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Plant microbiome

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https://www.readbyqxmd.com/read/28735410/rhizosphere-sampling-protocols-for-microbiome-16s-18s-its-rrna-library-preparation-and-enrichment-for-the-isolation-of-drought-tolerance-promoting-microbes
#1
Venkatachalam Lakshmanan, Prasun Ray, Kelly D Craven
Natural plant microbiomes are abundant and have a remarkably robust composition, both as epiphytes on the plant surface and as endophytes within plant tissues. Microbes in the former "habitat" face limited nutrients and harsh environmental conditions, while those in the latter likely lead a more sheltered existence. The most populous and diverse of these microbiomes are associated with the zone around the plant roots, commonly referred to as the rhizosphere. A majority of recent studies characterize these plant-associated microbiomes by community profiling of bacteria and fungi, using amplicon-based marker genes and next-generation sequencing (NGS)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28735391/toward-a-resilient-functional-microbiome-drought-tolerance-alleviating-microbes-for-sustainable-agriculture
#2
Venkatachalam Lakshmanan, Prasun Ray, Kelly D Craven
In recent years, the utilization of novel sequencing techniques opened a new field of research into plant microbiota and was used to explore a wide diversity of microorganisms both inside and outside of plant host tissues, i.e., the endosphere and rhizosphere, respectively. An early realization from such research was that species richness and diversity of the plant microbiome are both greater than believed even a few years ago, and soil is likely home to the most abundant and diverse microbial habitats known...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28732267/understanding-the-holobiont-the-interdependence-of-plants-and-their-microbiome
#3
REVIEW
Carmen Sánchez-Cañizares, Beatriz Jorrín, Philip S Poole, Andrzej Tkacz
The holobiont is composed by the plant and its microbiome. In a similar way to ecological systems of higher organisms, the holobiont shows interdependent and complex dynamics [1,2]. While plants originate from seeds, the microbiome has a multitude of sources. The assemblage of these communities depends on the interaction between the emerging seedling and its surrounding environment, with soil being the main source. These microbial communities are controlled by the plant through different strategies, such as the specific profile of root exudates and its immune system...
July 18, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28732264/insights-into-plant-phosphate-sensing-and-signaling
#4
REVIEW
Byung-Kook Ham, Jieyu Chen, Yan Yan, William J Lucas
Phosphorus (P) is a macronutrient essential for plant growth, therefore, soil P level is critical to crop yield potential in agriculture. As Pi levels limit crop yield under many soil conditions, it is crucial to understand the mechanisms by which plants adapt to low-phosphate (Pi) soil conditions and interact with their soil microbiome to improve crop P use efficiency, in order to ensure global food security. Recent advances have been made towards achieving this goal through advancing our understanding of the plant's response to limiting Pi conditions to maintain P homeostasis...
July 18, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28731473/ninety-nine-de-novo-assembled-genomes-from-the-moose-alces-alces-rumen-microbiome-provide-new-insights-into-microbial-plant-biomass-degradation
#5
Olov Svartström, Johannes Alneberg, Nicolas Terrapon, Vincent Lombard, Ino de Bruijn, Jonas Malmsten, Ann-Marie Dalin, Emilie El Muller, Pranjul Shah, Paul Wilmes, Bernard Henrissat, Henrik Aspeborg, Anders F Andersson
The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28730551/pseudomonas-fluorescens-r68-assisted-enhancement-in-growth-and-fertilizer-utilization-of-amaranthus-tricolor-l
#6
C Jimtha John, P Jishma, N R Karthika, K S Nidheesh, J G Ray, Jyothis Mathew, E K Radhakrishnan
Plant probiotic potential of rhizosphere microbiome and its role in phytofertilizer mobilization are largely unexplored. In the current study, the rhizobacterium Pseudomonas fluorescens R68 (PFR68) isolated from Western Ghat was analyzed for its growth enhancement effect on the leafy vegetable Amaranthus tricolor (L.). One month of field growth of PFR68 inoculated A. tricolor has found to have enhanced growth parameters such as leaf number (1.57 fold), root number (1.76 fold), shoot length (1.28 fold) and fresh weight (2...
August 2017: 3 Biotech
https://www.readbyqxmd.com/read/28729641/the-rhizosphere-microbiome-of-burned-holm-oak-potential-role-of-the-genus-arthrobacter-in-the-recovery-of-burned-soils
#7
Antonio J Fernández-González, Pilar Martínez-Hidalgo, José F Cobo-Díaz, Pablo J Villadas, Eustoquio Martínez-Molina, Nicolás Toro, Susannah G Tringe, Manuel Fernández-López
After a forest wildfire, the microbial communities have a transient alteration in their composition. The role of the soil microbial community in the recovery of an ecosystem following such an event remains poorly understood. Thus, it is necessary to understand the plant-microbe interactions that occur in burned soils. By high-throughput sequencing, we identified the main bacterial taxa of burnt holm-oak rhizosphere, then we obtained an isolate collection of the most abundant genus and its growth promoting activities were characterised...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28728852/in%C3%A2-vitro-characteristics-of-an-atlantic-salmon-salmo-salar-l-hind-gut-microbial-community-in-relation-to-different-dietary-treatments
#8
Kamarul Zaman Zarkasi, Richard S Taylor, Brett D Glencross, Guy C J Abell, Mark L Tamplin, John P Bowman
In this study, microbial community dynamics were assessed within a simple in vitro model system in order to understand those changes influenced by diet. The abundance and diversity of bacteria were monitored within different treatment slurries inoculated with salmon faecal samples in order to mimic the effects of dietary variables. A total of five complete diets and two ingredients (plant meal) were tested. The total viable counts (TVCs) and sequencing data revealed that there was very clear separation between the complete diets and the plant meal treatments, suggesting a dynamic response by the allochthonous bacteria to the treatments...
July 17, 2017: Research in Microbiology
https://www.readbyqxmd.com/read/28727425/the-database-and-bioinformatics-studies-of-probiotics
#9
Lin Tao, Bohua Wang, Yafen Zhong, Siok Hoon Pow, Xian Zeng, Chu Qin, Peng Zhang, Shangying Chen, Weidong He, Ying Tan, Hongxia Liu, Yuyang Jiang, Weiping Chen, Yu Zong Chen
Probiotics have been widely explored for health benefits, animal cares, and agricultural applications. Recent advances in microbiome, microbiota and microbial dark matter research have fueled greater interests in and paved ways for the study of the mechanisms of probiotics and the discovery of new probiotics from uncharacterized microbial sources. A probiotics database named PROBIO was developed to facilitate these efforts and the need for the information of the known probiotics, which provides the comprehensive information about the probiotic functions of 448 marketed, 167 clinical trial/field trial and 382 research probiotics for use or being studied for use in humans, animals, and plants...
July 20, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28720730/drought-stress-results-in-a-compartment-specific-restructuring-of-the-rice-root-associated-microbiomes
#10
Christian Santos-Medellín, Joseph Edwards, Zachary Liechty, Bao Nguyen, Venkatesan Sundaresan
Plant roots support complex microbial communities that can influence plant growth, nutrition, and health. While extensive characterizations of the composition and spatial compartmentalization of these communities have been performed in different plant species, there is relatively little known about the impact of abiotic stresses on the root microbiota. Here, we have used rice as a model to explore the responses of root microbiomes to drought stress. Using four distinct genotypes, grown in soils from three different fields, we tracked the drought-induced changes in microbial composition in the rhizosphere (the soil immediately surrounding the root), the endosphere (the root interior), and unplanted soils...
July 18, 2017: MBio
https://www.readbyqxmd.com/read/28715992/the-hibernator-microbiome-host-bacterial-interactions-in-an-extreme-nutritional-symbiosis
#11
Hannah V Carey, Fariba M Assadi-Porter
Animals that undergo seasonal cycles of feeding and fasting have adaptations that maintain integrity of organ systems when dietary nutrients are lacking. Food deprivation also challenges the gut microbiota, which relies heavily on host diet for metabolic substrates and the gastrointestinal tract, which is influenced by enteral nutrients and microbial activity. Winter fasting in hibernators shifts the microbiota to favor taxa with the capacity to degrade and utilize host-derived substrates and disfavor taxa that prefer complex plant polysaccharides...
July 17, 2017: Annual Review of Nutrition
https://www.readbyqxmd.com/read/28710849/long-distance-dispersal-of-fungi
#12
Jacob J Golan, Anne Pringle
Dispersal is a fundamental biological process, operating at multiple temporal and spatial scales. Despite an increasing understanding of fungal biodiversity, most research on fungal dispersal focuses on only a small fraction of species. Thus, any discussion of the dispersal dynamics of fungi as a whole is problematic. While abundant morphological and biogeographic data are available for hundreds of species, researchers have yet to integrate this information into a unifying paradigm of fungal dispersal, especially in the context of long-distance dispersal (LDD)...
July 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28702033/how-streptomyces-anulatus-primes-grapevine-defenses-to-cope-with-gray-mold-a-study-of-the-early-responses-of-cell-suspensions
#13
Parul Vatsa-Portugal, Aziz Aziz, Marine Rondeau, Sandra Villaume, Hamid Morjani, Christophe Clément, Essaid Ait Barka
Gray mold, caused by Botrytis cinerea, is one of the most destructive diseases of grapevine and is controlled with an intense application of fungicides. As alternatives to chemicals, beneficial microbes may promote plant health by stimulating the plant's immune system. An actinomycete, Streptomyces anulatus S37, has been screened from the rhizosphere microbiome of healthy Vitis vinifera on the basis of its ability to promote grapevine growth and to induce resistance against various phytopathogens, including B...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28696777/therapeutic-uses-of-triphala-in-ayurvedic-medicine
#14
Christine Tara Peterson, Kate Denniston, Deepak Chopra
AIM: The aim of this article is to review the current literature on the therapeutic uses and efficacy of Triphala. Herbal remedies are among the most ancient medicines used in traditional systems of healthcare such as Ayurveda. Triphala, a well-recognized and highly efficacious polyherbal Ayurvedic medicine consisting of fruits of the plant species Emblica officinalis (Amalaki), Terminalia bellerica (Bibhitaki), and Terminalia chebula (Haritaki), is a cornerstone of gastrointestinal and rejuvenative treatment...
July 11, 2017: Journal of Alternative and Complementary Medicine: Research on Paradigm, Practice, and Policy
https://www.readbyqxmd.com/read/28696064/harnessing-microbiome-based-biotechnologies-for-sustainable-mitigation-of-nitrous-oxide-emissions
#15
Hang-Wei Hu, Ji-Zheng He, Brajesh K Singh
Achieving the Sustainable Development Goal of climate change mitigation within this century will require adoption of new innovative technologies to control emissions of nitrous oxide (N2 O), an important greenhouse gas leading to global warming. This is particularly important in the face of growing fertilizer consumption and continuous land degradation. Currently used tools to mitigate N2 O emissions are based on agrochemical inputs and agronomic practices. Emerging technologies include plant breeding approaches to manipulate microbiome activities in agro-ecosystems, and microbial biotechnology approaches for in situ microbiome manipulation and engineering via use of biochemical, cellular and genome-editing methods...
July 11, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28696041/the-contribution-of-microbial-biotechnology-to-sustainable-development-goals-microbiome-therapies
#16
Paul W O'Toole, Max Paoli
Complex communities of microbes live on and in plants, humans and other animals. These communities are collectively referred to as the microbiota or microbiome. Plants and animals evolved to co-exist with these microbes. In mammals, particular kinds of alteration of the microbiome (dysbiosis) are associated with loss of health, most likely due to loss of microbial metabolites, signalling molecules, or regulators of host pathways. Modern life-style diseases such as Inflammatory Bowel Disease (IBD), Irritable Bowel Syndrome (IBS), type 2 diabetes, obesity and metabolic syndrome have been linked to dysbiosis...
July 11, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28690680/from-grass-to-gas-microbiome-dynamics-of-grass-biomass-acidification-under-mesophilic-and-thermophilic-temperatures
#17
Christian Abendroth, Claudia Simeonov, Juli Peretó, Oreto Antúnez, Raquel Gavidia, Olaf Luschnig, Manuel Porcar
BACKGROUND: Separating acidification and methanogenic steps in anaerobic digestion processes can help to optimize the process and contribute to producing valuable sub-products such as methane, hydrogen and organic acids. However, the full potential of this technology has not been fully explored yet. To assess the underlying fermentation process in more detail, a combination of high-throughput sequencing and proteomics on the acidification step of plant material (grass) at both mesophilic and thermophilic temperatures (37 and 55 °C, respectively) was applied for the first time...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28688926/microbes-from-mined-sites-harnessing-their-potential-for-reclamation-of-derelict-mine-sites
#18
REVIEW
Palanisami Thavamani, R Amos Samkumar, Viswanathan Satheesh, Suresh R Subashchandrabose, Kavitha Ramadass, Ravi Naidu, Kadiyala Venkateswarlu, Mallavarapu Megharaj
Derelict mines pose potential risks to environmental health. Several factors such as soil structure, organic matter, and nutrient content are the greatly affected qualities in mined soils. Soil microbial communities are an important element for successful reclamation because of their major role in nutrient cycling, plant establishment, geochemical transformations, and soil formation. Yet, microorganisms generally remain an undervalued asset in mined sites. The microbial diversity in derelict mine sites consists of diverse species belonging to four key phyla: Proteobacteria, Acidobacteria, Firmicutes, and Bacteroidetes...
July 6, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28686570/using-metagenomics-to-connect-microbial-community-biodiversity-and-functions
#19
Lucas William Mendes, Lucas Peres Palma Braga, Acacio Aparecido Navarrete, Dennis Goss de Souza, Genivaldo Gueiros Zacarias Silva, Siu Mui Tsai
Microbes constitute about a third of the Earth's biomass and are composed by an enormous genetic diversity. In a majority of environments the microbial communities play crucial roles for the ecosystem functioning, where a drastic biodiversity alteration or loss could lead to negative effects on the environment and sustainability. A central goal in microbiome studies is to elucidate the relation between microbial diversity to functions. A better understanding of the relation diversity-function would increase the ability to manipulate that diversity to improve plant and animal health and also setting conservation priorities...
July 6, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28680437/knots-untie-molecular-determinants-involved-in-knot-formation-induced-by-pseudomonas-savastanoi-in-woody-hosts
#20
REVIEW
Eloy Caballo-Ponce, Jesús Murillo, Marta Martínez-Gil, Alba Moreno-Pérez, Adrián Pintado, Cayo Ramos
The study of the molecular basis of tree diseases is lately receiving a renewed attention, especially with the emerging perception that pathogens require specific pathogenicity and virulence factors to successfully colonize woody hosts. Pathosystems involving woody plants are notoriously difficult to study, although the use of model bacterial strains together with genetically homogeneous micropropagated plant material is providing a significant impetus to our understanding of the molecular determinants leading to disease...
2017: Frontiers in Plant Science
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