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Plant microbiome

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https://www.readbyqxmd.com/read/27924137/exercise-induced-stress-behavior-gut-microbiota-brain-axis-and-diet-a-systematic-review-for-athletes
#1
REVIEW
Allison Clark, Núria Mach
Fatigue, mood disturbances, under performance and gastrointestinal distress are common among athletes during training and competition. The psychosocial and physical demands during intense exercise can initiate a stress response activating the sympathetic-adrenomedullary and hypothalamus-pituitary-adrenal (HPA) axes, resulting in the release of stress and catabolic hormones, inflammatory cytokines and microbial molecules. The gut is home to trillions of microorganisms that have fundamental roles in many aspects of human biology, including metabolism, endocrine, neuronal and immune function...
2016: Journal of the International Society of Sports Nutrition
https://www.readbyqxmd.com/read/27917166/temporal-metagenomic-and-metabolomic-characterization-of-fresh-perennial-ryegrass-degradation-by-rumen-bacteria
#2
Olga L Mayorga, Alison H Kingston-Smith, Eun J Kim, Gordon G Allison, Toby J Wilkinson, Matthew J Hegarty, Michael K Theodorou, Charles J Newbold, Sharon A Huws
Understanding the relationship between ingested plant material and the attached microbiome is essential for developing methodologies to improve ruminant nutrient use efficiency. We have previously shown that perennial ryegrass (PRG) rumen bacterial colonization events follow a primary (up to 4 h) and secondary (after 4 h) pattern based on the differences in diversity of the attached bacteria. In this study, we investigated temporal niche specialization of primary and secondary populations of attached rumen microbiota using metagenomic shotgun sequencing as well as monitoring changes in the plant chemistry using mid-infrared spectroscopy (FT-IR)...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27898265/prospects-for-biological-soil-borne-disease-control-application-of-indigenous-versus-synthetic-microbiomes
#3
Mark Mazzola, Shiri Freilich
Biological disease control of soil-borne plant diseases has traditionally employed the biopesticide approach whereby single strains or strain mixtures are introduced into production systems through inundative/inoculative release. The approach has significant barriers that have long been recognized, including a generally limited spectrum of target pathogens for any given biocontrol agent andinadequate colonization of the host rhizosphere, which can plague progress in the utilization of this resource in commercial field-based crop production systems...
November 29, 2016: Phytopathology
https://www.readbyqxmd.com/read/27892611/towards-a-bacterial-treatment-for-armpit-malodour
#4
Chris Callewaert, Jo Lambert, Tom Van de Wiele
Axillary malodour is a frustrating condition for many people. It can lead to significant discomforts and various psychological effects. The underarm microbiome generally plays a major role in axillary malodour formation. Not only the bacteria on the armpit epidermis, but especially those living in the sweat glands, sweat pores and hair follicles play a pivotal role in malodour development. In order to treat underarm malodour, this viewpoint paper envisions a bacterial treatment. Replacing the autochthonous malodour causing microbiome with a non-odour causing microbiome, through an armpit bacterial transplantation or direct application of probiotics/non-odour causing bacteria could resolve the condition...
November 28, 2016: Experimental Dermatology
https://www.readbyqxmd.com/read/27890087/molecular-phylogeny-diversity-community-structure-and-plant-growth-promoting-properties-of-fungal-endophytes-associated-with-the-corms-of-saffron-plant-an-insight-into-the-microbiome-of-crocus-sativus-linn
#5
Zahoor Ahmed Wani, Dania Nazir Mirza, Palak Arora, Syed Riyaz-Ul-Hassan
A total of 294 fungal endophytes were isolated from the corms of Crocus sativus at two stages of crocus life cycle collected from 14 different saffron growing sites in Jammu and Kashmir (J & K) State, India. Molecular phylogeny assigned them into 36 distinct internal transcribed spacer (ITS) genotypes which spread over 19 genera. The diversity of endophytes was higher at the dormant than at the vegetative stage. The Saffron microbiome was dominated by Phialophora mustea and Cadophora malorum, both are dark septate endophytes (DSEs)...
December 2016: Fungal Biology
https://www.readbyqxmd.com/read/27888459/comparative-analysis-of-bacterial-diversity-in-the-rhizosphere-of-tomato-by-culture-dependent-and-independent-approaches
#6
Shin Ae Lee, Jiyoung Park, Bora Chu, Jeong Myeong Kim, Jae-Ho Joa, Mee Kyung Sang, Jaekyeong Song, Hang-Yeon Weon
The microbiome in the rhizosphere-the region surrounding plant roots-plays a key role in plant growth and health, enhancing nutrient availability and protecting plants from biotic and abiotic stresses. To assess bacterial diversity in the tomato rhizosphere, we performed two contrasting approaches: culture-dependent and -independent. In the culture-dependent approach, two culture media (Reasoner's 2A agar and soil extract agar) were supplemented with 12 antibiotics for isolating diverse bacteria from the tomato rhizosphere by inhibiting predominant bacteria...
December 2016: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/27879004/plant-domestication-and-the-assembly-of-bacterial-and-fungal-communities-associated-with-strains-of-the-common-sunflower-helianthus-annuus
#7
Jonathan W Leff, Ryan C Lynch, Nolan C Kane, Noah Fierer
Root and rhizosphere microbial communities can affect plant health, but it remains undetermined how plant domestication may influence these bacterial and fungal communities. We grew 33 sunflower (Helianthus annuus) strains (n = 5) that varied in their extent of domestication and assessed rhizosphere and root endosphere bacterial and fungal communities. We also assessed fungal communities in the sunflower seeds to investigate the degree to which root and rhizosphere communities were influenced by vertical transmission of the microbiome through seeds...
November 23, 2016: New Phytologist
https://www.readbyqxmd.com/read/27871147/shared-and-host-specific-microbiome-diversity-and-functioning-of-grapevine-and-accompanying-weed-plants
#8
Abdul Samad, Friederike Trognitz, Stéphane Compant, Livio Antonielli, Angela Sessitsch
Weeds and crop plants select their microbiota from the same pool of soil microorganisms, however, the ecology of weed microbiomes is poorly understood. We analyzed the microbiomes associated with roots and rhizospheres of grapevine and four weed species (Lamium amplexicaule L., Veronica arvensis L., Lepidium draba L. and Stellaria media L.) growing in proximity in the same vineyard using 16S rRNA gene sequencing. We also isolated and characterized 500 rhizobacteria and root endophytes from L. draba and grapevine...
November 21, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27853518/metagenomic-analysis-of-medicinal-cannabis-samples-pathogenic-bacteria-toxigenic-fungi-and-beneficial-microbes-grow-in-culture-based-yeast-and-mold-tests
#9
Kevin McKernan, Jessica Spangler, Yvonne Helbert, Ryan C Lynch, Adrian Devitt-Lee, Lei Zhang, Wendell Orphe, Jason Warner, Theodore Foss, Christopher J Hudalla, Matthew Silva, Douglas R Smith
Background: The presence of bacteria and fungi in medicinal or recreational Cannabis poses a potential threat to consumers if those microbes include pathogenic or toxigenic species. This study evaluated two widely used culture-based platforms for total yeast and mold (TYM) testing marketed by 3M Corporation and Biomérieux, in comparison with a quantitative PCR (qPCR) approach marketed by Medicinal Genomics Corporation. Methods: A set of 15 medicinal Cannabis samples were analyzed using 3M and Biomérieux culture-based platforms and by qPCR to quantify microbial DNA...
2016: F1000Research
https://www.readbyqxmd.com/read/27833995/cultivation-versus-molecular-analysis-of-banana-musa-sp-shoot-tip-tissue-reveals-enormous-diversity-of-normally-uncultivable-endophytic-bacteria
#10
Pious Thomas, Aparna Chandra Sekhar
The interior of plants constitutes a unique environment for microorganisms with various organisms inhabiting as endophytes. Unlike subterranean plant parts, aboveground parts are relatively less explored for endophytic microbial diversity. We employed a combination of cultivation and molecular approaches to study the endophytic bacterial diversity in banana shoot-tips. Cultivable bacteria from 20 sucker shoot-tips of cv. Grand Naine included 37 strains under 16 genera and three phyla (Proteobacteria, Actinobacteria, Firmicutes)...
November 10, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27833797/root-bacterial-endophytes-alter-plant-phenotype-but-not-physiology
#11
Jeremiah A Henning, David J Weston, Dale A Pelletier, Collin M Timm, Sara S Jawdy, Aimée T Classen
Plant traits, such as root and leaf area, influence how plants interact with their environment and the diverse microbiota living within plants can influence plant morphology and physiology. Here, we explored how three bacterial strains isolated from the Populus root microbiome, influenced plant phenotype. We chose three bacterial strains that differed in predicted metabolic capabilities, plant hormone production and metabolism, and secondary metabolite synthesis. We inoculated each bacterial strain on a single genotype of Populus trichocarpa and measured the response of plant growth related traits (root:shoot, biomass production, root and leaf growth rates) and physiological traits (chlorophyll content, net photosynthesis, net photosynthesis at saturating light-Asat, and saturating CO2-Amax)...
2016: PeerJ
https://www.readbyqxmd.com/read/27824111/sensitive-responders-among-bacterial-and-fungal-microbiome-to-pyrogenic-organic-matter-biochar-addition-differed-greatly-between-rhizosphere-and-bulk-soils
#12
Zhongmin Dai, Jiajie Hu, Xingkun Xu, Lujun Zhang, Philip C Brookes, Yan He, Jianming Xu
Sensitive responses among bacterial and fungal communities to pyrogenic organic matter (PyOM) (biochar) addition in rhizosphere and bulk soils are poorly understood. We conducted a pot experiment with manure and straw PyOMs added to an acidic paddy soil, and identified the sensitive "responders" whose relative abundance was significantly increased/decreased among the whole microbial community following PyOM addition. Results showed that PyOMs significantly (p < 0.05) increased root growth, and simultaneously changed soil chemical parameters by decreasing soil acidity and increasing biogenic resource...
November 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27822530/moleculo-long-read-sequencing-facilitates-assembly-and-genomic-binning-from-complex-soil-metagenomes
#13
Richard Allen White, Eric M Bottos, Taniya Roy Chowdhury, Jeremy D Zucker, Colin J Brislawn, Carrie D Nicora, Sarah J Fansler, Kurt R Glaesemann, Kevin Glass, Janet K Jansson
Soil metagenomics has been touted as the "grand challenge" for metagenomics, as the high microbial diversity and spatial heterogeneity of soils make them unamenable to current assembly platforms. Here, we aimed to improve soil metagenomic sequence assembly by applying the Moleculo synthetic long-read sequencing technology. In total, we obtained 267 Gbp of raw sequence data from a native prairie soil; these data included 109.7 Gbp of short-read data (~100 bp) from the Joint Genome Institute (JGI), an additional 87...
May 2016: MSystems
https://www.readbyqxmd.com/read/27822524/from-sample-to-multi-omics-conclusions-in-under-48-hours
#14
Robert A Quinn, Jose A Navas-Molina, Embriette R Hyde, Se Jin Song, Yoshiki Vázquez-Baeza, Greg Humphrey, James Gaffney, Jeremiah J Minich, Alexey V Melnik, Jakob Herschend, Jeff DeReus, Austin Durant, Rachel J Dutton, Mahdieh Khosroheidari, Clifford Green, Ricardo da Silva, Pieter C Dorrestein, Rob Knight
Multi-omics methods have greatly advanced our understanding of the biological organism and its microbial associates. However, they are not routinely used in clinical or industrial applications, due to the length of time required to generate and analyze omics data. Here, we applied a novel integrated omics pipeline for the analysis of human and environmental samples in under 48 h. Human subjects that ferment their own foods provided swab samples from skin, feces, oral cavity, fermented foods, and household surfaces to assess the impact of home food fermentation on their microbial and chemical ecology...
March 2016: MSystems
https://www.readbyqxmd.com/read/27821517/tree-invasions-and-biosecurity-eco-evolutionary-dynamics-of-hitchhiking-fungi
#15
Treena I Burgess, Casparus J Crous, Bernard Slippers, Jarkko Hantula, Michael J Wingfield
When non-native plants reach novel environments, they typically arrive with hidden microbiomes. In general, most of these hitchhikers remain on their co-evolved hosts, some contribute to the invasiveness of their hosts, and a small number can undergo host shifts and move onto native hosts. Invasion success can vary depending upon the different categories of fungal associates. When an invader tree relies on a fungal mutualism to survive in the new environment, there is a fundamentally lower likelihood of either the tree, or the fungus, establishing novel associations...
November 7, 2016: AoB Plants
https://www.readbyqxmd.com/read/27819730/rhizosphere-bacteriome-of-the-medicinal-plant-sapindus-saponaria-l-revealed-by-pyrosequencing
#16
A Garcia, J C Polonio, A D Polli, C M Santos, S A Rhoden, M C Quecine, J L Azevedo, J A Pamphile
Sapindus saponaria L. of Sapindaceae family is popularly known as soldier soap and is found in Central and South America. A study of such medicinal plants might reveal a more complex diversity of microorganisms as compared to non-medicinal plants, considering their metabolic potential and the chemical communication between their natural microbiota. Rhizosphere is a highly diverse microbial habitat with respect to both the diversity of species and the size of the community. Rhizosphere bacteriome associated with medicinal plant S...
November 3, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/27805014/microbial-community-dynamics-in-the-rhizosphere-of-a-cadmium-hyper-accumulator
#17
J L Wood, C Zhang, E R Mathews, C Tang, A E Franks
Phytoextraction is influenced by the indigenous soil microbial communities during the remediation of heavy metal contaminated soils. Soil microbial communities can affect plant growth, metal availability and the performance of phytoextraction-assisting inocula. Understanding the basic ecology of indigenous soil communities associated with the phytoextraction process, including the interplay between selective pressures upon the communities, is an important step towards phytoextraction optimization. This study investigated the impact of cadmium (Cd), and the presence of a Cd-accumulating plant, Carpobrotus rossii (Haw...
November 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27804103/rhizobacteria-with-nematicide-aptitude-enzymes-and-compounds-associated
#18
REVIEW
C Castaneda-Alvarez, E Aballay
The use of rhizobacteria to control plant parasitic nematodes has been widely studied. Currently, the research focuses on bacteria-nematode interactions that can mitigate this complex microbiome in agriculture. Various enzymes, toxins and metabolic by-products from rhizobacteria antagonize plant parasitic nematodes, and many different modes of action have been proposed. Hydrolytic enzymes, primarily proteases, collagenases and chitinases, have been related to the nematicide effect in rhizobacteria, proving to be an important factor involved in the degradation of different chemical constituents of nematodes at distinct developmental stages...
December 2016: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/27797857/plant-microbiomes-and-sustainable-agriculture-deciphering-the-plant-microbiome-and-its-role-in-nutrient-supply-and-plant-immunity-has-great-potential-to-reduce-the-use-of-fertilizers-and-biocides-in-agriculture
#19
https://www.readbyqxmd.com/read/27795313/the-influence-of-the-host-plant-is-the-major-ecological-determinant-of-soil-presence-of-the-nitrogen-fixing-root-nodule-symbiont-cluster-ii-frankia
#20
Kai Battenberg, Jannah A Wren, Janell Hillman, Joseph Edwards, Liujing Huang, Alison M Berry
: The actinobacterial genus Frankia establishes nitrogen-fixing root nodule symbioses with specific hosts within the nitrogen-fixing plant clade. Of four genetically distinct subgroups of Frankia, Clusters I, II, and III are capable of forming effective nitrogen-fixing symbiotic associations, while Cluster IV strains generally do not. Cluster II Frankia has rarely been detected in soil devoid of host plants, unlike Cluster I or III, suggesting a stronger association with their host. To investigate the degree of host influence, we characterized the Cluster II Frankia distribution in rhizosphere soil in three locations in northern California...
October 21, 2016: Applied and Environmental Microbiology
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