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crop metagenomic

Dennis Goss-Souza, Lucas William Mendes, Clovis Daniel Borges, Jorge L M Rodrigues, Siu Mui Tsai
The conversion of native forest to agriculture is the main cause of microbial biodiversity loss in Amazon soils. In order to better understand this effect, we used metagenomics to investigate microbial patterns and functions in bulk soil and rhizosphere of soybean, in a long-term forest-to-agriculture conversion. Long-term forest-to-agriculture led to microbial homogenization and loss of diversity in both bulk soil and rhizosphere, mainly driven by decreasing aluminum concentration and increased cations saturation in soil, due liming and fertilization in long-term no-till cropping...
February 1, 2019: FEMS Microbiology Ecology
Fabio Pasin, Wulf Menzel, José-Antonio Daròs
Recent metagenomic studies have provided an unprecedented wealth of data, which is revolutionizing our understanding of virus diversity. A redrawn landscape highlights viruses as active players in the phytobiome, and surveys have uncovered their positive roles in environmental stress tolerance of plants. Viral infectious clones are key tools for functional characterization of known and newly identified viruses. Knowledge of viruses and their components has been instrumental for the development of modern plant molecular biology and biotechnology...
January 24, 2019: Plant Biotechnology Journal
J Musembi Mutuku, Francis O Wamonje, Gerardine Mukeshimana, Joyce Njuguna, Mark Wamalwa, Seung-Kook Choi, Trisna Tungadi, Appolinaire Djikeng, Krys Kelly, Jean-Baka Domelevo Entfellner, Sita R Ghimire, Hodeba D Mignouna, John P Carr, Jagger J W Harvey
Two closely related potyviruses, bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV), are regarded as major constraints on production of common bean ( Phaseolus vulgaris L.) in Eastern and Central Africa, where this crop provides a high proportion of dietary protein as well as other nutritional, agronomic, and economic benefits. Previous studies using antibody-based assays and indicator plants indicated that BCMV and BCMNV are both prevalent in bean fields in the region but these approaches cannot distinguish between these potyviruses or detect other viruses that may threaten the crop...
2018: Frontiers in Microbiology
Jin Xu, Yunzeng Zhang, Pengfan Zhang, Pankaj Trivedi, Nadia Riera, Yayu Wang, Xin Liu, Guangyi Fan, Jiliang Tang, Helvécio D Coletta-Filho, Jaime Cubero, Xiaoling Deng, Veronica Ancona, Zhanjun Lu, Balian Zhong, M Caroline Roper, Nieves Capote, Vittoria Catara, Gerhard Pietersen, Christian Vernière, Abdullah M Al-Sadi, Lei Li, Fan Yang, Xun Xu, Jian Wang, Huanming Yang, Tao Jin, Nian Wang
Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome is thought to play an important role in promoting citrus growth and health. Here, we report a comprehensive analysis of the structural and functional composition of the citrus rhizosphere microbiome. We use both amplicon and deep shotgun metagenomic sequencing of bulk soil and rhizosphere samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes...
November 20, 2018: Nature Communications
Hoe-Han Goh, Chyan Leong Ng, Kok-Keong Loke
Functional genomics encompasses diverse disciplines in molecular biology and bioinformatics to comprehend the blueprint, regulation, and expression of genetic elements that define the physiology of an organism. The deluge of sequencing data in the postgenomics era has demanded the involvement of computer scientists and mathematicians to create algorithms, analytical software, and databases for the storage, curation, and analysis of biological big data. In this chapter, we discuss on the concept of functional genomics in the context of systems biology and provide examples of its application in human genetic disease studies, molecular crop improvement, and metagenomics for antibiotic discovery...
2018: Advances in Experimental Medicine and Biology
Xiaogang Li, Alexandre Jousset, Wietse de Boer, Víctor J Carrión, Taolin Zhang, Xingxiang Wang, Eiko E Kuramae
Microorganisms associated with roots are thought to be part of the so-called extended plant phenotypes with roles in the acquisition of nutrients, production of growth hormones, and defense against diseases. Since the crops selectively enrich most rhizosphere microbes out of the bulk soil, we hypothesized that changes in the composition of bulk soil communities caused by agricultural management affect the extended plant phenotype. In the current study, we performed shotgun metagenome sequencing of the rhizosphere microbiome of the peanut (Arachis hypogaea) and metatranscriptome analysis of the roots of peanut plants grown in the soil with different management histories, peanut monocropping and crop rotation...
October 27, 2018: ISME Journal
Srinivasa Chaluvadi, Jeffrey L Bennetzen
The rhizosphere microbiome is known to play a crucial role in promoting plant growth, partly by countering soil-borne phytoparasites and by improving nutrient uptake. The abundance and composition of the rhizosphere and root-associated microbiota are influenced by several factors, including plant species and genotype. We hypothesize that crop domestication might influence the composition and diversity of plant-associated microbiomes. We tested the contribution of domestication to the bacterial and archaeal root and soil composition associated with six genotypes of domesticated Setaria italica and four genotypes of its wild ancestor, S...
2018: Frontiers in Plant Science
Huan Zhang, Jingwei Wu, Lijuan Gao, Jiadong Yu, Xufeng Yuan, Wanbin Zhu, Xiaofen Wang, Zongjun Cui
Ensilage is a commonly used method of preserving energy crops for biogas production. However, aerobic deterioration of silage is an inevitable problem. This study investigated the effect of aerobic deterioration on methane production and microbial community dynamics through anaerobic digestion (AD) of maize stalk silage, following 9days air exposure of silage. After air exposure, hydrolytic activity and methanogenic archaea amount in AD were reduced, decreasing the specific methane yield (SMY); whereas lignocellulose decomposition during exposure improved the degradability of silage in AD and enhanced SMY, partially compensating the dry matter (DM) loss...
February 2018: Bioresource Technology
Sohini Claverie, Pauline Bernardo, Simona Kraberger, Penelope Hartnady, Pierre Lefeuvre, Jean-Michel Lett, Serge Galzi, Denis Filloux, Gordon W Harkins, Arvind Varsani, Darren P Martin, Philippe Roumagnac
The number of plant viruses that are known likely remains only a vanishingly small fraction of all extant plant virus species. Consequently, the distribution and population dynamics of plant viruses within even the best-studied ecosystems have only ever been studied for small groups of virus species. Even for the best studied of these groups very little is known about virus diversity at spatial scales ranging from an individual host, through individual local host populations to global host populations. To date, metagenomics studies that have assessed the collective or metagenomes of viruses at the ecosystem scale have revealed many previously unrecognized viral species...
2018: Advances in Virus Research
Joana G Desiderato, Danillo O Alvarenga, Milena T L Constancio, Lucia M C Alves, Alessandro M Varani
Cellulose and its associated polymers are structural components of the plant cell wall, constituting one of the major sources of carbon and energy in nature. The carbon cycle is dependent on cellulose- and lignin-decomposing microbial communities and their enzymatic systems acting as consortia. These microbial consortia are under constant exploration for their potential biotechnological use. Herein, we describe the characterization of the genome of Dyella jiangningensis FCAV SCS01, recovered from the metagenome of a lignocellulose-degrading microbial consortium, which was isolated from a sugarcane crop soil under mechanical harvesting and covered by decomposing straw...
April 2018: Genetics and Molecular Biology
Afnan Khalil Ahmad Suleiman, Késia Silva Lourenço, Leonardo Machado Pitombo, Lucas William Mendes, Luiz Fernando Wurdig Roesch, Agata Pijl, Janaína Braga Carmo, Heitor Cantarella, Eiko Eurya Kuramae
Recycling residues is a sustainable alternative to improve soil structure and increase the stock of nutrients. However, information about the magnitude and duration of disturbances caused by crop and industrial wastes on soil microbial community structure and function is still scarce. The objective of this study was to investigate how added residues from industry and crops together with nitrogen (N) fertiliser affect the microbial community structure and function, and nitrous oxide (N2 O) emissions. The experimental sugarcane field had the following treatments: (I) control with nitrogen, phosphorus, and potassium (NPK), (II) sugarcane straw with NPK, (III) vinasse (by-product of ethanol industry) with NP, and (IV) vinasse plus sugarcane straw with NP...
August 1, 2018: Science of the Total Environment
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...
June 2018: Applied Microbiology and Biotechnology
Gui-Hua Lu, Xiao-Mei Hua, Li Liang, Zhong-Ling Wen, Mei-Hang Du, Fan-Fan Meng, Yan-Jun Pang, Jin-Liang Qi, Cheng-Yi Tang, Yong-Hua Yang
The worldwide commercial cultivation of transgenic crops, including glyphosate-tolerant (GT) soybeans, has increased widely during the past 20 years. However, it is accompanied with a growing concern about potential effects of transgenic crops on the soil microbial communities, especially on rhizosphere bacterial communities. Our previous study found that the GT soybean line NZL06-698 (N698) significantly affected rhizosphere bacteria, including some unidentified taxa, through 16S rRNA gene (16S rDNA) V4 region amplicon deep sequencing via Illumina MiSeq...
April 16, 2018: Genes
Tao Lu, Mingjing Ke, W J G M Peijnenburg, Youchao Zhu, Meng Zhang, Liwei Sun, Zhengwei Fu, Haifeng Qian
The plant rhizosphere microbiota plays multiple roles in plant growth. We investigated the taxonomic and functional variations in the rhizosphere microbial community, examining both prokaryotes and eukaryotes, of four crops at the seedling stage: wheat, barley, and two rice varieties ( indica and japonica) seeded in paddy soil. The diversity of rhizosphere communities in these four species was determined. Results showed that wheat and barley had much stronger selection effects than rice for the rhizosphere microbial community...
March 21, 2018: Journal of Agricultural and Food Chemistry
Vasim Ahmed, Manoj K Verma, Shashank Gupta, Vibha Mandhan, Nar S Chauhan
Osmotolerance is one of the critical factors for successful survival and colonization of microbes in saline environments. Nonetheless, information about these osmotolerance mechanisms is still inadequate. Exploration of the saline soil microbiome for its community structure and novel genetic elements is likely to provide information on the mechanisms involved in osmoadaptation. The present study explores the saline soil microbiome for its native structure and novel genetic elements involved in osmoadaptation...
2018: Frontiers in Microbiology
Nathálya Farias, Isabela Almeida, Carlos Meneses
Alkaline phytases from uncultured microorganisms, which hydrolyze phytate to less phosphorylated myo-inositols and inorganic phosphate, have great potential as additives in agricultural industry. The development of metagenomics has stemmed from the ineluctable evidence that as-yet-uncultured microorganisms represent the vast majority of organisms in most environments on earth. In this study, a gene encoding a phytase was cloned from red rice crop residues and castor bean cake using a metagenomics strategy. The amino acid identity between this gene and its closest published counterparts is lower than 60%...
February 17, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Kiran G Bapatla, Arjun Singh, Srujana Yeddula, Ramanagouda H Patil
The insect gut has been the house of many taxonomically and physiologically diverse groups of microbial colonizers as symbionts and commensals, which are evolving to support the physiological requirement of insects. Lepidoptera is one of the important family of class hexapoda, comprising agriculture insect pest Spodoptera litura and Spilosoma obliqua. Information on gut microbiota and their functional role in these insects was meager to elucidate the wide-ranging survivalist mechanisms. In this context, we analyzed the composition, diversity and functional role of gut bacteria in S...
March 2018: Journal of Basic Microbiology
Chanyarat Paungfoo-Lonhienne, Weijin Wang, Yun Kit Yeoh, Neil Halpin
Nitrifying microorganisms play an important role in nitrogen (N) cycling in agricultural soils as nitrification leads to accumulation of nitrate (NO3 - ) that is readily lost through leaching and denitrification, particularly in high rainfall regions. Legume crop rotation in sugarcane farming systems can suppress soil pathogens and improve soil health, but its effects on soil nitrifying microorganisms are not well understood. Using shotgun metagenomic sequencing, we investigated the impact of two legume break crops, peanut (Arachis hypogaea) and soybean (Glycine max), on the nitrifying communities in a sugarcane cropping soil...
December 1, 2017: Scientific Reports
Yanfen Cheng, Ying Wang, Yuanfei Li, Yipeng Zhang, Tianyi Liu, Yu Wang, Thomas J Sharpton, Weiyun Zhu
The aim of this study was to improve the utilization of rice straw as forage in ruminants by investigating the degradation pattern of rice straw in the dairy cow rumen. Ground up rice straw was incubated in situ in the rumens of three Holstein cows over a period of 72 h. The rumen fluid at 0 h and the rice straw at 0.5, 1, 2, 4, 6, 12, 24, 48, and 72 h were collected for analysis of the bacterial community and the degradation of the rice straw. The bacterial community and the carbohydrate-active enzymes in the rumen fluid were analyzed by metagenomics...
2017: Frontiers in Microbiology
Luis H Orellana, Joanne C Chee-Sanford, Robert A Sanford, Frank E Löffler, Konstantinos T Konstantinidis
The dynamics of individual microbial populations and their gene functions in agricultural soils, especially after major activities such as nitrogen (N) fertilization, remain elusive but are important for better understanding nutrient cycling. Here, we analyzed 20 short-read metagenomes collected at four time points across one year from two depths (0-5 and 20-30 cm) in two Midwestern agricultural sites representing contrasting soil textures (sandy versus silty-loam), with similar cropping histories. Although microbial community taxonomic and functional compositions differed between the two locations and depths, they were more stable within a depth/site throughout the year than communities in natural water-based ecosystems...
November 3, 2017: Applied and Environmental Microbiology
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