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Plant microbiome

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https://www.readbyqxmd.com/read/29155257/contrasting-the-microbiomes-from-forest-rhizosphere-and-deeper-bulk-soil-from-an-amazon-rainforest-reserve
#1
Jose Pedro Fonseca, Luisa Hoffmann, Bianca Catarina Azeredo Cabral, Victor Hugo Giordano Dias, Marcio Rodrigues Miranda, Allan Cezar de Azevedo Martins, Clarissa Boschiero, Wanderley Rodrigues Bastos, Rosane Silva
Pristine forest ecosystems provide a unique perspective for the study of plant-associated microbiota since they host a great microbial diversity. Although the Amazon forest is one of the hotspots of biodiversity around the world, few metagenomic studies described its microbial community diversity thus far. Understanding the environmental factors that can cause shifts in microbial profiles is key to improving soil health and biogeochemical cycles. Here we report a taxonomic and functional characterization of the microbiome from the rhizosphere of Brosimum guianense (Snakewood), a native tree, and bulk soil samples from a pristine Brazilian Amazon forest reserve (Cuniã), for the first time by the shotgun approach...
November 15, 2017: Gene
https://www.readbyqxmd.com/read/29153474/impacts-of-environmental-factors-on-the-whole-microbial-communities-in-the-rhizosphere-of-a-metal-tolerant-plant-elsholtzia-haichowensis-sun
#2
Songqiang Deng, Tan Ke, Longtai Li, Shenwen Cai, Yuyue Zhou, Yue Liu, Limin Guo, Lanzhou Chen, Dayi Zhang
Rhizospheric microbes play important roles in plant growth and heavy metals (HMs) transformation, possessing great potential for the successful phytoremediation of environmental pollutants. In the present study, the rhizosphere of Elsholtzia haichowensis Sun was comprehensively studied to uncover the influence of environmental factors (EFs) on the whole microbial communities including bacteria, fungi and archaea, via quantitative polymerase chain reaction (qPCR) and high-throughput sequencing. By analyzing molecular ecological network and multivariate regression trees (MRT), we evaluated the distinct impacts of 37 EFs on soil microbial community...
November 15, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/29146930/previous-crop-and-rotation-history-effects-on-maize-seedling-health-and-associated-rhizosphere-microbiome
#3
Maria-Soledad Benitez, Shannon L Osborne, R Michael Lehman
To evaluate crop rotation effects on maize seedling performance and its associated microbiome, maize plants were grown in the greenhouse in soils preceded by either maize, pea, soybean or sunflower. Soils originated from a replicated field experiment evaluating different four-year rotation combinations. In the greenhouse, a stressor was introduced by soil infestation with western corn rootworm (WCR) or Fusarium graminearum. Under non-infested conditions, maize seedlings grown in soils preceded by sunflower or pea had greater vigor...
November 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29145592/soil-bacterial-community-response-to-altered-precipitation-and-temperature-regimes-in-an-old-field-grassland-are-mediated-by-plants
#4
Akihiro Koyama, J Megan Steinweg, Michelle L Haddix, Jeffrey S Dukes, Matthew D Wallenstein
The structure and function of soil microbiomes often change in response to experimental climate manipulations, suggesting an important role in ecosystem feedbacks. However, it is difficult to know if microbes are responding directly to environmental changes or are more strongly impacted by plant responses. We investigated soil microbial responses to precipitation and temperature manipulations at the Boston-Area Climate Experiment in Massachusetts, USA in both vegetated and bare plots to parse direct vs plant-mediated response to multi-factor climate change...
November 14, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29144774/strategies-for-enhanced-crop-resistance-to-insect-pests
#5
Angela E Douglas
Insect pests are responsible for substantial crop losses worldwide through direct damage and transmission of plant diseases, and novel approaches that complement or replace broad-spectrum chemical insecticides will facilitate the sustainable intensification of food production in the coming decades. Multiple strategies for improved crop resistance to insect pests, especially strategies relating to plant secondary metabolism and immunity and microbiome science, are becoming available. Recent advances in metabolic engineering of plant secondary chemistry offer the promise of specific toxicity or deterrence to insect pests; improved understanding of plant immunity against insects provides routes to optimize plant defenses against insects; and the microbiomes of insect pests can be exploited, either as a target or as a vehicle for delivery of insecticidal agents...
November 16, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/29140397/progress-in-the-understanding-of-the-pathology-of-allergic-asthma-and-the-potential-of-fruit-proanthocyanidins-as-modulators-of-airway-inflammation
#6
REVIEW
Sara L Coleman, Odette M Shaw
Allergic asthma is a chronic inflammatory lung disease characterized by sensitization of the airways, and the development of immunoglobulin E antibodies, to benign antigens. The established pathophysiology of asthma includes recurrent lung epithelial inflammation, excessive mucus production, bronchial smooth muscle hyperreactivity, and chronic lung tissue remodeling, resulting in reversible airflow restriction. Immune cells, including eosinophils and the recently characterized type 2 innate lymphoid cells, infiltrate into the lung tissue as part of the inflammatory response in allergic asthma...
November 15, 2017: Food & Function
https://www.readbyqxmd.com/read/29138485/evaluating-the-impact-of-domestication-and-captivity-on-the-horse-gut-microbiome
#7
Jessica L Metcalf, Se Jin Song, James T Morton, Sophie Weiss, Andaine Seguin-Orlando, Frédéric Joly, Claudia Feh, Pierre Taberlet, Eric Coissac, Amnon Amir, Eske Willerslev, Rob Knight, Valerie McKenzie, Ludovic Orlando
The mammal gut microbiome, which includes host microbes and their respective genes, is now recognized as an essential second genome that provides critical functions to the host. In humans, studies have revealed that lifestyle strongly influences the composition and diversity of the gastrointestinal microbiome. We hypothesized that these trends in humans may be paralleled in mammals subjected to anthropogenic forces such as domestication and captivity, in which diets and natural life histories are often greatly modified...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29134155/foliar-microbiome-transplants-confer-disease-resistance-in-a-critically-endangered-plant
#8
Geoffrey Zahn, Anthony S Amend
There has been very little effort to incorporate foliar microbiomes into plant conservation efforts even though foliar endophytes are critically important to the fitness and function of hosts. Many critically endangered plants that have been extirpated from the wild are dependent on regular fungicidal applications in greenhouses that cannot be maintained for remote out-planted populations, which quickly perish. These fungicides negatively impact potentially beneficial fungal symbionts, which may reduce plant defenses to pathogens once fungicide treatments are stopped...
2017: PeerJ
https://www.readbyqxmd.com/read/29125552/transmission-of-bacterial-endophytes
#9
REVIEW
Anna Carolin Frank, Jessica Paola Saldierna Guzmán, Jackie E Shay
Plants are hosts to complex communities of endophytic bacteria that colonize the interior of both below- and aboveground tissues. Bacteria living inside plant tissues as endophytes can be horizontally acquired from the environment with each new generation, or vertically transmitted from generation to generation via seed. A better understanding of bacterial endophyte transmission routes and modes will benefit studies of plant-endophyte interactions in both agricultural and natural ecosystems. In this review, we provide an overview of the transmission routes that bacteria can take to colonize plants, including vertically via seeds and pollen, and horizontally via soil, atmosphere, and insects...
November 10, 2017: Microorganisms
https://www.readbyqxmd.com/read/29123512/alternative-growth-promoters-modulate-broiler-gut-microbiome-and-enhance-body-weight-gain
#10
Serajus Salaheen, Seon-Woo Kim, Bradd J Haley, Jo Ann S Van Kessel, Debabrata Biswas
Antibiotic growth promoters (AGPs) are frequently used to enhance weight-gain in poultry production. However, there has been increasing concern over the impact of AGP on the emergence of antibiotic resistance in zoonotic bacterial pathogens in the microbial community of the poultry gut. In this study, we adopted mass-spectrophotometric, phylogenetic, and shotgun-metagenomic approaches to evaluate bioactive phenolic extracts (BPE) from blueberry (Vaccinium corymbosum) and blackberry (Rubus fruticosus) pomaces as AGP alternatives in broilers...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29118851/targeted-metatranscriptomics-of-compost-derived-consortia-reveals-a-gh11-exerting-an-unusual-exo-1-4-%C3%AE-xylanase-activity
#11
Bruno L Mello, Anna M Alessi, Diego M Riaño-Pachón, Eduardo R deAzevedo, Francisco E G Guimarães, Melissa C Espirito Santo, Simon McQueen-Mason, Neil C Bruce, Igor Polikarpov
Background: Using globally abundant crop residues as a carbon source for energy generation and renewable chemicals production stand out as a promising solution to reduce current dependency on fossil fuels. In nature, such as in compost habitats, microbial communities efficiently degrade the available plant biomass using a diverse set of synergistic enzymes. However, deconstruction of lignocellulose remains a challenge for industry due to recalcitrant nature of the substrate and the inefficiency of the enzyme systems available, making the economic production of lignocellulosic biofuels difficult...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29117584/environmental-and-health-effects-of-the-herbicide-glyphosate
#12
REVIEW
A H C Van Bruggen, M M He, K Shin, V Mai, K C Jeong, M R Finckh, J G Morris
The herbicide glyphosate, N-(phosphonomethyl) glycine, has been used extensively in the past 40years, under the assumption that side effects were minimal. However, in recent years, concerns have increased worldwide about the potential wide ranging direct and indirect health effects of the large scale use of glyphosate. In 2015, the World Health Organization reclassified glyphosate as probably carcinogenic to humans. A detailed overview is given of the scientific literature on the movement and residues of glyphosate and its breakdown product aminomethyl phosphonic acid (AMPA) in soil and water, their toxicity to macro- and microorganisms, their effects on microbial compositions and potential indirect effects on plant, animal and human health...
November 5, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29112136/gut-microbiome-and-putative-resistome-of-inca-and-italian-nobility-mummies
#13
Tasha M Santiago-Rodriguez, Gino Fornaciari, Stefania Luciani, Gary A Toranzos, Isolina Marota, Valentina Giuffra, Raul J Cano
Little is still known about the microbiome resulting from the process of mummification of the human gut. In the present study, the gut microbiota, genes associated with metabolism, and putative resistome of Inca and Italian nobility mummies were characterized by using high-throughput sequencing. The Italian nobility mummies exhibited a higher bacterial diversity as compared to the Inca mummies when using 16S ribosomal (rRNA) gene amplicon sequencing, but both groups showed bacterial and fungal taxa when using shotgun metagenomic sequencing that may resemble both the thanatomicrobiome and extant human gut microbiomes...
November 7, 2017: Genes
https://www.readbyqxmd.com/read/29106611/mvoc-2-0-a-database-of-microbial-volatiles
#14
Marie C Lemfack, Bjoern-Oliver Gohlke, Serge M T Toguem, Saskia Preissner, Birgit Piechulla, Robert Preissner
Metabolic capabilities of microorganisms include the production of secondary metabolites (e.g. antibiotics). The analysis of microbial volatile organic compounds (mVOCs) is an emerging research field with huge impact on medical, agricultural and biotechnical applied and basic science. The mVOC database (v1) has grown with microbiome research and integrated species information with data on emitted volatiles. Here, we present the mVOC 2.0 database with about 2000 compounds from almost 1000 species and new features to work with the database...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29101364/shifts-in-microbial-communities-in-soil-rhizosphere-and-roots-of-two-major-crop-systems-under-elevated-co2-and-o3
#15
Peng Wang, Ellen L Marsh, Elizabeth A Ainsworth, Andrew D B Leakey, Amy M Sheflin, Daniel P Schachtman
Rising atmospheric concentrations of CO2 and O3 are key features of global environmental change. To investigate changes in the belowground bacterial community composition in response to elevated CO2 and O3 (eCO2 and eO3) the endosphere, rhizosphere and soil were sampled from soybeans under eCO2 and maize under eO3. The maize rhizosphere and endosphere α-diversity was higher than soybean, which may be due to a high relative abundance of Rhizobiales. Only the rhizosphere microbiome composition of the soybeans changed in response to eCO2, associated with an increased abundance of nitrogen fixing microbes...
November 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29081767/strong-regionality-and-dominance-of-anaerobic-bacterial-taxa-characterize-diazotrophic-bacterial-communities-of-the-arcto-alpine-plant-species-oxyria-digyna-and-saxifraga-oppositifolia
#16
Manoj Kumar, Jan Dirk van Elsas, Riitta Nissinen
Arctic and alpine biomes are most often strongly nitrogen-limited, and hence biological nitrogen fixation is a strong driver of these ecosystems. Both biomes are characterized by low temperatures and short growing seasons, but they differ in seasonality of solar radiation and in soil water balance due to underlying permafrost in the Arctic. Arcto-alpine plant species are well-adapted to the low temperatures that prevail in their habitats, and plant growth is mainly limited by the availability of nutrients, in particular nitrogen, due to slow mineralization...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29076547/the-sphagnome-project-enabling-ecological-and-evolutionary-insights-through-a-genus-level-sequencing-project
#17
David J Weston, Merritt R Turetsky, Matthew G Johnson, Gustaf Granath, Zoë Lindo, Lisa R Belyea, Steven K Rice, David T Hanson, Katharina A M Engelhardt, Jeremy Schmutz, Ellen Dorrepaal, Eugénie S Euskirchen, Hans K Stenøien, Péter Szövényi, Michelle Jackson, Bryan T Piatkowski, Wellington Muchero, Richard J Norby, Joel E Kostka, Jennifer B Glass, Håkan Rydin, Juul Limpens, Eeva-Stiina Tuittila, Kristian K Ullrich, Alyssa Carrell, Brian W Benscoter, Jin-Gui Chen, Tobi A Oke, Mats B Nilsson, Priya Ranjan, Daniel Jacobson, Erik A Lilleskov, R S Clymo, A Jonathan Shaw
Considerable progress has been made in ecological and evolutionary genetics with studies demonstrating how genes underlying plant and microbial traits can influence adaptation and even 'extend' to influence community structure and ecosystem level processes. Progress in this area is limited to model systems with deep genetic and genomic resources that often have negligible ecological impact or interest. Thus, important linkages between genetic adaptations and their consequences at organismal and ecological scales are often lacking...
October 27, 2017: New Phytologist
https://www.readbyqxmd.com/read/29073903/characterizing-endophytic-competence-and-plant-growth-promotion-of-bacterial-endophytes-inhabiting-the-seed-endosphere-of-rice
#18
Denver I Walitang, Kiyoon Kim, Munusamy Madhaiyan, Young Kee Kim, Yeongyeong Kang, Tongmin Sa
BACKGROUND: Rice (Oryza sativa L. ssp. indica) seeds as plant microbiome present both an opportunity and a challenge to colonizing bacterial community living in close association with plants. Nevertheless, the roles and activities of bacterial endophytes remain largely unexplored and insights into plant-microbe interaction are compounded by its complexity. In this study, putative functions or physiological properties associated with bacterial endophytic nature were assessed. Also, endophytic roles in plant growth and germination that may allow them to be selectively chosen by plants were also studied...
October 26, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/29067007/insights-into-microalga-and-bacteria-interactions-of-selected-phycosphere-biofilms-using-metagenomic-transcriptomic-and-proteomic-approaches
#19
Ines Krohn-Molt, Malik Alawi, Konrad U Förstner, Alena Wiegandt, Lia Burkhardt, Daniela Indenbirken, Melanie Thieß, Adam Grundhoff, Julia Kehr, Andreas Tholey, Wolfgang R Streit
Microalga are of high relevance for the global carbon cycling and it is well-known that they are associated with a microbiota. However, it remains unclear, if the associated microbiota, often found in phycosphere biofilms, is specific for the microalga strains and which role individual bacterial taxa play. Here we provide experimental evidence that Chlorella saccharophila, Scenedesmus quadricauda, and Micrasterias crux-melitensis, maintained in strain collections, are associated with unique and specific microbial populations...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29065162/endosphere-microbiome-comparison-between-symptomatic-and-asymptomatic-roots-of-brassica-napus-infected-with-plasmodiophora-brassicae
#20
COMPARATIVE STUDY
Ying Zhao, Zhixiao Gao, Binnian Tian, Kai Bi, Tao Chen, Huiquan Liu, Jiatao Xie, Jiasen Cheng, Yanping Fu, Daohong Jiang
Clubroot caused by Plasmodiophora brassicae, is a severe disease of cruciferous crops that causes large hypertrophic galls in the roots. The plant microbiome is important for growth promotion and disease suppression. In this study, using 16S rRNA and internal transcribed spacer (ITS) sequencing techniques, we compared the endosphere microbiome of symptomatic and asymptomatic B. napus roots infected with P. brassicae collected from the same natural clubroot field. The results showed that the microbial population and its relative abundance in the asymptomatic roots was far higher than that in the symptomatic roots, and that many microorganisms in asymptomatic roots have biological control and plant growth promotion functions that may be related to clubroot symptoms...
2017: PloS One
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