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Plant microbiome

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https://www.readbyqxmd.com/read/29327481/the-genome-and-microbiome-of-a-dikaryotic-fungus-inocybe-terrigena-inocybaceae-revealed-by-metagenomics
#1
Mohammad Bahram, Dan Vanderpool, Mari Pent, Markus Hiltunen, Martin Ryberg
Recent advances in molecular methods have increased our understanding of various fungal symbioses. However, little is known about genomic and microbiome features of most uncultured symbiotic fungal clades. Here, we analysed the genome and microbiome of Inocybaceae (Agaricales, Basidiomycota), a largely uncultured ectomycorrhizal clade known to form symbiotic associations with a wide variety of plant species. We used metagenomic sequencing and assembly of dikaryotic fruiting-body tissues from Inocybe terrigena (Fr...
January 12, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/29327437/intra-species-variation-in-a-widely-distributed-tree-species-regulates-the-responses-of-soil-microbiome-to-different-temperature-regimes
#2
Cui-Jing Zhang, Manuel Delgado-Baquerizo, John E Drake, Peter B Reich, Mark G Tjoelker, David T Tissue, Jun-Tao Wang, Ji-Zheng He, Brajesh K Singh
Plant characteristics in different provenances within a single species may vary in response to climate change, which might alter soil microbial communities and ecosystem functions. We conducted a glasshouse experiment and grew seedlings of three provenances (temperate, subtropical and tropical origins) of a tree species (i.e. Eucalyptus tereticornis) at different growth temperatures (18, 21.5, 25, 28.5, 32 and 35.5°C) for 54 days. At the end of the experiment, bacterial and fungal community composition, diversity and abundance were characterized...
January 12, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/29319512/comparison-of-microbial-communities-associated-with-halophyte-salsola-stocksii-and-non-halophyte-triticum-aestivum-using-culture-independent-approaches
#3
Salma Mukhtar, Ayesha Ishaq, Sara Hassan, Samina Mehnaz, Muhammad S Mirza, Kauser A Malik
Halophyte microbiome contributes significantly to plant performance and can provide information regarding complex ecological processes involved in osmoregulation of these plants. The objective of this study is to investigate the microbiomes associated with belowground (rhizosphere), internal (endosphere) and aboveground (phyllosphere) tissues of halophyte (Salsola stocksii) through metagenomics approach. Plant samples were collected from Khewra Salt Mines. The metagenomic DNA from soil, root and shoot samples was isolated with the help of FastDNA spin kit...
September 27, 2017: Polish Journal of Microbiology
https://www.readbyqxmd.com/read/29314469/beneficial-changes-in-rumen-bacterial-community-profile-in-sheep-and-dairy-calves-as-a-result-of-feeding-the-probiotic-bacillus-amyloliquefaciens-h57
#4
Benjamin J Schofield, Nancy Lachner, Oanh T Le, David M McNeill, Peter Dart, Diane Ouwerkerk, Philip Hugenholtz, Athol V Klieve
AIMS: The probiotic Bacillus amyloliquefaciens H57 increased weight gain, increased nitrogen retention and increased feed intake in ruminants when administered to the diet. This study aims to develop a better understanding of this probiotic effect by analysing changes in the rumen prokaryotic community. METHODS AND RESULTS: Sequencing the 16S rRNA gene PCR amplicons of the rumen microbiome, revealed that ewes fed H57 had a significantly different rumen microbial community structure to Control sheep...
January 3, 2018: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/29310579/gene-trait-matching-across-the-bifidobacterium-longum-pan-genome-reveals-considerable-diversity-in-carbohydrate-catabolism-among-human-infant-strains
#5
Silvia Arboleya, Francesca Bottacini, Mary O'Connell-Motherway, C Anthony Ryan, R Paul Ross, Douwe van Sinderen, Catherine Stanton
BACKGROUND: Bifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, thus indicative of a close symbiotic host-microbe relationship. Different mechanisms may be responsible for the high competitiveness of this taxon in its human host to allow stable establishment in the complex and dynamic intestinal microbiota environment. The objective of this study was to assess the genetic and metabolic diversity in a set of 20 B...
January 8, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29298729/grapevine-rootstocks-shape-underground-bacterial-microbiome-and-networking-but-not-potential-functionality
#6
Ramona Marasco, Eleonora Rolli, Marco Fusi, Grégoire Michoud, Daniele Daffonchio
BACKGROUND: The plant compartments of Vitis vinifera, including the rhizosphere, rhizoplane, root endosphere, phyllosphere and carposphere, provide unique niches that drive specific bacterial microbiome associations. The majority of phyllosphere endophytes originate from the soil and migrate up to the aerial compartments through the root endosphere. Thus, the soil and root endosphere partially define the aerial endosphere in the leaves and berries, contributing to the terroir of the fruit...
January 3, 2018: Microbiome
https://www.readbyqxmd.com/read/29291559/spatiotemporal-changes-in-bacterial-community-and-microbial-activity-in-a-full-scale-drinking-water-treatment-plant
#7
Luanfeng Hou, Qin Zhou, Qingping Wu, Qihui Gu, Ming Sun, Jumei Zhang
To gain insight into the bacterial dynamics present in drinking water treatment (DWT) systems, the microbial community and activity in a full-scale DWT plant (DWTP) in Guangzhou, South China, were investigated using Illumina Hiseq sequencing analyses combined with cultivation-based techniques during the wet and dry seasons. Illumina sequencing analysis of 16S rRNA genes revealed a large shift in the proportion of Actinobacteria, Proteobacteria and Firmicutes during the treatment process, with the proportion of Actinobacteria decreased sharply, whereas that of Proteobacteria and Firmicutes increased and predominated in treated water...
December 29, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29282153/under-control-how-a-dietary-additive-can-restore-the-gut-microbiome-and-proteomic-profile-and-improve-disease-resilience-in-a-marine-teleostean-fish-fed-vegetable-diets
#8
María Carla Piazzon, Josep Alvar Calduch-Giner, Belén Fouz, Itziar Estensoro, Paula Simó-Mirabet, Mónica Puyalto, Vasileios Karalazos, Oswaldo Palenzuela, Ariadna Sitjà-Bobadilla, Jaume Pérez-Sánchez
BACKGROUND: The constant increase of aquaculture production and wealthy seafood consumption has forced the industry to explore alternative and more sustainable raw aquafeed materials, and plant ingredients have been used to replace marine feedstuffs in many farmed fish. The objective of the present study was to assess whether plant-based diets can induce changes in the intestinal mucus proteome, gut autochthonous microbiota and disease susceptibility of fish, and whether these changes could be reversed by the addition of sodium butyrate to the diets...
December 28, 2017: Microbiome
https://www.readbyqxmd.com/read/29281673/taxonomic-differences-of-gut-microbiomes-drive-cellulolytic-enzymatic-potential-within-hind-gut-fermenting-mammals
#9
Emma C L Finlayson-Trick, Landon J Getz, Patrick D Slaine, Mackenzie Thornbury, Emily Lamoureux, Jamie Cook, Morgan G I Langille, Lois E Murray, Craig McCormick, John R Rohde, Zhenyu Cheng
Host diet influences the diversity and metabolic activities of the gut microbiome. Previous studies have shown that the gut microbiome provides a wide array of enzymes that enable processing of diverse dietary components. Because the primary diet of the porcupine, Erethizon dorsatum, is lignified plant material, we reasoned that the porcupine microbiome would be replete with enzymes required to degrade lignocellulose. Here, we report on the bacterial composition in the porcupine microbiome using 16S rRNA sequencing and bioinformatics analysis...
2017: PloS One
https://www.readbyqxmd.com/read/29274958/mining-metagenomic-and-metatranscriptomic-data-for-clues-about-microbial-metabolic-functions-in-ruminants
#10
Fuyong Li, Andre L A Neves, Bibaswan Ghoshal, Le Luo Guan
Metagenomics and metatranscriptomics can capture the whole genome and transcriptome repertoire of microorganisms through sequencing total DNA/RNA from various environmental samples, providing both taxonomic and functional information with high resolution. The unique and complex rumen microbial ecosystem is receiving great research attention because the rumen microbiota coevolves with the host and equips ruminants with the ability to convert cellulosic plant materials to high-protein products for human consumption...
December 20, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29247170/harnessing-the-microbiomes-of-brassica-vegetables-for-health-issues
#11
Birgit Wassermann, Daria Rybakova, Christina Müller, Gabriele Berg
Plant health is strongly connected with plants´ microbiome. In case of raw-eaten plants, the microbiome can also affect human health. To study potential impacts on health issues of both hosts, the microbiome composition of seven different Brassica vegetables, originating from different food processing pathways, was analyzed by a combined approach of amplicon sequencing, metagenomic mining and cultivation. All Brassica vegetables harbored a highly diverse microbiota as identified by 16S rRNA gene amplicon sequencing...
December 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29244059/the-mediterranean-diet-metabolic-and-molecular-mechanisms
#12
Valeria Tosti, Beatrice Bertozzi, Luigi Fontana
Consuming a Mediterranean diet rich in minimally processed plant foods has been associated with a reduced risk of developing multiple chronic diseases and increased life expectancy. Data from several randomized clinic trials have demonstrated a beneficial effect in the primary and secondary prevention of cardiovascular disease, type 2 diabetes, atrial fibrillation and breast cancer. The exact mechanism by which an increased adherence to the traditional Mediterranean diet exerts its favorable effects is not known...
December 13, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/29238751/tree-leaf-bacterial-community-structure-and-diversity-differ-along-a-gradient-of-urban-intensity
#13
Isabelle Laforest-Lapointe, Christian Messier, Steven W Kembel
Tree leaf-associated microbiota have been studied in natural ecosystems but less so in urban settings, where anthropogenic pressures on trees could impact microbial communities and modify their interaction with their hosts. Additionally, trees act as vectors spreading bacterial cells in the air in urban environments due to the density of microbial cells on aerial plant surfaces. Characterizing tree leaf bacterial communities along an urban gradient is thus key to understand the impact of anthropogenic pressures on urban tree-bacterium interactions and on the overall urban microbiome...
November 2017: MSystems
https://www.readbyqxmd.com/read/29238353/rhizosphere-microbiome-recruited-from-a-suppressive-compost-improves-plant-fitness-and-increases-protection-against-vascular-wilt-pathogens-of-tomato
#14
Anastasis Antoniou, Maria-Dimitra Tsolakidou, Ioannis A Stringlis, Iakovos S Pantelides
Suppressive composts represent a sustainable approach to combat soilborne plant pathogens and an alternative to the ineffective chemical fungicides used against those. Nevertheless, suppressiveness to plant pathogens and reliability of composts are often inconsistent with unpredictable effects. While suppressiveness is usually attributed to the compost's microorganisms, the mechanisms governing microbial recruitment by the roots and the composition of selected microbial communities are not fully elucidated...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29236466/honokiol-inspired-analogs-as-inhibitors-of-oral-bacteria
#15
Amy E Solinski, Cristian Ochoa, Young Eun Lee, Thomas Paniak, Marisa C Kozlowski, William M Wuest
The oral microbiome is a complex ecological niche where both commensal and pathogenic bacteria coexist. Previous reports have cited that the plant isolate honokiol is a potent inhibitor of S. mutans biofilms. Herein we report a cross-coupling method that provides access to a concise library of honokiol-inspired analogs. Through this work we determined that the inhibitory activity of honokiol is highly dependent on the growth conditions. Further, we identify a series of analogs that display significant potency against oral bacteria leading to the discovery of a potent antimicrobial...
December 13, 2017: ACS Infectious Diseases
https://www.readbyqxmd.com/read/29218571/culturable-endophytic-bacteria-of-ginger-rhizome%C3%A2-and-their-remarkable-multi-trait-plant-growth-promoting-features
#16
Sabu Rohini, R Aswani, M Kannan, V P Sylas, E K Radhakrishnan
Functional contribution of endophytic bacteria towards plant growth is highly impressive due to their species diversity and array of probiotic mechanisms. In the study, 96 endophytic bacteria isolated from rhizome of ginger (Zingiber officinale) were screened for phosphate solubilisation, 1-amino cyclopropane-1-carboxylate (ACC) deaminase activity, nitrogen fixation, ammonia and IAA production. Among these, sixteen endophytes with multiple plant growth-promoting activities were identified by 16S rDNA sequencing and all of them showed growth enhancement in Vigna unguiculata var Lola which make the study remarkably significant...
December 7, 2017: Current Microbiology
https://www.readbyqxmd.com/read/29215202/context-dependent-vertical-transmission-shapes-strong-endosymbiont-community-structure-in-the-pea-aphid-acyrthosiphon-pisum
#17
Danielle I Rock, Andrew H Smith, Jonah Joffe, Amie Albertus, Narayan Wong, Michael O'Connor, Kerry M Oliver, Jacob A Russell
Animal-associated microbiomes are often comprised of structured, multi-species communities, with particular microbes showing trends of co-occurrence or exclusion. Such structure suggests variable community stability, or variable costs and benefits-possibilities with implications for symbiont-driven host adaptation. In this study, we performed systematic screening for maternally transmitted, facultative endosymbionts of the pea aphid, Acyrthosiphon pisum. Sampling across six locales, with up to five years of collection in each, netted significant and consistent trends of community structure...
December 7, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29200959/polyphenols-and-health-interactions-between-fibre-plant-polyphenols-and-the-gut-microbiota
#18
C A Edwards, J Havlik, W Cong, W Mullen, T Preston, D J Morrison, E Combet
A high-fibre diet and one rich in fruit and vegetables have long been associated with lower risk of chronic disease. There are several possible mechanisms underpinning these associations, but one likely important factor is the production of bioactive molecules from plant-based foods by the bacteria in the colon. This links to our growing understanding of the role of the gut microbiome in promoting health. Polyphenolic-rich plant foods have been associated with potential health effects in many studies, but the bioavailability of polyphenol compounds, as eaten, is often very low...
December 2017: Nutrition Bulletin
https://www.readbyqxmd.com/read/29192219/symbionts-protect-aphids-from-parasitic-wasps-by-attenuating-herbivore-induced-plant-volatiles
#19
Enric Frago, Mukta Mala, Berhane T Weldegergis, Chenjiao Yang, Ailsa McLean, H Charles J Godfray, Rieta Gols, Marcel Dicke
Plants respond to insect attack by releasing blends of volatile chemicals that attract their herbivores' specific natural enemies, while insect herbivores may carry endosymbiotic microorganisms that directly improve herbivore survival after natural enemy attack. Here we demonstrate that the two phenomena can be linked. Plants fed upon by pea aphids release volatiles that attract parasitic wasps, and the pea aphid can carry facultative endosymbiotic bacteria that prevent the development of the parasitic wasp larva and thus markedly improve aphid survival after wasp attack...
November 30, 2017: Nature Communications
https://www.readbyqxmd.com/read/29191163/antibiotic-resistant-bacteria-in-the-guts-of-insects-feeding-on-plants-prospects-for-discovering-plant-derived-antibiotics
#20
Katarzyna Ignasiak, Anthony Maxwell
BACKGROUND: Although plants produce many secondary metabolites, currently none of these are commercial antibiotics. Insects feeding on specific plants can harbour bacterial strains resistant to known antibiotics suggesting that compounds in the plant have stimulated resistance development. We sought to determine whether the occurrence of antibiotic-resistant bacteria in insect guts was a widespread phenomenon, and whether this could be used as a part of a strategy to identify antibacterial compounds from plants...
December 1, 2017: BMC Microbiology
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