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Metatranscriptome

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https://www.readbyqxmd.com/read/29782790/magnetite-triggering-enhanced-diet-a-scavenger-for-the-blockage-of-electron-transfer-in-anaerobic-digestion-of-high-solids-sewage-sludge
#1
Tao Wang, Dong Zhang, Lingling Dai, Bin Dong, Xiaohu Dai
At present, high-solids anaerobic digestion of sewage sludge has drawn great attention due to the superiority of its small land area footprint and low energy consumption. However, a high organic loading rate may cause acids accumulation and ammonia inhibition, thus leading to an inhibited pseudo-steady state in which electron transfer through interspecies hydrogen transfer (IHT) between acetogens and methanogens is blocked. In this study, adding 50 mg/g TS (total solid) magnetite clearly reduced the accumulation of short-chain fatty acids and accelerated methane production by 26...
May 21, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29780371/comparative-metatranscriptomics-of-wheat-rhizosphere-microbiomes-in-disease-suppressive-and-non-suppressive-soils-for-rhizoctonia-solani-ag8
#2
Helen L Hayden, Keith W Savin, Jenny Wadeson, Vadakattu V S R Gupta, Pauline M Mele
The soilborne fungus Rhizoctonia solani anastomosis group (AG) 8 is a major pathogen of grain crops resulting in substantial production losses. In the absence of resistant cultivars of wheat or barley, a sustainable and enduring method for disease control may lie in the enhancement of biological disease suppression. Evidence of effective biological control of R. solani AG8 through disease suppression has been well documented at our study site in Avon, South Australia. A comparative metatranscriptomic approach was applied to assess the taxonomic and functional characteristics of the rhizosphere microbiome of wheat plants grown in adjacent fields which are suppressive and non-suppressive to the plant pathogen R...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29767724/fluctuations-in-populations-of-subsurface-methane-oxidizers-in-coordination-with-changes-in-electron-acceptor-availability
#3
C Magnabosco, P H A Timmers, M C Y Lau, G Borgonie, B Linage-Alvarez, O Kuloyo, R Alleva, T L Kieft, G F Slater, E van Heerden, B Sherwood Lollar, T C Onstott
The concentrations of electron donors and acceptors in the terrestrial subsurface biosphere fluctuate due to migration and mixing of subsurface fluids, but the mechanisms and rates at which microbial communities respond to these changes are largely unknown. Subsurface microbial communities exhibit long cellular turnover times and are often considered relatively static-generating just enough ATP for cellular maintenance. Here, we investigated how subsurface populations of CH4 oxidizers respond to changes in electron acceptor availability by monitoring the biological and geochemical composition in a 1,339 meters-below-land-surface (mbls) fluid-filled fracture over the course of both longer (2...
May 14, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29753651/integrated-metatranscriptomics-and-metaproteomics-for-the-characterization-of-bacterial-microbiota-in-unfed-ixodes-ricinus
#4
Angélica Hernández-Jarguín, Sandra Díaz-Sánchez, Margarita Villar, José de la Fuente
An innovative metaomics approach integrating metatranscriptomics and metaproteomics was used to characterize bacterial communities in the microbiota of the Lyme borreliosis spirochete vector, Ixodes ricinus (Acari: Ixodidae). Whole internal tissues and salivary glands from unfed larvae and female ticks, respectively were used. Reused I. ricinus RNA-sequencing data for metranscriptomics analysis together with metaproteomics provided a better characterization of tick bacterial microbiota by increasing bacteria identification and support for identified bacteria with putative functional implications...
May 5, 2018: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/29739901/compositional-and-functional-differences-in-the-human-gut-microbiome-correlate-with-clinical-outcome-following-infection-with-wild-type-salmonella-enterica-serovar-typhi
#5
Yan Zhang, Arthur Brady, Cheron Jones, Yang Song, Thomas C Darton, Claire Jones, Christoph J Blohmke, Andrew J Pollard, Laurence S Magder, Alessio Fasano, Marcelo B Sztein, Claire M Fraser
Insights into disease susceptibility as well as the efficacy of vaccines against typhoid and other enteric pathogens may be informed by better understanding the relationship between the effector immune response and the gut microbiota. In the present study, we characterized the composition (16S rRNA gene profiling) and function (RNA sequencing [RNA-seq]) of the gut microbiota following immunization and subsequent exposure to wild-type Salmonella enterica serovar Typhi in a human challenge model to further investigate the central hypothesis that clinical outcomes may be linked to the gut microbiota...
May 8, 2018: MBio
https://www.readbyqxmd.com/read/29739469/biomarkers-for-monitoring-intestinal-health-in-poultry-present-status-and-future-perspectives
#6
REVIEW
Richard Ducatelle, Evy Goossens, Fien De Meyer, Venessa Eeckhaut, Gunther Antonissen, Freddy Haesebrouck, Filip Van Immerseel
Intestinal health is determined by host (immunity, mucosal barrier), nutritional, microbial and environmental factors. Deficiencies in intestinal health are associated with shifts in the composition of the intestinal microbiome (dysbiosis), leakage of the mucosal barrier and/or inflammation. Since the ban on growth promoting antimicrobials in animal feed, these dysbiosis-related problems have become a major issue, especially in intensive animal farming. The economical and animal welfare consequences are considerable...
May 8, 2018: Veterinary Research
https://www.readbyqxmd.com/read/29730401/metatranscriptome-analysis-of-the-intestinal-microorganisms-in-pardosa-pseudoannulata-in-response-to-cadmium-stress
#7
Huilin Yang, Juan Wang, Zhiyue Lv, Jianxiang Tian, Yuande Peng, Xianjin Peng, Xiang Xu, Qisheng Song, Bo Lv, Zhaoyang Chen, Zhiying Sun, Zhi Wang
Cadmium (Cd) generates a variety of physiological and ecological toxicity to spiders. However, little is known about the effects of Cd on symbiotic bacteria of spiders. Metatranscriptomics is increasing our knowledge of microorganisms in environment. To better understand the impact of Cd on the symbiotic bacteria of spiders, we generated and compared the metatranscriptomes of the intestinal microorganisms of Pardosa pseudoannulata with and without Cd stress. The community structure of intestinal microorganisms in P...
May 3, 2018: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/29713790/metagenome-metatranscriptome-and-metaproteome-approaches-unraveled-compositions-and-functional-relationships-of-microbial-communities-residing-in-biogas-plants
#8
REVIEW
Julia Hassa, Irena Maus, Sandra Off, Alfred Pühler, Paul Scherer, Michael Klocke, Andreas Schlüter
The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters...
April 30, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29713376/genome-centric-metatranscriptomes-and-ecological-roles-of-the-active-microbial-populations-during-cellulosic-biomass-anaerobic-digestion
#9
Yangyang Jia, Siu-Kin Ng, Hongyuan Lu, Mingwei Cai, Patrick K H Lee
Background: Although anaerobic digestion for biogas production is used worldwide in treatment processes to recover energy from carbon-rich waste such as cellulosic biomass, the activities and interactions among the microbial populations that perform anaerobic digestion deserve further investigations, especially at the population genome level. To understand the cellulosic biomass-degrading potentials in two full-scale digesters, this study examined five methanogenic enrichment cultures derived from the digesters that anaerobically digested cellulose or xylan for more than 2 years under 35 or 55 °C conditions...
2018: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29708635/shifting-metabolic-priorities-among-key-protistan-taxa-within-and-below-the-euphotic-zone
#10
Sarah K Hu, Zhenfeng Liu, Harriet Alexander, Victoria Campbell, Paige E Connell, Sonya T Dyhrman, Karla B Heidelberg, David A Caron
A metatranscriptome study targeting the protistan community was conducted off the coast of Southern California, at the San Pedro Ocean Time-series station at the surface, 150 m (oxycline), and 890 m to link putative metabolic patterns to distinct protistan lineages. Comparison of relative transcript abundances revealed depth-related shifts in the nutritional modes of key taxonomic groups. Eukaryotic gene expression in the sunlit surface environment was dominated by phototrophs, such as diatoms and chlorophytes, and high abundances of transcripts associated with synthesis pathways (e...
April 30, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29706947/circadian-disruption-changes-gut-microbiome-taxa-and-functional-gene-composition
#11
Jessica A Deaver, Sung Y Eum, Michal Toborek
Disrupted circadian rhythms and alterations of the gut microbiome composition were proposed to affect host health. Therefore, the aim of this research was to identify whether these events are connected and if circadian rhythm disruption by abnormal light-dark (LD) cycles affects microbial community gene expression and host vulnerability to intestinal dysfunction. Mice were subjected to either a 4-week period of constant 24-h light or of normal 12-h LD cycles. Stool samples were collected at the beginning and after the circadian rhythm disruption...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29703736/distribution-and-diversity-of-rhodopsin-producing-microbes-in-the-chesapeake-bay
#12
Julia A Maresca, Kelsey J Miller, Jessica L Keffer, Chandran R Sabanayagam, Barbara J Campbell
Although sunlight is an abundant source of energy in surface environments, less than 0.5% of the available photons are captured by (bacterio)chlorophyll dependent photosynthesis in plants and bacteria. Metagenomic data indicate that 30-60% of the bacterial genomes in some environments encode rhodopsins, retinal-based photosystems found in heterotrophs, suggesting that sunlight may provide energy for more life than previously suspected. However, quantitative data on the number of cells that produce rhodopsins in environmental systems is limited...
April 27, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29685277/silage-review-using-molecular-approaches-to-define-the-microbial-ecology-of-silage
#13
REVIEW
T A McAllister, L Dunière, P Drouin, S Xu, Y Wang, K Munns, R Zaheer
Ensiling of forages was recognized as a microbial-driven process as early as the late 1800s, when it was associated with the production of "sweet" or "sour" silage. Classical microbiological plating techniques defined the epiphytic microbial populations associated with fresh forage, the pivotal role of lactic acid-producing bacteria in the ensiling process, and the contribution of clostridia, bacilli, yeast, and molds to the spoilage of silage. Many of these classical studies focused on the enumeration and characterization of a limited number of microbial species that could be readily isolated on selective media...
May 2018: Journal of Dairy Science
https://www.readbyqxmd.com/read/29679511/light-availability-impacts-structure-and-function-of-phototrophic-stream-biofilms-across-domains-and-trophic-levels
#14
Mia M Bengtsson, Karoline Wagner, Clarissa Schwab, Tim Urich, Tom J Battin
Phototrophic biofilms are ubiquitous in freshwater and marine environments where they are critical for biogeochemical cycling, food webs and in industrial applications. In streams, phototrophic biofilms dominate benthic microbial life and harbor an immense prokaryotic and eukaryotic microbial biodiversity with biotic interactions across domains and trophic levels. Here, we examine how community structure and function of these biofilms respond to varying light availability, as the crucial energy source for phototrophic biofilms...
April 21, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29666288/microbiota-and-metatranscriptome-changes-accompanying-the-onset-of-gingivitis
#15
Emily M Nowicki, Raghav Shroff, Jacqueline A Singleton, Diane E Renaud, Debra Wallace, Julie Drury, Jolene Zirnheld, Brock Colleti, Andrew D Ellington, Richard J Lamont, David A Scott, Marvin Whiteley
Over half of adults experience gingivitis, a mild yet treatable form of periodontal disease caused by the overgrowth of oral microbes. Left untreated, gingivitis can progress to a more severe and irreversible disease, most commonly chronic periodontitis. While periodontal diseases are associated with a shift in the oral microbiota composition, it remains unclear how this shift impacts microbiota function early in disease progression. Here, we analyzed the transition from health to gingivitis through both 16S v4-v5 rRNA amplicon and metatranscriptome sequencing of subgingival plaque samples from individuals undergoing an experimental gingivitis treatment...
April 17, 2018: MBio
https://www.readbyqxmd.com/read/29666229/drought-delays-development-of-the-sorghum-root-microbiome-and-enriches-for-monoderm-bacteria
#16
Ling Xu, Dan Naylor, Zhaobin Dong, Tuesday Simmons, Grady Pierroz, Kim K Hixson, Young-Mo Kim, Erika M Zink, Kristin M Engbrecht, Yi Wang, Cheng Gao, Stephanie DeGraaf, Mary A Madera, Julie A Sievert, Joy Hollingsworth, Devon Birdseye, Henrik V Scheller, Robert Hutmacher, Jeffery Dahlberg, Christer Jansson, John W Taylor, Peggy G Lemaux, Devin Coleman-Derr
Drought stress is a major obstacle to crop productivity, and the severity and frequency of drought are expected to increase in the coming century. Certain root-associated bacteria have been shown to mitigate the negative effects of drought stress on plant growth, and manipulation of the crop microbiome is an emerging strategy for overcoming drought stress in agricultural systems, yet the effect of drought on the development of the root microbiome is poorly understood. Through 16S rRNA amplicon and metatranscriptome sequencing, as well as root metabolomics, we demonstrate that drought delays the development of the early sorghum root microbiome and causes increased abundance and activity of monoderm bacteria, which lack an outer cell membrane and contain thick cell walls...
April 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29664912/metatranscriptome-analysis-of-the-microbial-fermentation-of-dietary-milk-proteins-in-the-murine-gut
#17
Floor Hugenholtz, Mark Davids, Jessica Schwarz, Michael Müller, Daniel Tomé, Peter Schaap, Guido J E J Hooiveld, Hauke Smidt, Michiel Kleerebezem
Undigestible food ingredients are converted by the microbiota into a large range of metabolites, predominated by short chain fatty acids (SCFA). These microbial metabolites are subsequently available for absorption by the host mucosa and can serve as an energy source. Amino acids fermentation by the microbiota expands the spectrum of fermentation end-products beyond acetate, propionate and butyrate, to include in particular branched-SCFA. Here the long-term effects of high protein-diets on microbial community composition and functionality in mice were analyzed...
2018: PloS One
https://www.readbyqxmd.com/read/29662480/comparative-analysis-of-the-microbiota-between-sheep-rumen-and-rabbit-cecum-provides-new-insight-into-their-differential-methane-production
#18
Lan Mi, Bin Yang, Xialu Hu, Yang Luo, Jianxin Liu, Zhongtang Yu, Jiakun Wang
The rumen and the hindgut represent two different fermentation organs in herbivorous mammals, with the former producing much more methane than the latter. The objective of this study was to elucidate the microbial underpinning of such differential methane outputs between these two digestive organs. Methane production was measured from 5 adult sheep and 15 adult rabbits, both of which were placed in open-circuit respiratory chambers and fed the same diet (alfalfa hay). The sheep produced more methane than the rabbits per unit of metabolic body weight, digestible neutral detergent fiber, and acid detergent fiber...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29662147/a-methanotrophic-archaeon-couples-anaerobic-oxidation-of-methane-to-fe-iii-reduction
#19
Chen Cai, Andy O Leu, Guo-Jun Xie, Jianhua Guo, Yuexing Feng, Jian-Xin Zhao, Gene W Tyson, Zhiguo Yuan, Shihu Hu
Microbially mediated anaerobic oxidation of methane (AOM) is a key process in the regulation of methane emissions to the atmosphere. Iron can serve as an electron acceptor for AOM, and it has been suggested that Fe(III)-dependent AOM potentially comprises a major global methane sink. Although it has been proposed that anaerobic methanotrophic (ANME) archaea can facilitate this process, their active metabolic pathways have not been confirmed. Here we report the enrichment and characterisation of a novel archaeon in a laboratory-scale bioreactor fed with Fe(III) oxide (ferrihydrite) and methane...
April 16, 2018: ISME Journal
https://www.readbyqxmd.com/read/29660711/the-rhizosphere-microbiome-significance-in-rhizoremediation-of-polyaromatic-hydrocarbon-contaminated-soil
#20
REVIEW
Rhitu Kotoky, Jina Rajkumari, Piyush Pandey
Microbial communities are an essential part of plant rhizosphere and participate in the functioning of plants, including rhizoremediation of petroleum contaminants. Rhizoremediation is a promising technology for removal of polyaromatic hydrocarbons based on interactions between plants and microbiome in the rhizosphere. Root exudation in the rhizosphere provides better nutrient uptake for rhizosphere microbiome, and therefore it is considered to be one of the major factors of microbial community function in the rhizosphere that plays a key role in the enhanced PAH biodegradation...
April 13, 2018: Journal of Environmental Management
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