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Plant microbiome

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https://www.readbyqxmd.com/read/28326066/beneficial-microorganisms-for-corals-bmc-proposed-mechanisms-for-coral-health-and-resilience
#1
REVIEW
Raquel S Peixoto, Phillipe M Rosado, Deborah Catharine de Assis Leite, Alexandre S Rosado, David G Bourne
The symbiotic association between the coral animal and its endosymbiotic dinoflagellate partner Symbiodinium is central to the success of corals. However, an array of other microorganisms associated with coral (i.e., Bacteria, Archaea, Fungi, and viruses) have a complex and intricate role in maintaining homeostasis between corals and Symbiodinium. Corals are sensitive to shifts in the surrounding environmental conditions. One of the most widely reported responses of coral to stressful environmental conditions is bleaching...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28320784/mechanisms-to-mitigate-the-tradeoff-between-growth-and-defense
#2
Talia Karasov, Eunyoung Chae, Jacob Herman, Joy Bergelson
Plants have evolved an array of defenses against pathogens. However, mounting a defense response frequently comes with the cost of a reduction in growth and reproduction, carrying critical implications for natural and agricultural populations. How costs are generated, and whether and how they can be mitigated is the focus of this review. Most well-characterized growth-defense tradeoffs stem from antagonistic crosstalk among hormones rather than an identified metabolic expenditure. A primary way plants mitigate such costs is through restricted expression of resistance; this can be achieved through inducible expression of defense genes or by the concentration of defense to particular times or tissues...
March 20, 2017: Plant Cell
https://www.readbyqxmd.com/read/28318994/more-flavor-for-flavonoid-based-interventions
#3
Nadeem O Kaakoush, Margaret J Morris
Poor diets are associated with obesity and a decline in cognitive function. Flavonoids are plant compounds that have been associated with improved metabolic parameters in obesity and reversal of cognitive decline. Given that microbial flavonoid conversion is important for bioactivity, flavonoid-derived neuroactive compounds may be functionally crucial in the gut microbiome-brain axis.
March 17, 2017: Trends in Molecular Medicine
https://www.readbyqxmd.com/read/28298918/host-parasite-bacteria-triangle-the-microbiome-of-the-parasitic-weed-phelipanche-aegyptiaca-and-tomato-solanum-lycopersicum-mill-as-a-host
#4
Lilach Iasur Kruh, Tamar Lahav, Jacline Abu-Nassar, Guy Achdari, Raghda Salami, Shiri Freilich, Radi Aly
Broomrapes (Phelipanche/Orobanche spp.) are holoparasitic plants that subsist on the roots of a variety of agricultural crops, establishing direct connections with the host vascular system. This connection allows for the exchange of various substances and a possible exchange of endophytic microorganisms that inhabit the internal tissues of both plants. To shed some light on bacterial interactions occurring between the parasitic Phelipanche aegyptiaca and its host tomato, we characterized the endophytic composition in the parasite during the parasitization process and ascertained if these changes were accompanied by changes to endophytes in the host root...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28297714/root-microbiota-drive-direct-integration-of-phosphate-stress-and-immunity
#5
Gabriel Castrillo, Paulo José Pereira Lima Teixeira, Sur Herrera Paredes, Theresa F Law, Laura de Lorenzo, Meghan E Feltcher, Omri M Finkel, Natalie W Breakfield, Piotr Mieczkowski, Corbin D Jones, Javier Paz-Ares, Jeffery L Dangl
Plants live in biogeochemically diverse soils with diverse microbiota. Plant organs associate intimately with a subset of these microbes, and the structure of the microbial community can be altered by soil nutrient content. Plant-associated microbes can compete with the plant and with each other for nutrients, but may also carry traits that increase the productivity of the plant. It is unknown how the plant immune system coordinates microbial recognition with nutritional cues during microbiome assembly. Here we establish that a genetic network controlling the phosphate stress response influences the structure of the root microbiome community, even under non-stress phosphate conditions...
March 23, 2017: Nature
https://www.readbyqxmd.com/read/28296930/seasonal-changes-in-the-digesta-adherent-rumen-bacterial-communities-of-dairy-cattle-grazing-pasture
#6
Samantha J Noel, Graeme T Attwood, Jasna Rakonjac, Christina D Moon, Garry C Waghorn, Peter H Janssen
The complex microbiota that resides within the rumen is responsible for the break-down of plant fibre. The bacteria that attach to ingested plant matter within the rumen are thought to be responsible for initial fibre degradation. Most studies examining the ecology of this important microbiome only offer a 'snapshot' in time. We monitored the diversity of rumen bacteria in four New Zealand dairy cows, grazing a rye-grass and clover pasture over five consecutive seasons, using high throughput pyrosequencing of bacterial 16S rRNA genes...
2017: PloS One
https://www.readbyqxmd.com/read/28293229/fungal-root-microbiome-from-healthy-and-brittle-leaf-diseased-date-palm-trees-phoenix-dactylifera-l-reveals-a-hidden-untapped-arsenal-of-antibacterial-and-broad-spectrum-antifungal-secondary-metabolites
#7
Fedia B Mefteh, Amal Daoud, Ali Chenari Bouket, Faizah N Alenezi, Lenka Luptakova, Mostafa E Rateb, Adel Kadri, Neji Gharsallah, Lassaad Belbahri
In this study, we aimed to explore and compare the composition, metabolic diversity and antimicrobial potential of endophytic fungi colonizing internal tissues of healthy and brittle leaf diseased (BLD) date palm trees (Phoenix dactylifera L.) widely cultivated in arid zones of Tunisia. A total of 52 endophytic fungi were isolated from healthy and BLD roots of date palm trees, identified based on internal transcribed spacer-rDNA sequence analysis and shown to represent 13 species belonging to five genera. About 36...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28285599/microbiome-and-metabolome-modifying-effects-of-several-cardiovascular-disease-interventions-in-apo-e-mice
#8
Paul M Ryan, Lis E E London, Trent C Bjorndahl, Rupasri Mandal, Kiera Murphy, Gerald F Fitzgerald, Fergus Shanahan, R Paul Ross, David S Wishart, Noel M Caplice, Catherine Stanton
BACKGROUND: There is strong evidence indicating that gut microbiota have the potential to modify, or be modified by the drugs and nutritional interventions that we rely upon. This study aims to characterize the compositional and functional effects of several nutritional, neutraceutical, and pharmaceutical cardiovascular disease interventions on the gut microbiome, through metagenomic and metabolomic approaches. Apolipoprotein-E-deficient mice were fed for 24 weeks either high-fat/cholesterol diet alone (control, HFC) or high-fat/cholesterol in conjunction with one of three dietary interventions, as follows: plant sterol ester (PSE), oat β-glucan (OBG) and bile salt hydrolase-active Lactobacillus reuteri APC 2587 (BSH), or the drug atorvastatin (STAT)...
March 13, 2017: Microbiome
https://www.readbyqxmd.com/read/28279152/the-altered-gut-microbiota-in-adults-with-cystic-fibrosis
#9
D G Burke, F Fouhy, M J Harrison, M C Rea, P D Cotter, O O'Sullivan, C Stanton, C Hill, F Shanahan, B J Plant, R P Ross
BACKGROUND: Cystic Fibrosis (CF) is an autosomal recessive disease that affects the function of a number of organs, principally the lungs, but also the gastrointestinal tract. The manifestations of cystic fibrosis transmembrane conductance regulator (CFTR) dysfunction in the gastrointestinal tract, as well as frequent antibiotic exposure, undoubtedly disrupts the gut microbiota. To analyse the effects of CF and its management on the microbiome, we compared the gut microbiota of 43 individuals with CF during a period of stability, to that of 69 non-CF controls using 454-pyrosequencing of the 16S rRNA gene...
March 9, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28275097/simplified-and-representative-bacterial-community-of-maize-roots
#10
Ben Niu, Joseph Nathaniel Paulson, Xiaoqi Zheng, Roberto Kolter
Plant-associated microbes are important for the growth and health of their hosts. As a result of numerous prior studies, we know that host genotypes and abiotic factors influence the composition of plant microbiomes. However, the high complexity of these communities challenges detailed studies to define experimentally the mechanisms underlying the dynamics of community assembly and the beneficial effects of such microbiomes on plant hosts. In this work, from the distinctive microbiota assembled by maize roots, through host-mediated selection, we obtained a greatly simplified synthetic bacterial community consisting of seven strains (Enterobacter cloacae, Stenotrophomonas maltophilia, Ochrobactrum pituitosum, Herbaspirillum frisingense, Pseudomonas putida, Curtobacterium pusillum, and Chryseobacterium indologenes) representing three of the four most dominant phyla found in maize roots...
March 8, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28261928/revegetation-rewilds-the-soil-bacterial-microbiome-of-an-old-field
#11
Nicholas J C Gellie, Jacob G Mills, Martin F Breed, Andrew J Lowe
Ecological restoration is a globally important and well-financed management intervention used to combat biodiversity declines and land degradation. Most restoration aims to increase biodiversity towards a reference state, but there are concerns that intended outcomes are not reached due to unsuccessful interventions and land use legacy issues. Monitoring biodiversity recovery is essential to measure success, however most projects remain insufficiently monitored. Current field-based methods are hard to standardise and are limited in their ability to assess important components of ecosystems, such as bacteria...
March 5, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28239038/effect-of-ageratina-adenophora-invasion-on-the-composition-and-diversity-of-soil-microbiome
#12
Yunhong Kong, James Kong, Dingkang Wang, Heping Huang, Kaiyou Geng, Yonxia Wang, Yun Xia
In the present study, high throughput 16S rRNA gene sequencing was used to investigate soil invaded by the aggressive weed Ageratina adenophora to determine its effect on the species composition, distribution, and biodiversity of the bacterial communities. Soil samples from 12 micro-sites containing a monoculture of A. adenophora plants, mixtures of A. adenophora and different native plant species, and native species alone were studied. We found that the invasion of this weed resulted in a selection of bacteria belonging to phyla Acidobacteria and Verrucomicrobia and the lack of bacteria belonging to phyla Actinobacteria and Planctomycetes, but did not affect significantly the percentage abundances of members of other phyla...
February 24, 2017: Journal of General and Applied Microbiology
https://www.readbyqxmd.com/read/28230180/assessment-of-chicken-carcass-microbiome-responses-during-processing-in-the-presence-of-commercial-antimicrobials-using-a-next-generation-sequencing-approach
#13
Sun Ae Kim, Si Hong Park, Sang In Lee, Casey M Owens, Steven C Ricke
The purpose of this study was to 1) identify microbial compositional changes on chicken carcasses during processing, 2) determine the antimicrobial efficacy of peracetic acid (PAA) and Amplon (blend of sulfuric acid and sodium sulfate) at a poultry processing pilot plant scale, and 3) compare microbial communities between chicken carcass rinsates and recovered bacteria from media. Birds were collected from each processing step and rinsates were applied to estimate aerobic plate count (APC) and Campylobacter as well as Salmonella prevalence...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28198425/organic-nitrogen-rearranges-both-structure-and-activity-of-the-soil-borne-microbial-seedbank
#14
Márcio F A Leite, Yao Pan, Jaap Bloem, Hein Ten Berge, Eiko E Kuramae
Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28195358/parkinson-s-disease-and-parkinson-s-disease-medications-have-distinct-signatures-of-the-gut-microbiome
#15
Erin M Hill-Burns, Justine W Debelius, James T Morton, William T Wissemann, Matthew R Lewis, Zachary D Wallen, Shyamal D Peddada, Stewart A Factor, Eric Molho, Cyrus P Zabetian, Rob Knight, Haydeh Payami
BACKGROUND: There is mounting evidence for a connection between the gut and Parkinson's disease (PD). Dysbiosis of gut microbiota could explain several features of PD. OBJECTIVE: The objective of this study was to determine if PD involves dysbiosis of gut microbiome, disentangle effects of confounders, and identify candidate taxa and functional pathways to guide research. METHODS: A total of 197 PD cases and 130 controls were studied. Microbial composition was determined by 16S rRNA gene sequencing of DNA extracted from stool...
February 14, 2017: Movement Disorders: Official Journal of the Movement Disorder Society
https://www.readbyqxmd.com/read/28190522/bioaugmentation-with-bacteria-selected-from-the-microbiome-enhances-arthrocnemum-macrostachyum-metal-accumulation-and-tolerance
#16
Salvadora Navarro-Torre, José M Barcia-Piedras, Miguel A Caviedes, Eloísa Pajuelo, Susana Redondo-Gómez, Ignacio D Rodríguez-Llorente, Enrique Mateos-Naranjo
A glasshouse experiment was designed to investigate the role of bacterial consortia isolated from the endosphere (CE) and rhizosphere (CR) of Arthrocnemum macrostachyum on its metal uptake capacity and tolerance in plants grown in metal polluted sediments. A. macrostachyum plants were randomly assigned to three bioaugmentation treatments (CE, CR and without inoculation) during 120days. Bioaugmentation with both bacterial consortia enhanced A. macrostachyum capacity to accumulate ions in its roots, while shoot ions concentration only increased with CE treatment...
February 10, 2017: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/28188207/use-of-endophytic-and-rhizosphere-bacteria-to-improve-phytoremediation-of-arsenic-contaminated-industrial-soils-by-autochthonous-betula-celtiberica
#17
Victoria Mesa, Alejandro Navazas, Ricardo González-Gil, Aida González, Nele Weyens, Béatrice Lauga, Jose Luis R Gallego, Jesús Sánchez, Ana Isabel Peláez
The aim of the study was to investigate the potential of indigenous arsenic-tolerant bacteria to enhance arsenic phytoremediation by autochthonous pseudometallophyte Betula celtiberica The first goal was to perform an initial analysis of the entire rhizosphere and endophytic bacterial communities of the above-named accumulator plant, including the cultivable bacterial species. B. celtiberica's microbiome was dominated by taxa related to Flavobacteriales, Burkholderiales, and Pseudomonadales, specially the Pseudomonas and Flavobacterium genera...
February 10, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28184370/metaproteomics-as-a-complementary-approach-to-gut-microbiota-in-health-and-disease
#18
REVIEW
Bernardo A Petriz, Octávio L Franco
Classic studies on phylotype profiling are limited to the identification of microbial constituents, where information is lacking about the molecular interaction of these bacterial communities with the host genome and the possible outcomes in host biology. A range of OMICs approaches have provided great progress linking the microbiota to health and disease. However, the investigation of this context through proteomic mass spectrometry-based tools is still being improved. Therefore, metaproteomics or community proteogenomics has emerged as a complementary approach to metagenomic data, as a field in proteomics aiming to perform large-scale characterization of proteins from environmental microbiota, such as the human gut...
2017: Frontiers in Chemistry
https://www.readbyqxmd.com/read/28177413/selenium-biofortification-and-phytoremediation-phytotechnologies-a-review
#19
Michela Schiavon, Elizabeth A H Pilon-Smits
The element selenium (Se) is both essential and toxic for most life forms, with a narrow margin between deficiency and toxicity. Phytotechnologies using plants and their associated microbes can address both of these problems. To prevent Se toxicity due to excess environmental Se, plants may be used to phytoremediate Se from soil or water. To alleviate Se deficiency in humans or livestock, crops may be biofortified with Se. These two technologies may also be combined: Se-enriched plant material from phytoremediation could be used as green fertilizer or as fortified food...
January 2017: Journal of Environmental Quality
https://www.readbyqxmd.com/read/28173617/specificity-of-root-microbiomes-in-native-grown-nicotiana-attenuata-and-plant-responses-to-uvb-increase-deinococcus-colonization
#20
Rakesh Santhanam, Youngjoo Oh, Ramesh Kumar, Arne Weinhold, Van Thi Luu, Karin Groten, Ian T Baldwin
Plants recruit microbial communities from the soil in which they germinate. Our understanding of the recruitment process and the factors affecting it is still limited for most microbial taxa. We analyzed several factors potentially affecting root microbiome structure - the importance of geographic location of natural populations, the microbiome of native seeds as putative source of colonization and the effect of a plant's response to UVB-exposure on root colonization of highly abundant species. The microbiome of Nicotiana attenuata seeds was determined by a culture-dependent and independent approach, and the root microbiome of natural N...
February 7, 2017: Molecular Ecology
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