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https://www.readbyqxmd.com/read/28929212/an-insight-into-phage-diversity-at-environmental-habitats-using-comparative-metagenomics-approach
#1
Krupa Parmar, Nishant Dafale, Rajesh Pal, Hitesh Tikariha, Hemant Purohit
Bacteriophages play significant role in driving microbial diversity; however, little is known about the diversity of phages in different ecosystems. A dynamic predator-prey mechanism called "kill the winner" suggests the elimination of most active bacterial populations through phages. Thus, interaction between phage and host has an effect on the composition of microbial communities in ecosystems. In this study, secondary phage metagenome data from aquatic habitats: wastewater treatment plant (WWTP), fresh, marine, and hot water spring habitat were analyzed using MG-RAST and STAMP tools to explore the diversity of the viruses...
September 19, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28926236/biofilms-benefiting-plants-exposed-to-zno-and-cuo-nps-studied-with-a-root-mimetic-hollow-fiber-membrane
#2
Michelle Bonebrake, Kaitlyn C Anderson, Jonathan Valiente, Astrid Rosa Jacobson, Joan E McLean, Anne J Anderson, David W Britt
Plants exist with a consortium of microbes that influence plant health, including response to biotic and abiotic stress. While nanoparticle (NP) - plant interactions are increasingly studied, the effect of NPs on the plant microbiome is less researched. Here a root-mimetic hollow fiber membrane (HFM) is presented for generating biofilms of plant-associated microbes nurtured by artificial root exudates (AREs) to correlate exudate composition with biofilm formation and response to NPs. Two microbial isolates from field-grown wheat, a bacillus endophyte and a pseudomonad root surface colonizer, were examined on HFMs fed with AREs varying in N and C composition...
September 19, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28905991/target-of-rapamycin-signaling-orchestrates-growth-defense-trade-offs-in-plants
#3
David De Vleesschauwer, Osvaldo Filipe, Gena Hoffman, Hamed Soren Seifi, Ashley Haeck, Patrick Canlas, Jonas Van Bockhaven, Evelien De Waele, Kristof Demeestere, Pamela Ronald, Monica Hofte
Plant defense to microbial pathogens is often accompanied by significant growth inhibition. How plants merge immune system function with normal growth and development is still poorly understood. Here, we investigated the role of target of rapamycin (TOR), an evolutionary conserved serine/threonine kinase, in the plant defense response. We used rice as a model system and applied a combination of chemical, genetic, genomic and cell-based analyses. We demonstrate that ectopic expression of TOR and Raptor (regulatory-associated protein of mTOR), a protein previously demonstrated to interact with TOR in Arabidopsis, positively regulates growth and development in rice...
September 14, 2017: New Phytologist
https://www.readbyqxmd.com/read/28900218/sources-of-variation-in-the-gut-microbial-community-of-lycaeides-melissa-caterpillars
#4
Samridhi Chaturvedi, Alexandre Rego, Lauren K Lucas, Zachariah Gompert
Microbes can mediate insect-plant interactions and have been implicated in major evolutionary transitions to herbivory. Whether microbes also play a role in more modest host shifts or expansions in herbivorous insects is less clear. Here we evaluate the potential for gut microbial communities to constrain or facilitate host plant use in the Melissa blue butterfly (Lycaeides melissa). We conducted a larval rearing experiment where caterpillars from two populations were fed plant tissue from two hosts. We used 16S rRNA sequencing to quantify the relative effects of sample type (frass versus whole caterpillar), diet (plant species), butterfly population and development (caterpillar age) on the composition and diversity of the caterpillar gut microbial communities, and secondly, to test for a relationship between microbial community and larval performance...
September 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28900190/soil-microbial-carbon-utilization-enzyme-activities-and-nutrient-availability-responses-to-bidens-pilosa-and-a-non-invasive-congener-under-different-irradiances
#5
Hui Wei, Wenbin Yan, Guoming Quan, Jiaen Zhang, Kaiming Liang
Two Bidens species (Bidens pilosa and B. bipinnata) that originate from America have been introduced widely in pan-tropics, with the former regarded as a noxious invasive weed whereas the latter naturalized as a plant resource. Whether the two species exhibit different effects on the belowground system remains rarely studied. This study was conducted to investigate soil microbial carbon (C) utilization, enzyme activities and available nitrogen, phosphorus and potassium contents under the two species in a subtropical garden soil of southern China under different levels of light intensity...
September 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28892269/bacteria-utilising-plant-derived-carbon-in-the-rhizosphere-of-triticum-aestivum-change-in-different-depths-of-an-arable-soil
#6
Marie Uksa, Franz Buegger, Silvia Gschwendtner, Tillmann Lueders, Susanne Kublik, Timo Kautz, Miriam Athmann, Ulrich Köpke, Jean Charles Munch, Michael Schloter, Doreen Fischer
Root exudates shape microbial communities at the plant soil interface. Here we compared bacterial communities that utilise plant-derived carbon in the rhizosphere of wheat in different soil depths, including topsoil, as well as two subsoil layers up to 1 m depth. The experiment was performed in a green house using soil monoliths with intact soil structure taken from an agricultural field. To identify bacteria utilizing plant derived carbon, (13) C-CO2 labelling of plants was performed for two weeks at the EC50 stage, followed by stable isotope probing of extracted DNA from the rhizosphere combined with 16S rRNA gene-based amplicon sequencing...
September 11, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28887483/responses-of-plant-species-diversity-and-soil-physical-chemical-microbial-properties-to-phragmites-australis-invasion-along-a-density-gradient
#7
M D Nazim Uddin, Randall William Robinson
The invasion of ecosystems by strongly colonising plants such as Phragmites australis is viewed as one of the greatest threats to plant diversity and soil properties. This study compared a range of diversity measures including soil properties and mycorrhizal potential under different degrees of Phragmites density among three populations in coastal wetland, Victoria, Australia. Species richness, evenness and Shanon-Wiener index had significantly higher values in low degree of Phragmites density in all populations...
September 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28886679/microbial-expansins
#8
Daniel J Cosgrove
Expansins are small proteins that loosen plant cell walls and cellulosic materials without lytic activity. First discovered in plants, expansin genes are found in the genomes of numerous bacteria and fungi that interact with plants in pathogenic and mutualistic patterns, as well as in microbes that feed on plant debris. Horizontal gene transfer from plants to microbes and between microbes accounts for expansins' irregular taxonomic distribution. Expansins facilitate plant colonization by Bacillus, Clavibacter, and Trichoderma species, a list likely to grow as knowledge of microbial expansin function deepens...
September 8, 2017: Annual Review of Microbiology
https://www.readbyqxmd.com/read/28880994/live-long-and-prosper-plant-soil-feedback-lifespan-and-landscape-abundance-covary
#9
Andrew Kulmatiski, Karen H Beard, Jeanette Norton, Justin Heavilin, Leslie Forero, Josephine Grenzer
Plant soil feedbacks (PSFs) are thought to be important to plant growth and species coexistence, but most support for these hypotheses is derived from short-term greenhouse experiments. Here we use a seven-year, common garden experiment to measure PSFs for seven native and six non-native species common to the western USA. We use these long-term, field-based estimates to test correlations between PSF and plant landscape abundance, species origin, functional type and lifespan. To assess potential PSF mechanisms, we also measured soil microbial community composition, root biomass, nitrogen cycling, bulk density, penetration resistance, and shear strength...
September 7, 2017: Ecology
https://www.readbyqxmd.com/read/28878756/analysis-of-microbial-functions-in-the-rhizosphere-using-a-metabolic-network-based-framework-for-metagenomics-interpretation
#10
Shany Ofaim, Maya Ofek-Lalzar, Noa Sela, Jiandong Jinag, Yechezkel Kashi, Dror Minz, Shiri Freilich
Advances in metagenomics enable high resolution description of complex bacterial communities in their natural environments. Consequently, conceptual approaches for community level functional analysis are in high need. Here, we introduce a framework for a metagenomics-based analysis of community functions. Environment-specific gene catalogs, derived from metagenomes, are processed into metabolic-network representation. By applying established ecological conventions, network-edges (metabolic functions) are assigned with taxonomic annotations according to the dominance level of specific groups...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28878351/tillage-and-nitrogen-fertilization-enhanced-belowground-carbon-allocation-and-plant-nitrogen-uptake-in-a-semi-arid-canola-crop-soil-system
#11
Jharna Rani Sarker, Bhupinder Pal Singh, Xinhua He, Yunying Fang, Guangdi D Li, Damian Collins, Annette L Cowie
Carbon (C) and nitrogen (N) allocation and assimilation are coupled processes, likely influencing C accumulation, N use efficiency and plant productivity in agro-ecosystems. However, dynamics and responses of these processes to management practices in semi-arid agro-ecosystems are poorly understood. A field-based (13)CO2 and urea-(15)N pulse labelling experiment was conducted to track how C and N allocation and assimilation during canola growth from flowering to maturity were affected by short-term (2-year) tillage (T) and no-till (NT) with or without 100 kg urea-N ha(-1) (T-0, T-100, NT-0, NT-100) on a Luvisol in an Australian semi-arid region...
September 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28875273/host-genotype-and-nitrogen-form-shape-the-root-microbiome-of-pinus-radiata
#12
Marta Gallart, Karen L Adair, Jonathan Love, Dean F Meason, Peter W Clinton, Jianming Xue, Matthew H Turnbull
A central challenge in community ecology is understanding the role that phenotypic variation among genotypes plays in structuring host-associated communities. While recent studies have investigated the relationship between plant genotype and the composition of soil microbial communities, the effect of genotype-by-environment interactions on the plant microbiome remains unclear. In this study, we assessed the influence of tree genetics (G), nitrogen (N) form and genotype-by-environment interaction (G x N) on the composition of the root microbiome...
September 5, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28869082/development-of-botanicals-to-combat-antibiotic-resistance
#13
REVIEW
Pooja D Gupta, Tannaz J Birdi
The discovery of antibiotics in the previous century lead to reduction in mortality and morbidity due to infectious diseases but their inappropriate and irrational use has resulted in emergence of resistant microbial populations. Alteration of target sites, active efflux of drugs and enzymatic degradations are the strategies employed by the pathogenic bacteria to develop intrinsic resistance to antibiotics. This has led to an increased interest in medicinal plants since 25-50% of current pharmaceuticals are plant derived...
August 30, 2017: Journal of Ayurveda and Integrative Medicine
https://www.readbyqxmd.com/read/28865272/rhizoremediation-half-lives-of-pcbs-role-of-congener-composition-organic-carbon-forms-bioavailability-microbial-activity-plant-species-and-soil-conditions-on-the-prediction-of-fate-and-persistence-in-soil
#14
REVIEW
Elisa Terzaghi, Elisabetta Zanardini, Cristiana Morosini, Giuseppe Raspa, Sara Borin, Francesca Mapelli, Lorenzo Vergani, Antonio Di Guardo
Polychlorinated biphenyls (PCBs) are persistent organic pollutants widely produced and used in many countries until the increasing concern about their environmental risk lead to their ban in the 1980s. Although their emissions decreased, PCBs are nowadays still present in the environment and can be reemitted from reservoir compartments such as contaminated soils. In the last two decades, there has been a growing interest in bioremediation technologies that use plants and microorganisms (i.e. rhizoremediation) to degrade organic chemicals in contaminated sites...
August 30, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28860535/ecological-and-functional-adaptations-to-water-management-in-a-semiarid-agroecosystem-a-soil-metaproteomics-approach
#15
Robert Starke, Felipe Bastida, Joaquín Abadía, Carlos García, Emilio Nicolás, Nico Jehmlich
Climate change models point to a decrease in water availability in semiarid areas that would compromise the maintenance of sustainable agriculture. Here, we used a grapefruit agroecosystem model to evaluate the responses of the active soil microbial community - as a microbial subset directly involved in soil functionality- undergoing strategies to cope with the low water availability in south-east Spain. For this purpose, we tested the impacts of: (i) water quality: transfer-water from a river (TW) or reclaimed-water from a wastewater-treatment plant (RW); and (ii) water quantity: continuous optimal amount of water or reduced irrigation (RDI) in the temporal frame when the crop is less sensitive; and their interactions...
August 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28852143/microbial-communities-in-marine-sediments-modify-success-of-an-invasive-macrophyte
#16
Paul E Gribben, Shaun Nielsen, Justin R Seymour, Daniel J Bradley, Matthew N West, Torsten Thomas
Invasive plants have extensive impacts on ecosystem function and biodiversity globally. Our inability to manage invasive species stems in part from a lack of understanding of the processes that control their successful establishment and spread. To date, studies have largely considered how above-ground processes control native/invasive plant interactions. Emerging research from terrestrial and wetland ecosystems demonstrates that below-ground processes under microbial control can determine the outcome of interactions between native and invasive plants...
August 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28846968/phosphate-enhanced-abiotic-and-biotic-arsenic-mobilization-in-the-wetland-rhizosphere
#17
Zheyun Zhang, Hee Sun Moon, Satish C B Myneni, Peter R Jaffé
Although abiotic process of competitive sorption between phosphate (P) and arsenate (As(V)), especially onto iron oxides, are well understood, P-mediated biotic processes of Fe and As redox transformation contributing to As mobilization and speciation in wetlands remain poorly defined. To gain new insights into the effects of P on As mobility, speciation, and bioavailability in wetlands, well-controlled greenhouse experiments were conducted. As expected, increased P levels contributed to more As desorption, but more interestingly the interactions between P and wetland plants played a synergistic role in the microbially-mediated As mobilization and enhanced As uptake by plants...
August 21, 2017: Chemosphere
https://www.readbyqxmd.com/read/28840959/tiny-microbes-big-yields-enhancing-food-crop-production-with-biological-solutions
#18
Pankaj Trivedi, Peer M Schenk, Matthew D Wallenstein, Brajesh K Singh
Plant-associated microbiomes have tremendous potential to improve plant resilience and yields in farming systems. There is increasing evidence that biological technologies that use microbes or their metabolites can enhance nutrient uptake and yield, control pests and mitigate plant stress responses. However, to fully realize the potential of microbial technology, their efficacy and consistency under the broad range of real-world conditions need to be improved. While the optimization of microbial biofertilizers and biopesticides is advancing rapidly to enable use in various soils, crop varieties and environments, crop breeding programmes have yet to incorporate the selection of beneficial plant-microbe interactions to breed 'microbe-optimized plants'...
August 25, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28839137/the-powdery-mildew-resistant-arabidopsis-mlo2-mlo6-mlo12-triple-mutant-displays-altered-infection-phenotypes-with-diverse-types-of-phytopathogens
#19
Johanna Acevedo-Garcia, Katrin Gruner, Anja Reinstädler, Ariane Kemen, Eric Kemen, Lingxue Cao, Frank L W Takken, Marco U Reitz, Patrick Schäfer, Richard J O'Connell, Stefan Kusch, Hannah Kuhn, Ralph Panstruga
Arabidopsis thaliana mlo2 mlo6 mlo12 triple mutant plants exhibit complete immunity against infection by otherwise virulent obligate biotrophic powdery mildew fungi such as Golovinomyces orontii. While this phenotype is well documented, the interaction profile of the triple mutant with other microbes is underexplored and incomplete. Here, we thoroughly assessed and quantified the infection phenotypes of two independent powdery mildew-resistant triple mutant lines with a range of microbes. These microorganisms belong to three kingdoms of life, engage in diverse trophic lifestyles, and deploy different infection strategies...
August 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28832648/matrix-metalloproteinases-operate-redundantly-in-arabidopsis-immunity-against-necrotrophic-and-biotrophic-fungal-pathogens
#20
Puyan Zhao, Fei Zhang, Dilin Liu, Jafargholi Imani, Gregor Langen, Karl-Heinz Kogel
Matrix metalloproteinases (MMPs) are evolutionarily conserved and multifunctional effector molecules playing pivotal roles in development and homeostasis. In this study we explored the involvement of the five Arabidopsis thaliana At-MMPs in plant defence against microbial pathogens. Expression of At2-MMP was most responsive to inoculation with fungi and a bacterial pathogen followed by At3-MMP and At5-MMP, while At1-MMP and At4-MMP were non-responsive to these biotic stresses. Loss-of-function mutants for all tested At-MMPs displayed increased susceptibility to the necrotrophic fungus Botrytis cinerea and double mutant at2,3-mmp and triple mutant at2,3,5-mmp plants developed even stronger symptoms...
2017: PloS One
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