-mitochondrial-genome-of-the-endophytic-fungus-pestalotiopsis-fici-features-and-evolution
#11
Shu Zhang, Xiu-Na Wang, Xiao-Ling Zhang, Xing-Zhong Liu, Yong-Jie Zhang
Endophytic fungi (EF) live within plants and have profound impacts on plant communities. They are astonishingly diverse but poorly studied at the genome level. Herein, we assembled the mitochondrial genome (mitogenome) of the EF Pestalotiopsis fici, annotated and compared it with those of other relatives to better understand the evolution of the EF lineage. Except for standard fungal mitochondrial genes, the 69,529-bp circular mitogenome of P. fici harbors 18 introns acquired possibly through lateral transfer from other fungi and nine free-standing open reading frames with some scarcely seen in fungal mitogenomes...
January 17, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28097076/a-critical-issue-in-model-based-inference-for-studying-trait-based-community-assembly-and-a-solution
#12
Cajo J F Ter Braak, Pedro Peres-Neto, Stéphane Dray
Statistical testing of trait-environment association from data is a challenge as there is no common unit of observation: the trait is observed on species, the environment on sites and the mediating abundance on species-site combinations. A number of correlation-based methods, such as the community weighted trait means method (CWM), the fourth-corner correlation method and the multivariate method RLQ, have been proposed to estimate such trait-environment associations. In these methods, valid statistical testing proceeds by performing two separate resampling tests, one site-based and the other species-based and by assessing significance by the largest of the two p-values (the pmax test)...
2017: PeerJ
https://www.readbyqxmd.com/read/28097055/comprehensive-transcriptome-analysis-provides-new-insights-into-nutritional-strategies-and-phylogenetic-relationships-of-chrysophytes
#13
Daniela Beisser, Nadine Graupner, Christina Bock, Sabina Wodniok, Lars Grossmann, Matthijs Vos, Bernd Sures, Sven Rahmann, Jens Boenigk
BACKGROUND: Chrysophytes are protist model species in ecology and ecophysiology and important grazers of bacteria-sized microorganisms and primary producers. However, they have not yet been investigated in detail at the molecular level, and no genomic and only little transcriptomic information is available. Chrysophytes exhibit different trophic modes: while phototrophic chrysophytes perform only photosynthesis, mixotrophs can gain carbon from bacterial food as well as from photosynthesis, and heterotrophs solely feed on bacteria-sized microorganisms...
2017: PeerJ
https://www.readbyqxmd.com/read/28095190/-but-oh-what-tales-portraying-the-middle-east-in-u-s-homophile-periodicals-of-the-1950s-and-1960s
#14
Marva Milo
This essay examines Middle East representation in U.S. homophile periodicals from 1953 to 1964. The essay uses more than 120 Middle East related items that were published in ONE, Mattachine Review, and The Ladder to address the periodicals' engagement with the region (particularly ancient history and biblical themes) and discuss the types of sexual "knowledge" that the homophile periodicals created about the region. It then assesses the role of periodicals as a genre in the creation of a transnational homophile community, showing both their potential for democratizing participation in this community and their limits...
January 17, 2017: Journal of Homosexuality
https://www.readbyqxmd.com/read/28094795/impacts-of-chemical-gradients-on-microbial-community-structure
#15
Jianwei Chen, Anna Hanke, Halina E Tegetmeyer, Ines Kattelmann, Ritin Sharma, Emmo Hamann, Theresa Hargesheimer, Beate Kraft, Sabine Lenk, Jeanine S Geelhoed, Robert L Hettich, Marc Strous
Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the 'redox tower'. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat...
January 17, 2017: ISME Journal
https://www.readbyqxmd.com/read/28092966/avian-influenza-prevalence-among-hunter-harvested-birds-in-a-remote-canadian-first-nation-community
#16
Eric N Liberda, Richard Meldrum, Nadia A Charania, Robert Davey, Leonard Js Tsuji
INTRODUCTION: Avian influenza virus (AIV) prevalence has been associated with wild game and other bird species. The contamination of these birds may pose a greater risk to those who regularly hunt and consumed infected species. Due to resident concerns communicated by local Band Council, hunter-harvested birds from a remote First Nation community in subArctic Ontario, Canada were assessed for AIV. Hunters, and especially those who live a subsistence lifestyle, are at higher risk of AIV exposure due to their increased contact with wild birds, which represent an important part of their diet...
January 2017: Rural and Remote Health
https://www.readbyqxmd.com/read/28092680/utilizing-somatic-mutation-data-from-numerous-studies-for-cancer-research-proof-of-concept-and-applications
#17
D Amar, S Izraeli, R Shamir
Large cancer projects measure somatic mutations in thousands of samples, gradually assembling a catalog of recurring mutations in cancer. Many methods analyze these data jointly with auxiliary information with the aim of identifying subtype-specific results. Here, we show that somatic gene mutations alone can reliably and specifically predict cancer subtypes. Interpretation of the classifiers provides useful insights for several biomedical applications. We analyze the COSMIC database, which collects somatic mutations from The Cancer Genome Atlas (TCGA) as well as from many smaller scale studies...
January 16, 2017: Oncogene
https://www.readbyqxmd.com/read/28090692/a-high-resolution-reference-genetic-map-positioning-8-8k-genes-for-the-conifer-white-spruce-structural-genomics-implications-and-correspondence-with-physical-distance
#18
Nathalie Pavy, Manuel Lamothe, Betty Pelgas, France Gagnon, Inanç Birol, Joerg Bohlmann, John Mackay, Nathalie Isabel, Jean Bousquet
Over the last decade, extensive genetic and genomic resources have been developed for the conifer white spruce (Picea glauca, Pinaceae), which has one of the largest plant genomes (20 Gbp). Draft genome sequences of white spruce and other conifers have recently been produced, but dense genetic maps are needed to comprehend genome macrostructure, delineate regions involved in quantitative traits, complement functional genomic investigations, and assist the assembly of fragmented genomic sequences. A greatly expanded P...
January 15, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28087661/disturbance-by-an-endemic-rodent-in-an-arid-shrubland-is-a-habitat-filter-effects-on-plant-invasion-and-taxonomical-functional-and-phylogenetic-community-structure
#19
Víctor M Escobedo, Rodrigo S Rios, Cristian Salgado-Luarte, Gisela C Stotz, Ernesto Gianoli
BACKGROUND AND AIMS: Disturbance often drives plant invasion and may modify community assembly. However, little is known about how these modifications of community patterns occur in terms of taxonomic, functional and phylogenetic structure. This study evaluated in an arid shrubland the influence of disturbance by an endemic rodent on community functional divergence and phylogenetic structure as well as on plant invasion. It was expected that disturbance would operate as a habitat filter favouring exotic species with short life cycles...
January 12, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28070812/plant-species-diversity-reduces-n2o-but-not-ch4-emissions-from-constructed-wetlands-under-high-nitrogen-levels
#20
Wenjuan Han, Mengmeng Shi, Jie Chang, Yuan Ren, Ronghua Xu, Chongbang Zhang, Ying Ge
Constructed wetlands (CWs) have been widely used for treating wastewater. CWs also are the sources of greenhouse gas (GHG) due to high pollutant load. It has been reported that plant species diversity can enhance nitrogen (N) removal efficiency in CWs for treating wastewater. However, the influence of plant species diversity on GHG emissions from CWs in habitats with high N levels still lack research. This study established four species richness levels (1, 2, 3, 4) and 15 species compositions by using 75 simulated vertical flow CWs microcosms to investigate the effects of plant species diversity on the GHG emissions and N removal efficiency of CWs with a high N level...
January 9, 2017: Environmental Science and Pollution Research International
keyword
keyword
22603
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"