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Community assembly

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https://www.readbyqxmd.com/read/28440800/the-trichodesmium-consortium-conserved-heterotrophic-co-occurrence-and-genomic-signatures-of-potential-interactions
#1
Michael D Lee, Nathan G Walworth, Erin L McParland, Fei-Xue Fu, Tracy J Mincer, Naomi M Levine, David A Hutchins, Eric A Webb
The nitrogen (N)-fixing cyanobacterium Trichodesmium is globally distributed in warm, oligotrophic oceans, where it contributes a substantial proportion of new N and fuels primary production. These photoautotrophs form macroscopic colonies that serve as relatively nutrient-rich substrates that are colonized by many other organisms. The nature of these associations may modulate ocean N and carbon (C) cycling, and can offer insights into marine co-evolutionary mechanisms. Here we integrate multiple omics-based and experimental approaches to investigate Trichodesmium-associated bacterial consortia in both laboratory cultures and natural environmental samples...
April 25, 2017: ISME Journal
https://www.readbyqxmd.com/read/28439034/teleosts-as-model-organisms-to-understand-host-microbe-interactions
#2
Emily A Lescak, Kathryn C Milligan-Myhre
Host-microbe interactions are influenced by complex host genetics and environment. Studies across animal taxa have aided our understanding of how intestinal microbiota influence vertebrate development, disease, and physiology. However, traditional mammalian studies can be limited by use of isogenic strains, husbandry constraints that result in small sample sizes and limited statistical power, reliance on indirect characterization of gut microbial communities from fecal samples, and concerns whether observations in artificial conditions are actually reflective of what occurs in the wild...
April 24, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28438921/null-expectations-for-disease-dynamics-in-shrinking-habitat-dilution-or-amplification
#3
Christina L Faust, Andrew P Dobson, Nicole Gottdenker, Laura S P Bloomfield, Hamish I McCallum, Thomas R Gillespie, Maria Diuk-Wasser, Raina K Plowright
As biodiversity declines with anthropogenic land-use change, it is increasingly important to understand how changing biodiversity affects infectious disease risk. The dilution effect hypothesis, which points to decreases in biodiversity as critical to an increase in infection risk, has received considerable attention due to the allure of a win-win scenario for conservation and human well-being. Yet some empirical data suggest that the dilution effect is not a generalizable phenomenon. We explore the response of pathogen transmission dynamics to changes in biodiversity that are driven by habitat loss using an allometrically scaled multi-host model...
June 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28438910/lyme-disease-ecology-in-a-changing-world-consensus-uncertainty-and-critical-gaps-for-improving-control
#4
REVIEW
A Marm Kilpatrick, Andrew D M Dobson, Taal Levi, Daniel J Salkeld, Andrea Swei, Howard S Ginsberg, Anne Kjemtrup, Kerry A Padgett, Per M Jensen, Durland Fish, Nick H Ogden, Maria A Diuk-Wasser
Lyme disease is the most common tick-borne disease in temperate regions of North America, Europe and Asia, and the number of reported cases has increased in many regions as landscapes have been altered. Although there has been extensive work on the ecology and epidemiology of this disease in both Europe and North America, substantial uncertainty exists about fundamental aspects that determine spatial and temporal variation in both disease risk and human incidence, which hamper effective and efficient prevention and control...
June 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28437589/the-roles-of-ecology-behavior-and-effective-population-size-in-the-evolution-of-a-community
#5
Chih-Ming Hung, Sergei V Drovetski, Robert M Zink
Organismal traits such as ecological specialization and migratory behavior may affect colonization potential, population persistence, and degree of isolation, factors that determine the composition and genetic structure of communities. However, studies focusing on community assembly rarely consider these factors jointly. We sequenced 16 nuclear and one mitochondrial genes from Caucasian and European populations of 30 forest-dwelling avian species that represent diverse ecological (specialist-generalist) and behavioral (migratory-resident) backgrounds...
April 24, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28437572/nearly-a-decade-long-repeatable-seasonal-diversity-patterns-of-bacterioplankton-communities-in-the-eutrophic-lake-donghu-wuhan-china
#6
Qingyun Yan, James C Stegen, Yuhe Yu, Ye Deng, Xinghao Li, Shu Wu, LilI Dai, Xiang Zhang, Jinjin Li, Chun Wang, Jiajia Ni, Xuemei Li, Hongjuan Hu, Fanshu Xiao, Weisong Feng, Daliang Ning, Zhili H E, Joy D Van Nostrand, Liyou Wu, Jizhong Zhou
Uncovering which environmental factors govern community diversity patterns and how ecological processes drive community turnover are key questions related to understand the community assembly. However, the ecological mechanisms regulating long-term variations of bacterioplankton communities in lake ecosystems remains poorly understood. Here we present nearly a decade-long study of bacterioplankton communities from the eutrophic Lake Donghu (Wuhan, China) using 16S rRNA gene amplicon sequencing with MiSeq platform...
April 24, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28434188/drivers-of-community-assembly-in-tropical-forest-restoration-sites-role-of-local-environment-landscape-and-space
#7
Lívia D Audino, Stephen J Murphy, Ludimila Zambaldi, Julio Louzada, Liza S Comita
There is increasing recognition that community assembly theory can offer valuable insights for ecological restoration. We studied community assembly processes following tropical forest restoration efforts, using dung beetles (Scarabaeidae) as a focal taxon to investigate taxonomic and functional patterns of biodiversity recovery. We evaluated the relative importance of the local environment (i.e., canopy cover, understory cover, tree basal area, and soil texture), landscape context (i.e., habitat patch proximity and availability and percentage of surrounding area classified as natural forest or Eucalyptus spp...
April 23, 2017: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/28431521/a-reference-floral-transcriptome-of-sexual-and-apomictic-paspalum-notatum
#8
Juan Pablo A Ortiz, Santiago Revale, Lorena A Siena, Maricel Podio, Luciana Delgado, Juliana Stein, Olivier Leblanc, Silvina C Pessino
BACKGROUND: Paspalum notatum Flügge is a subtropical grass native to South America, which includes sexual diploid and apomictic polyploid biotypes. In the past decade, a number of apomixis-associated genes were discovered in this species through genetic mapping and differential expression surveys. However, the scarce information on Paspalum sequences available in public databanks limited annotations and functional predictions for these candidates. RESULTS: We used a long-read 454/Roche FLX+ sequencing strategy to produce robust reference transcriptome datasets from florets of sexual and apomictic Paspalum notatum genotypes and delivered a list of transcripts showing differential representation in both reproductive types...
April 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28431252/engineered-regulatory-systems-modulate-gene-expression-of-human-commensals-in-the-gut
#9
Bentley Lim, Michael Zimmermann, Natasha A Barry, Andrew L Goodman
The gut microbiota is implicated in numerous aspects of health and disease, but dissecting these connections is challenging because genetic tools for gut anaerobes are limited. Inducible promoters are particularly valuable tools because these platforms allow real-time analysis of the contribution of microbiome gene products to community assembly, host physiology, and disease. We developed a panel of tunable expression platforms for the prominent genus Bacteroides in which gene expression is controlled by a synthetic inducer...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28430893/congeneric-predaceous-diving-beetle-species-fail-to-segregate-in-a-floodplain-system-a-case-of-amplified-sympatry
#10
Courtney Holt McDaniel, Joseph V McHugh, Darold P Batzer
Coexistence of closely related species has long been a focus of biologists in their efforts to explain mechanisms that drive community assembly. Dytiscidae (predaceous diving beetles) are a group that shows a particularly high affinity for sympatry despite their relatedness. Our objective was to investigate the degree of overlap among Neoporus (Guignot) species (Coleoptera: Dytiscidae) in floodplains of the southeastern United States. We sampled two floodplain habitats (permanent oxbow lakes and temporarily flooded pools) of the Altamaha River (Georgia, USA) for Neoporus species over three years...
April 18, 2017: Environmental Entomology
https://www.readbyqxmd.com/read/28428978/20th-workshop-of-the-international-stroke-genetics-consortium-november-3-4-2016-milan-italy-2016-036-isgc-research-priorities
#11
Daniel Woo, Stephanie Debette, Christopher Anderson
OBJECTIVE: To develop a research priority list for the International Stroke Genetics Consortium (ISGC). BACKGROUND: Previously, stroke progress review groups and other activities provided an opportunity for members within the field to develop priorities for research. These filtered into larger categories which then published the top research priorities of their given field. However, these review groups are no longer forming and thus there has been no clear direction on what the research priorities and needs for stroke genetics research...
March 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28428841/reproductive-traits-associated-with-species-turnover-of-amphibians-in-amazonia-and-its-andean-slopes
#12
Octavio Jiménez-Robles, Juan M Guayasamin, Santiago R Ron, Ignacio De la Riva
Assembly of ecological communities is important for the conservation of ecosystems, predicting perturbation impacts, and understanding the origin and loss of biodiversity. We tested how amphibian communities are assembled by neutral and niche-based mechanisms, such as habitat filtering. Species richness, β-diversities, and reproductive traits of amphibians were evaluated at local scale in seven habitats at different elevation and disturbance levels in Wisui Biological Station, Morona-Santiago, Ecuador, on the foothills of the Cordillera del Kutukú; and at regional scale using 109 localities across evergreen forests of Amazonia and its Andean slopes (0-3,900 m a...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28424672/isolation-and-identification-of-the-indigenous-yeast-population-during-spontaneous-fermentation-of-isabella-vitis-labrusca-l-grape-must
#13
María L Raymond Eder, Cristina Reynoso, Santiago C Lauret, Alberto L Rosa
Grape must harbors a complex community of yeast species responsible for spontaneous alcoholic fermentation. Although there are detailed studies on the microbiota of Vitis vinifera L. grapes, less is known about the diversity and behavior of yeast communities present on fermenting grape must from other species of Vitis. In this work, we used a culture-dependent method to study the identity and dynamics of the indigenous yeast population present during the spontaneous fermentation of Isabella (Vitis labrusca L...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28423948/fermentation-at-non-conventional-conditions-in-food-and-bio-sciences-by-the-application-of-advanced-processing-technologies
#14
Maria J Mota, Rita P Lopes, Mohamed Koubaa, Shahin Roohinejad, Francisco J Barba, Ivonne Delgadillo, Jorge A Saraiva
The interest in improving the yield and productivity values of relevant microbial fermentations is an increasingly important issue for the scientific community. Therefore, several strategies have been tested for the stimulation of microbial growth and manipulation of their metabolic behavior. One promising approach involves the performance of fermentative processes during non-conventional conditions, which includes high pressure (HP), electric fields (EF) and ultrasound (US). These advanced technologies are usually applied for microbial inactivation in the context of food processing...
April 20, 2017: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/28419169/decomposing-functional-trait-associations-in-a-chinese-subtropical-forest
#15
Xuefei Li, Kequan Pei, Marc Kéry, Pascal A Niklaus, Bernhard Schmid
Functional traits, properties of organisms correlated with ecological performance, play a central role in plant community assembly and functioning. To some extents, functional traits vary in concert, reflecting fundamental ecological strategies. While "trait syndromes" characteristic of e.g. fast-growing, early-successional vs. competitive, late-successional species are recognized in principle, less is known about the environmental and genetic factors at the source of trait variation and covariation within plant communities...
2017: PloS One
https://www.readbyqxmd.com/read/28415075/hopbase-a-unified-resource-for-humulus-genomics
#16
Steven T Hill, Ramcharan Sudarsanam, John Henning, David Hendrix
Hop (Humulus lupulus L. var lupulus) is a dioecious plant of worldwide significance, used primarily for bittering and flavoring in brewing beer. Studies on the medicinal properties of several unique compounds produced by hop have led to additional interest from pharmacy and healthcare industries as well as livestock production as a natural antibiotic. Genomic research in hop has resulted a published draft genome and transcriptome assemblies. As research into the genomics of hop has gained interest, there is a critical need for centralized online genomic resources...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28411219/global-scale-structure-of-the-eelgrass-microbiome
#17
Ashkaan K Fahimipour, Melissa R Kardish, Jenna M Lang, Jessica L Green, Jonathan A Eisen, John J Stachowicz
Plant-associated microorganisms are essential for their hosts' survival and performance. Yet, most plant microbiome studies to date have focused on terrestrial species sampled across relatively small spatial scales. Here we report results of a global-scale analysis of microbial communities associated with leaf and root surfaces of the marine eelgrass Zostera marina throughout its range in the Northern Hemisphere. By contrasting host microbiomes with those of surrounding seawater and sediment, we uncovered the structure, composition and variability of microbial communities associated with eelgrass...
April 14, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28410385/structural-power-and-the-evolution-of-collective-fairness-in-social-networks
#18
Fernando P Santos, Jorge M Pacheco, Ana Paiva, Francisco C Santos
From work contracts and group buying platforms to political coalitions and international climate and economical summits, often individuals assemble in groups that must collectively reach decisions that may favor each part unequally. Here we quantify to which extent our network ties promote the evolution of collective fairness in group interactions, modeled by means of Multiplayer Ultimatum Games (MUG). We show that a single topological feature of social networks-which we call structural power-has a profound impact on the tendency of individuals to take decisions that favor each part equally...
2017: PloS One
https://www.readbyqxmd.com/read/28407798/utilization-of-defined-microbial-communities-enables-effective-evaluation-of-meta-genomic-assemblies
#19
William W Greenwald, Niels Klitgord, Victor Seguritan, Shibu Yooseph, J Craig Venter, Chad Garner, Karen E Nelson, Weizhong Li
BACKGROUND: Metagenomics is the study of the microbial genomes isolated from communities found on our bodies or in our environment. By correctly determining the relation between human health and the human associated microbial communities, novel mechanisms of health and disease can be found, thus enabling the development of novel diagnostics and therapeutics. Due to the diversity of the microbial communities, strategies developed for aligning human genomes cannot be utilized, and genomes of the microbial species in the community must be assembled de novo...
April 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28407248/evolutionary-priority-effects-persist-in-anthropogenically-created-habitats-but-not-through-nonnative-plant-invasion
#20
Angela J Brandt, William G Lee, Andrew J Tanentzap, Ella Hayman, Tadashi Fukami, Barbara J Anderson
Evolutionary priority effects, where early-arriving lineages occupy niche space via diversification and preclude dominance of later arrivals, have been observed in alpine and forest communities. However, the potential for evolutionary priority effects to persist in an era of rapid global change remains unclear. Here, we use a natural experiment of historical disturbance in New Zealand to test whether anthropogenic changes in available habitat and nonnative invasion eliminate the role of evolutionary priority effects in community assembly...
April 13, 2017: New Phytologist
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