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https://www.readbyqxmd.com/read/28646202/the-microbiome-of-endophytic-wood-colonizing-bacteria-from-pine-trees-as-affected-by-pine-wilt-disease
#1
Diogo Neves Proença, Romeu Francisco, Susanne Kublik, Anne Schöler, Gisle Vestergaard, Michael Schloter, Paula V Morais
Pine wilt disease (PWD) is a devastating forest disease present worldwide. In this study we analyzed the effects of the invasion of the pinewood nematode Bursaphelenchus xylophilus, the major pathogen causing PWD, on the endophytic microbiome of adult P. pinaster trees. Wood samples from trees with different degrees of PWD disease were collected at two sites (A and M) in Portugal. Endophytic bacteria were characterized based on directly extracted DNA by fingerprinting and barcoding using the 16S rRNA gene as marker...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28643880/effects-of-discrete-bioactive-microbial-volatiles-on-plants-and-fungi
#2
REVIEW
Birgit Piechulla, Marie-Chantal Lemfack, Marco Kai
Plants live in association with microorganisms, which are well known as a rich source of specialized metabolits, including volatile compounds. The increasing numbers of described plant microbiomes allowed manifold phylogenetic tree deductions, but less emphasis is presently put on the metabolic capacities of plant-associated microorganisms. With the focus on small volatile metabolites we summarize i) the knowledge of prominent bacteria of plant microbiomes, ii) present the state-of-the-art of individual (discrete) microbial organic and inorganic volatiles affecting plants and fungi, and iii) emphasize the high potential of microbial volatiles in mediating microbe-plant interactions...
June 23, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28640496/distance-decay-relationships-in-foliar-fungal-endophytes-are-driven-by-rare-taxa
#3
Ryoko Oono, Anna Rasmussen, Emilie Lefèvre
Foliar fungal endophytes represent a diverse and species-rich plant microbiome. Their biogeography provides essential clues to their cryptic relationship with hosts and the environment in which they disperse. We present species composition, diversity, and dispersal patterns of endophytic fungi associated with needles of Pinus taeda trees across regional scales in the absence of strong environmental gradients as well as within individual trees. An empirical designation of rare and abundant taxa enlightens us on the structure of endophyte communities...
May 18, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28638057/the-variation-in-the-rhizosphere-microbiome-of-cotton-with-soil-type-genotype-and-developmental-stage
#4
Qinghua Qiao, Furong Wang, Jingxia Zhang, Yu Chen, Chuanyun Zhang, Guodong Liu, Hui Zhang, Changle Ma, Jun Zhang
Plant roots and soil microorganisms interact with each other mainly in the rhizosphere. Changes in the community structure of the rhizosphere microbiome are influenced by many factors. In this study, we determined the community structure of rhizosphere bacteria in cotton, and studied the variation of rhizosphere bacterial community structure in different soil types and developmental stages using TM-1, an upland cotton cultivar (Gossypium hirsutum L.) and Hai 7124, a sea island cotton cultivar (G. barbadense L...
June 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28634640/the-microbiome-of-eucalyptus-roots-under-different-management-conditions-and-its-potential-for-biological-nitrogen-fixation
#5
Eduardo da Siva Fonseca, Raquel Silva Peixoto, Alexandre Soares Rosado, Fabiano de Carvalho Balieiro, James M Tiedje, Caio Tavora Coelho da Costa Rachid
Eucalyptus plantations offer a cost-effective and renewable source of raw material. There is substantial interest in improving forestry production, especially through sustainable strategies such as the use of plant growth-promoting bacteria. However, little is known about Eucalyptus microbiology. In this study, the endophytic bacterial community was assessed in Eucalyptus urograndis roots using culture-dependent and culture-independent techniques with plants grown under different conditions. Three phyla accounted for approximately 95% of the community, with Actinobacteria corresponding to approximately 59%...
June 21, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28630614/a-plant-based-diet-for-the-prevention-and-treatment-of-type-2-diabetes
#6
REVIEW
Michelle McMacken, Sapana Shah
The prevalence of type 2 diabetes is rising worldwide, especially in older adults. Diet and lifestyle, particularly plant-based diets, are effective tools for type 2 diabetes prevention and management. Plant-based diets are eating patterns that emphasize legumes, whole grains, vegetables, fruits, nuts, and seeds and discourage most or all animal products. Cohort studies strongly support the role of plant-based diets, and food and nutrient components of plant-based diets, in reducing the risk of type 2 diabetes...
May 2017: Journal of Geriatric Cardiology: JGC
https://www.readbyqxmd.com/read/28622659/understanding-and-exploiting-plant-beneficial-microbes
#7
REVIEW
Omri M Finkel, Gabriel Castrillo, Sur Herrera Paredes, Isai Salas González, Jeffery L Dangl
After a century of incremental research, technological advances, coupled with a need for sustainable crop yield increases, have reinvigorated the study of beneficial plant-microbe interactions with attention focused on how microbiomes alter plant phenotypes. We review recent advances in plant microbiome research, and describe potential applications for increasing crop productivity. The phylogenetic diversity of plant microbiomes is increasingly well characterized, and their functional diversity is becoming more accessible...
June 13, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28614633/differential-sensitivity-of-total-and-active-soil-microbial-communities-to-drought-and-forest-management
#8
F Bastida, I F Torres, M Andrés-Abellán, P Baldrian, R López-Mondéjar, T Větrovský, H H Richnow, R Starke, S Ondoño, C García, F R López-Serrano, N Jehmlich
Climate change will affect semiarid ecosystems through severe droughts that increase the competition for resources in plant and microbial communities. In these habitats, adaptations to climate change may consist of thinning - that reduces competition for resources through a decrease in tree density and the promotion of plant survival. We deciphered the functional and phylogenetic responses of the microbial community to six years of drought induced by rainfall exclusion and how forest management affects its resistance to drought, in a semiarid forest ecosystem dominated by Pinus halepensis Mill...
June 14, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28611735/the-effects-of-cropping-regimes-on-fungal-and-bacterial-communities-of-wheat-and-faba-bean-in-a-greenhouse-pot-experiment-differ-between-plant-species-and-compartment
#9
Sandra Granzow, Kristin Kaiser, Bernd Wemheuer, Birgit Pfeiffer, Rolf Daniel, Stefan Vidal, Franziska Wemheuer
Many bacteria and fungi in the plant rhizosphere and endosphere are beneficial to plant nutrient acquisition, health, and growth. Although playing essential roles in ecosystem functioning, our knowledge about the effects of multiple cropping regimes on the plant microbiome and their interactions is still limited. Here, we designed a pot experiment simulating different cropping regimes. For this purpose, wheat and faba bean plants were grown under controlled greenhouse conditions in monocultures and in two intercropping regimes: row and mixed intercropping...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28607843/ecophylogeny-of-the-endospheric-root-fungal-microbiome-of-co-occurring-agrostis-stolonifera
#10
Amandine Lê Van, Achim Quaiser, Marie Duhamel, Sophie Michon-Coudouel, Alexis Dufresne, Philippe Vandenkoornhuyse
BACKGROUND: Within the root endosphere, fungi are known to be important for plant nutrition and resistance to stresses. However, description and understanding of the rules governing community assembly in the fungal fraction of the plant microbiome remains scarce. METHODS: We used an innovative DNA- and RNA-based analysis of co-extracted nucleic acids to reveal the complexity of the fungal community colonizing the roots of an Agrostis stolonifera population. The normalized RNA/DNA ratio, designated the 'mean expression ratio', was used as a functional trait proxy...
2017: PeerJ
https://www.readbyqxmd.com/read/28597254/changes-in-structure-and-function-of-bacterial-communities-during-coconut-leaf-vermicomposting
#11
Murali Gopal, Shrikant S Bhute, Alka Gupta, S R Prabhu, George V Thomas, William B Whitman, Kamlesh Jangid
To understand bacterial community dynamics during the vermicomposting of lignin-rich coconut leaves using an indigenous isolate of an epigeic earthworm, Eudrilus sp., we employed amplicon-based pyrosequencing of the V1 to V3 region of the 16S rRNA genes. Total community DNA was isolated from two separate vermicomposting tanks in triplicate at four different stages of the process: pre-decomposition (15th day), initial vermicomposting (45th day), 50-70% vermicomposting (75th day) and mature vermicompost (105th day)...
June 9, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28595639/diet-shifts-provoke-complex-and-variable-changes-in-the-metabolic-networks-of-the-ruminal-microbiome
#12
Sara M Wolff, Melinda J Ellison, Yue Hao, Rebecca R Cockrum, Kathy J Austin, Michael Baraboo, Katherine Burch, Hyuk Jin Lee, Taylor Maurer, Rocky Patil, Andrea Ravelo, Tasia M Taxis, Huan Truong, William R Lamberson, Kristi M Cammack, Gavin C Conant
BACKGROUND: Grazing mammals rely on their ruminal microbial symbionts to convert plant structural biomass into metabolites they can assimilate. To explore how this complex metabolic system adapts to the host animal's diet, we inferred a microbiome-level metabolic network from shotgun metagenomic data. RESULTS: Using comparative genomics, we then linked this microbial network to that of the host animal using a set of interface metabolites likely to be transferred to the host...
June 8, 2017: Microbiome
https://www.readbyqxmd.com/read/28588643/molecular-cloning-expression-and-characterization-of-four-novel-thermo-alkaliphilic-enzymes-retrieved-from-a-metagenomic-library
#13
Mukil Maruthamuthu, Jan Dirk van Elsas
BACKGROUND: Enzyme discovery is a promising approach to aid in the deconstruction of recalcitrant plant biomass in an industrial process. Novel enzymes can be readily discovered by applying metagenomics on whole microbiomes. Our goal was to select, examine, and characterize eight novel glycoside hydrolases that were previously detected in metagenomic libraries, to serve biotechnological applications with high performance. RESULTS: Here, eight glycosyl hydrolase family candidate genes were selected from metagenomes of wheat straw-degrading microbial consortia using molecular cloning and subsequent gene expression studies in Escherichia coli...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28587078/morinda-citrifolia-linn-noni-and-its-potential-in-obesity-related-metabolic-dysfunction
#14
REVIEW
Aline Carla Inada, Priscila Silva Figueiredo, Rosângela Aparecida Dos Santos-Eichler, Karine de Cássia Freitas, Priscila Aiko Hiane, Alinne Pereira de Castro, Rita de Cássia Avellaneda Guimarães
Cultural and economic shifts in the early 19th century led to the rapid development of companies that made good profits from technologically-produced commodities. In this way, some habits changed in society, such as the overconsumption of processed and micronutrient-poor foods and devices that gave rise to a sedentary lifestyle. These factors influenced host-microbiome interactions which, in turn, mediated the etiopathogenesis of "new-era" disorders and diseases, which are closely related, such as obesity, type 2 diabetes mellitus, non-alcoholic fatty liver disease, hypertension, and inflammatory bowel disease, which are characterized by chronic dysregulation of metabolic and immune processes...
May 25, 2017: Nutrients
https://www.readbyqxmd.com/read/28585939/linking-rhizosphere-microbiome-composition-of-wild-and-domesticated-phaseolus-vulgaris-to-genotypic-and-root-phenotypic-traits
#15
Juan E Pérez-Jaramillo, Víctor J Carrión, Mirte Bosse, Luiz F V Ferrão, Mattias de Hollander, Antonio A F Garcia, Camilo A Ramírez, Rodrigo Mendes, Jos M Raaijmakers
Plant domestication was a pivotal accomplishment in human history, but also led to a reduction in genetic diversity of crop species compared to their wild ancestors. How this reduced genetic diversity affected plant-microbe interactions belowground is largely unknown. Here, we investigated the genetic relatedness, root phenotypic traits and rhizobacterial community composition of modern and wild accessions of common bean (Phaseolus vulgaris) grown in agricultural soil from the highlands of Colombia, one of the centers of common bean diversification...
June 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28583081/addition-of-plant-growth-promoting-bacillus-subtilis-pts-394-on-tomato-rhizosphere-has-no-durable-impact-on-composition-of-root-microbiome
#16
Junqing Qiao, Xiang Yu, Xuejie Liang, Yongfeng Liu, Rainer Borriss, Youzhou Liu
BACKGROUND: Representatives of the genus Bacillus are increasingly used in agriculture to promote plant growth and to protect against plant pathogens. Unfortunately, hitherto the impact of Bacillus inoculants on the indigenous plant microbiota has been investigated exclusively for the species Bacillus amyloliquefaciens and was limited to prokaryotes, whilst eukaryotic member of this community, e.g. fungi, were not considered. RESULTS: The root-colonizing Bacillus subtilis PTS-394 supported growth of tomato plants and suppressed soil-borne diseases...
June 5, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28569210/bacteriophage-prokaryote-dynamics-and-interaction-within-anaerobic-digestion-processes-across-time-and-space
#17
Junyu Zhang, Qun Gao, Qiuting Zhang, Tengxu Wang, Haowei Yue, Linwei Wu, Jason Shi, Ziyan Qin, Jizhong Zhou, Jiane Zuo, Yunfeng Yang
BACKGROUND: Bacteriophage-prokaryote dynamics and interaction are believed to be important in governing microbiome composition and ecosystem functions, yet our limited knowledge of the spatial and temporal variation in phage and prokaryotic community compositions precludes accurate assessment of their roles and impacts. Anaerobic digesters are ideal model systems to examine phage-host interaction, owing to easy access, stable operation, nutrient-rich environment, and consequently enormous numbers of phages and prokaryotic cells...
May 31, 2017: Microbiome
https://www.readbyqxmd.com/read/28561849/symbiosis-inspired-approaches-to-antibiotic-discovery
#18
REVIEW
Navid Adnani, Scott R Rajski, Tim S Bugni
Covering: 2010 up to 2017Life on Earth is characterized by a remarkable abundance of symbiotic and highly refined relationships among life forms. Defined as any kind of close, long-term association between two organisms, symbioses can be mutualistic, commensalistic or parasitic. Historically speaking, selective pressures have shaped symbioses in which one organism (typically a bacterium or fungus) generates bioactive small molecules that impact the host (and possibly other symbionts); the symbiosis is driven fundamentally by the genetic machineries available to the small molecule producer...
May 31, 2017: Natural Product Reports
https://www.readbyqxmd.com/read/28559882/bacterial-root-microbiome-of-plants-growing-in-oil-sands-reclamation-covers
#19
Eduardo K Mitter, J Renato de Freitas, James J Germida
Oil sands mining in northern Alberta impacts a large footprint, but the industry is committed to reclaim all disturbed land to an ecologically healthy state in response to environmental regulations. However, these newly reconstructed landscapes may be limited by several factors that include low soil nutrient levels and reduced microbial activity. Rhizosphere microorganisms colonize plant roots providing hosts with nutrients, stimulating growth, suppressing disease and increasing tolerance to abiotic stress...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28555641/a-parts-list-for-fungal-cellulosomes-revealed-by-comparative-genomics
#20
Charles H Haitjema, Sean P Gilmore, John K Henske, Kevin V Solomon, Randall de Groot, Alan Kuo, Stephen J Mondo, Asaf A Salamov, Kurt LaButti, Zhiying Zhao, Jennifer Chiniquy, Kerrie Barry, Heather M Brewer, Samuel O Purvine, Aaron T Wright, Matthieu Hainaut, Brigitte Boxma, Theo van Alen, Johannes H P Hackstein, Bernard Henrissat, Scott E Baker, Igor V Grigoriev, Michelle A O'Malley
Cellulosomes are large, multiprotein complexes that tether plant biomass-degrading enzymes together for improved hydrolysis(1). These complexes were first described in anaerobic bacteria, where species-specific dockerin domains mediate the assembly of enzymes onto cohesin motifs interspersed within protein scaffolds(1). The versatile protein assembly mechanism conferred by the bacterial cohesin-dockerin interaction is now a standard design principle for synthetic biology(2,3). For decades, analogous structures have been reported in anaerobic fungi, which are known to assemble by sequence-divergent non-catalytic dockerin domains (NCDDs)(4)...
May 30, 2017: Nature Microbiology
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