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Community assembly

Wei Xie, Haiwei Luo, Senthil K Murugapiran, Jeremy A Dodsworth, Songze Chen, Ying Sun, Brian P Hedlund, Peng Wang, Huaying Fang, Minghua Deng, Chuanlun Zhang
Marine group II archaea are widely distributed in global oceans and dominate the total archaeal community within the upper euphotic zone of temperate waters. However, factors controlling the distribution of MGII are poorly delineated and the physiology and ecological functions of these still-uncultured organisms remain elusive. In this study, we investigated the planktonic MGII associated with particles and in free-living forms in the Pearl River Estuary (PRE) over a 10-month period. We detected high abundance of particle-associated MGII in PRE (up to ∼108 16S rRNA gene copies/L), which was around 10-fold higher than the free-living MGII in the same region, and an order of magnitude higher than previously reported in other marine environments...
December 13, 2017: Environmental Microbiology
Chi Liu, Minjie Yao, James C Stegen, Junpeng Rui, Jiabao Li, Xiangzhen Li
How press disturbance (long-term) influences the phylogenetic turnover of soil microbial communities responding to pulse disturbances (short-term) is not fully known. Understanding the complex connections between the history of environmental conditions, assembly processes and microbial community dynamics is necessary to predict microbial response to perturbation. We started by investigating phylogenetic spatial turnover (based on DNA) of soil prokaryotic communities after long-term nitrogen (N) deposition and temporal turnover (based on RNA) of communities responding to pulse by conducting short-term rewetting experiments...
December 13, 2017: Scientific Reports
Kevin D Kohl, Denise M Dearing, Seth R Bordenstein
Host-associated microbial communities consist of stable and transient members that can assemble through purely stochastic processes associated with the environment or by interactions with the host. Phylosymbiosis predicts that if host-microbiota interactions impact assembly patterns, then one conceivable outcome is concordance between host evolutionary histories (phylogeny) and the ecological similarities in microbial community structures (microbiota dendrogram). This assembly pattern has been demonstrated in several clades of animal hosts in laboratory and natural populations, but in vertebrates it has only been investigated using samples from feces or the distal colon...
December 11, 2017: Molecular Ecology
He Zhao, Xuanzhen Li, Zhiming Zhang, Yong Zhao, Jiantao Yang, Yiwei Zhu
Arbuscular mycorrhizal fungi (AMF) play an essential role in complex ecosystems. However, the species diversity and composition of AMF communities remain unclear in semi-arid mountains. Further, it is not well understood if the characteristics of AMF community assemblies differ for different habitat types, e.g., agricultural arable land, artificial forest land, natural grassland, and bush/wood land. Here, using the high-throughput technology by Illumina sequencing on the MiSeq platform, we explored the species diversity and composition of soil AMF communities among different habitat types in a semi-arid mountain (Taihang Mountain, Mid-western region of China)...
2017: PeerJ
Yandong Xiao, Marco Tulio Angulo, Jonathan Friedman, Matthew K Waldor, Scott T Weiss, Yang-Yu Liu
Mapping the ecological networks of microbial communities is a necessary step toward understanding their assembly rules and predicting their temporal behavior. However, existing methods require assuming a particular population dynamics model, which is not known a priori. Moreover, those methods require fitting longitudinal abundance data, which are often not informative enough for reliable inference. To overcome these limitations, here we develop a new method based on steady-state abundance data. Our method can infer the network topology and inter-taxa interaction types without assuming any particular population dynamics model...
December 11, 2017: Nature Communications
Pacifica Sommers, John L Darcy, Eli M S Gendron, Lee F Stanish, Elizabeth A Bagshaw, Dorota L Porazinska, Steven K Schmidt
Ice-lidded cryoconite holes on glaciers in the Taylor Valley, Antarctica, provide a unique system of natural mesocosms for studying community structure and assembly. We used high-throughput DNA sequencing to characterize both microbial eukaryotic communities and bacterial communities within cryoconite holes across three glaciers to study similarities in their spatial patterns. We expected that the alpha (phylogenetic diversity) and beta (pairwise community dissimilarity) diversity patterns of eukaryotes in cryoconite holes would be related to those of bacteria, and that they would be related to the biogeochemical gradient within the Taylor Valley...
December 6, 2017: FEMS Microbiology Ecology
John Beaulaurier, Shijia Zhu, Gintaras Deikus, Ilaria Mogno, Xue-Song Zhang, Austin Davis-Richardson, Ronald Canepa, Eric W Triplett, Jeremiah J Faith, Robert Sebra, Eric E Schadt, Gang Fang
Shotgun metagenomics methods enable characterization of microbial communities in human microbiome and environmental samples. Assembly of metagenome sequences does not output whole genomes, so computational binning methods have been developed to cluster sequences into genome 'bins'. These methods exploit sequence composition, species abundance, or chromosome organization but cannot fully distinguish closely related species and strains. We present a binning method that incorporates bacterial DNA methylation signatures, which are detected using single-molecule real-time sequencing...
December 11, 2017: Nature Biotechnology
Felix Helmut Schacher, Johannes Brendel
The desire for increasing complexity while maintaining control over every aspect of the process itself - this might be used as a provocative description of the developments in block copolymer self-assembly in solution over the last decade. The community has witnessed tremendous progress, not only with regard to the design of building blocks, but also in terms of understanding assembly pathways, interfacial properties, or kinetic obstacles. In particular, the latter can be of interest (and actually turned into an advantage), if structures are targeted, which are not in thermodynamic equilibrium...
December 11, 2017: Chemistry, An Asian Journal
Michelle E Afkhami, D Luke Mahler, Jean H Burns, Marjorie G Weber, Martin F Wojciechowski, Janet Sprent, Sharon Y Strauss
How species interactions shape global biodiversity and influence diversification is a central - but also data-hungry - question in evolutionary ecology. Microbially-based mutualisms are widespread and could cause diversification by ameliorating stress and thus allowing organisms to colonize and adapt to otherwise unsuitable habitats. Yet the role of these interactions in generating species diversity has received limited attention, especially across large taxonomic groups. In the massive angiosperm family Leguminosae, plants often associate with root-nodulating bacteria that ameliorate nutrient stress by fixing atmospheric nitrogen...
December 11, 2017: Ecology
Hoa Thi Nguyen, Tinh Viet Luu, Gerald Leppert, Manuela De Allegri
Understanding public preferences in terms of health benefit packages (HBPs) remains limited, yet gathering community insights is an important endeavour when developing people-centred health systems and moving towards universal health coverage. Our study aimed to address this gap in knowledge by eliciting community preferences for the social health insurance benefit package among the uninsured in Vietnam. We adopted a mixed methods approach that included a ranking exercise followed by focus group discussions...
2017: BMJ Global Health
Jie Zhang, Shuo Jiao, Yahai Lu
Natural wetlands and anthropogenic paddy fields are the dominant biogenic sources of atmospheric methane emission which have been speculated as the most probable sources for the increase of post-2006 atmospheric methane. Regional differences in CH4 emission is possibly due to microbial biogeographic distribution. Here we collected soils from 19 wetlands from different regions in China. The methane production capacity (MPC) was measured for each soil samples and varied from 1.11 to 841.94mg/kg dry soil. High throughput sequencing was employed to investigate the diversity and composition of bacterial, archaeal and methanogenic communities...
December 6, 2017: Science of the Total Environment
Valeria Lencioni
The aim of this work was to highlight the main ecological predictors driving invertebrate distribution in eight glacier-fed streams in the Southern Alps. Thirty-five sites belonging to four stream types were sampled monthly during the ablation season of one, two or three years between 1996 and 2014. Taxa from glacial (kryal and glacio-rhithral) and non-glacial (kreno-rhithral and lake outlet) sites were separated by canonical correspondence analysis (CCA) along a glacial influence gradient and a hydrological-altitudinal gradient...
December 6, 2017: Science of the Total Environment
Tatjana Stojković, Olaf Rose, Ronja Woltersdorf, Valentina Marinković, Tanja Manser, Ulrich Jaehde
BACKGROUND: Medicine dispensing represents an error-prone activity, carrying a considerable risk for patients. OBJECTIVE: To prospectively identify and prioritize potential failure modes in the medicine dispensing process as well as to develop corrective actions for patient safety improvement in German community pharmacies. METHOD: Failure mode and effects analysis was performed in 2 community pharmacies in North Rhine-Westphalia, Germany, in October 2016...
December 7, 2017: International Journal of Health Planning and Management
Andrew L Chang, Christopher W Brown, Jeffrey A Crooks, Gregory M Ruiz
The impacts of changing climate regimes on emergent processes controlling the assembly of ecological communities remain poorly understood. Human alterations to the water cycle in the western United States have resulted in greater interannual variability and more frequent and severe extremes in freshwater flow. The specific mechanisms through which such extremes and climate regime shifts may alter ecological communities have rarely been demonstrated, and baseline information on current impacts of environmental variation is widely lacking for many habitats and communities...
December 7, 2017: Global Change Biology
Shengen Liu, Hang Wang, Ye Deng, Peng Tian, Qingkui Wang
World-wide conversion of natural forests to other land uses has profound effects on soil microbial communities. However, how soil microbial β-diversity responds to land-use change and its driving mechanisms remains poorly understood. In this study, therefore, we examined the effect of forest conversion from native broad-leaved forest to coniferous plantation on soil microbial β-diversity and its underlying mechanisms in both summer and winter in subtropical China. Microbial communities increasingly differed in structure as geographical distance between them increased, and the slope of the relationship among distances and community similarity differed among forest covers...
December 7, 2017: Environmental Microbiology
Jeannette Whitton, Christopher J Sears, Wayne P Maddison
We used randomizations to analyse patterns of co-occurrence of sexual and apomictic (asexual) members of the North American Crepis agamic complex (Asteraceae). We expect strong asymmetry in reproductive interactions in Crepis: apomicts produce clonal seeds with no need for pollination and are not subject to reproductive interference from co-occurring relatives. However, because they still produce some viable pollen, apomicts can reduce reproductive success of nearby sexual relatives, potentially leading to eventual local exclusion of sexuals...
December 6, 2017: Proceedings. Biological Sciences
Robert Šket, Nicole Treichel, Susanne Kublik, Tadej Debevec, Ola Eiken, Igor Mekjavić, Michael Schloter, Marius Vital, Jenna Chandler, James M Tiedje, Boštjan Murovec, Zala Prevoršek, Matevž Likar, Blaž Stres
We explored the assembly of intestinal microbiota in healthy male participants during the randomized crossover design of run-in (5 day) and experimental phases (21-day normoxic bed rest (NBR), hypoxic bed rest (HBR) and hypoxic ambulation (HAmb) in a strictly controlled laboratory environment, with balanced fluid and dietary intakes, controlled circadian rhythm, microbial ambiental burden and 24/7 medical surveillance. The fraction of inspired O2 (FiO2) and partial pressure of inspired O2 (PiO2) were 0.209 and 133...
2017: PloS One
Alejandro Morón-Ríos, Sergio Gómez-Cornelio, Benjamin Otto Ortega-Morales, Susana De la Rosa-García, Laila Pamela Partida-Martínez, Patricia Quintana, José Armando Alayón-Gamboa, Silvia Cappello-García, Santiago González-Gómez
The assembly of fungal communities on stone materials is mainly influenced by the differential bioreceptivity of such materials and environmental conditions. However, little is known about the role of fungal interactions in the colonization and establishment of fungal species. We analyzed the effects of intra- and interspecific interactions between 11 species of fungi in oligotrophic and copiotrophic media and on limestone coupons. In a previous study, these species were the most frequently isolated in the epilithic biofilms of limestone walls exposed to a subtropical climate...
2017: PloS One
Charmaine Ng, Martin Tay, Boonfei Tan, Thai-Hoang Le, Laurence Haller, Hongjie Chen, Tse H Koh, Timothy M S Barkham, Karina Y-H Gin
The dissemination of antimicrobial resistance (AMR) is an escalating problem and a threat to public health. Comparative metagenomics was used to investigate the occurrence of antibiotic resistant genes (ARGs) in wastewater and urban surface water environments in Singapore. Hospital and municipal wastewater (n = 6) were found to have higher diversity and average abundance of ARGs (303 ARG subtypes, 197,816 x/Gb) compared to treated wastewater effluent (n = 2, 58 ARG subtypes, 2,692 x/Gb) and surface water (n = 5, 35 subtypes, 7,985 x/Gb)...
2017: Frontiers in Microbiology
Muhammad Imran Qadir, Maria Zafar
HIV infection presents a major community health hazard, partially because the HIV virus is capable of evading antiretroviral therapies. Most anti-HIV drugs were intended to target virus-encoded mechanisms; however, some host-encoded molecules comparatively execute a vital role in the life cycle of virus. Thus, these might be considered as target sites for antiviral agents. TSG101 is important among these antiviral therapies because, as a cytoplasmic molecule, it facilitates viral budding and release. In this review, HIV-infected cells have TSG101 on their surface and thus can be used in antibody-based therapies...
2017: Critical Reviews in Eukaryotic Gene Expression
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