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An optmized protocol for simultaneous extraction of DNA and RNA from soils BJM
Costa,Rodrigo; Gomes,Newton C.M.; Milling,Annett; Smalla,Kornelia.
In this work we report an optimized protocol for simultaneous extraction of DNA and RNA from soil matrices. Treatment of soil matrices with ethanol followed by bead-beating worked as a successful strategy to lyse the cells without considerable degradation of nucleic acids, resulting in DNA and RNA of good yield and integrity. The reverse transcribed RNA could be amplified with primers targeting a glutamine synthetase (glnA) gene fragment. From both DNA and cDNA, 16S rDNA fragments were amplified and analyzed by Denaturing Gradient Gel Electrophoresis (DGGE). The method was applied to soil and rhizosphere (strawberry and oilseed rape) samples. Two other protocols for the extraction of nucleic acids from soil were applied to the same set of samples in order...
Tipo: Info:eu-repo/semantics/article Palavras-chave: RNA extraction; Nucleic acids; Rhizosphere; Microbial communities.
Ano: 2004 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822004000200011
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Aspergillus niveus Blochwitz 4128URM: new source for inulinase production BABT
Souza-Motta,Cristina Maria de; Cavalcanti,Maria Auxiliadora de Queiroz; Porto,Ana Lúcia Figueiredo; Moreira,Keila Aparecida; Lima Filho,José Luiz de.
Aspergillus niveus Blochwitz 4128 URM isolated from sunflower rhizosphere demonstrated a new source of inulinase. The enzyme was produced in culture medium containing inulin as substrate in the concentrations: 10, 15 and 20g L-1. Maximum enzyme activity was obtained in medium containing 20g L-1 inulin. The enzyme was partially purified using ammonium sulphate precipitation, followed by ion charge (DE-32) and molecular exclusion (Sephadex) chromatography. The results showed the optimal pH and temperature of inulinase from crude extract were 4.0 and 4.8 and 45ºC, respectively. The enzyme was purified 34.65 fold with yield of 53.63%. A. niveus 4128URM can be used in the inulinase production with use in the food industries.
Tipo: Info:eu-repo/semantics/article Palavras-chave: Aspergillus niveus; Rhizosphere; Inulinase; Inulin; Purification.
Ano: 2005 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132005000300003
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Assessing the diversity of bacterial communities associated with plants BJM
Andreote,Fernando Dini; Azevedo,João Lúcio; Araújo,Welington Luiz.
Plant-bacteria interactions result from reciprocal recognition between both species. These interactions are responsible for essential biological processes in plant development and health status. Here, we present a review of the methodologies applied to investigate shifts in bacterial communities associated with plants. A description of techniques is made from initial isolations to culture-independent approaches focusing on quantitative Polymerase Chain Reaction in real time (qPCR), Denaturing Gradient Gel Electrophoresis (DGGE), clone library construction and analysis, the application of multivariate analyses to microbial ecology data and the upcoming high throughput methodologies such as microarrays and pyrosequencing. This review supplies information...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Plant-bacteria interactions; Molecular techniques; Multivariate analysis; Endophytes; Rhizosphere.
Ano: 2009 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822009000300001
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Back to the roots: revealing beneficial interactions between the rhizosphere microbiome and wild wheat. Repositório Alice
ROSSMANN, M.; PÉREZ-JARAMILLO, J. E.; CHIARAMONTE, J. B.; KAVAMURA, V. N.; DUMACK, K.; FIORE-DONNO, A. M.; MENDES, L. W.; BONKOWSKI, M.; MAUCHLINE, T.; RAAIJMAKERS, J. M.; MENDES, R..
Domestication of plants may have impacted the interactions between plants and their rhizosphere microbiome. Considering that plants rely on the rhizosphere microbiome for functions related with plant growth, nutrition and health, the objective of this work was to analyse the rhizosphere microbiome of wild relatives and modern varieties of wheat and to investigate whether wild relatives recruit a higher proportion of beneficial microbes than modern cultivars. By 16S-rRNA gene amplicon, ITS and 18SrRNA gene amplicon, we assessed the bacterial, fungal and cercozoa rhizosphere community composition of five modern cultivars and three wheat ancestors cultivated in forest and agricultural soils. Results revealed a pronounced soil type and rhizosphere effect on...
Tipo: Separatas Palavras-chave: Wild wheat; Trigo; Rizosfera; Rhizosphere; Wheat; Microbiome.
Ano: 2018 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1103217
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Bacterial diversity associated with the rhizosphere of wheat plants (Triticum aestivum): Toward a metagenomic analysis Phyton
Velázquez-Sepúlveda,I; Orozco-Mosqueda,MC; Prieto-Barajas,CM; Santoyo,G.
Rhizospheric soil is one the largest reservoirs of microbial genetic diversity. Before conducting a large-scale metagenomic analysis of an environment, such as a rhizospheric soil, it is necessary to perform a pre-screening of the resident genetic diversity. In this study, we analyzed the bacterial diversity associated with the rhizosphere of wheat plants by PCR amplification, construction of a library and sequencing of 16S rDNA genes. Thirty OTUs were detected, including the Classes Alfaproteobacteria, Betaproteobacteria, Deltaproteobacteria, Gammaproteobateria, Actinobacteria, Bacilli, Clostridia and Uncultivable bacteria. Within the Gamma­proteobacteria class, the genera Pseudomonas, Stenotrophomonas and Bacillus were the most abundant, since they...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bacterial diversity; Rhizosphere; Wheat; 16S ribosomal genes.
Ano: 2012 URL: http://www.scielo.org.ar/scielo.php?script=sci_arttext&pid=S1851-56572012000100012
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Bacterial diversity in the rhizosphere of a transgenic versus a conventional maize (Zea mays) Phyton
Vital-López,L; Cruz-Hernández,MA; Fernández-Dávila,S; Mendoza-Herrera,A.
Genetically modified crops could cause negative effects on bacterial communities. In this study, we compared the bacterial community structure of two maize cultivars to determine whether the transgenic cultivar exerts a negative effect on bacterial communities inhabiting the rhizosphere. Cultivars included the genetically modified maize (Zea mays), with the pat-gene conferring resistance to the herbicide glufosinate (synonym: L-phosphinothricin), and the hybrid, conventional maize. Metagenomic DNA was extracted from the rhizosphere of plants grown in a greenhouse. Single-strand conformation polymorphism, based on polymerase chain reaction amplifying a partial subunit rRNA gene was used to characterize and generate genetic profiles that corresponded to the...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Zea mays; Glufosinate; Metagenomic DNA; Rhizosphere; Single-strand conformation polymorphism.
Ano: 2016 URL: http://www.scielo.org.ar/scielo.php?script=sci_arttext&pid=S1851-56572016000200006
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Biological nitrogen fixation and agronomic features of soybean (Glycine max (L.)Merr.) crop under different doses of inoculant Acta Agron. (Palmira)
Pedrozo,Alessandro; Girelli de Oliveira,Nelson João; Alberton,Odair.
Abstract Soybean is one of the most important crops in the world and presents great versatility. This study aims to investigate the effect of the Bradyrhizobium japonicum inoculant at 0, 600 and 1200 mL ha1 on soybean crop, with and without 1 L ha-1 calcium (Ca 41%) + 0.4 L ha-1 boron (B 14%). Plants were grown for 90 days in plastic pots with 3 kg of sand and vermiculite (v/v) autoclaved at 121oC for 1 h. The experiment was conducted in a completely randomized design with five replications in a greenhouse. Soybean yield parameters were evaluated, such as, dry weight of shoot, root and total; plant height, nitrogen in the shoot; number and dry weight of nodules; chlorophyll index in the leaves; number of pods per plant (NPPL); number of grains per pod...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bradyrhizobium; Inoculation; Plant-soil relations; Rhizosphere; Soil microbiology; Symbiosis.
Ano: 2018 URL: http://www.scielo.org.co/scielo.php?script=sci_arttext&pid=S0120-28122018000200297
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Breeding for resistance to soil-borne pathogen impacts rhizosphere microbiome functions in common bean. Repositório Alice
MENDES, L. W.; MENDES, R.; RAAIJMAKERS, J. M.; TSAI, S. M..
Over the past century, plant breeding programs have substantially improved plant growth and health, but have not yet considered the potential effects on the plant microbiome. Here, we conducted a metatranscriptome analysis to determine if and how breeding for resistance of common bean against the root pathogen Fusarium oxysporum (Fox) affected gene expression in the rhizobacterial community. Our data revealed that rhizobacterial community assembly of Fox-resistant and susceptible bean cultivars follows niche-based mechanisms, presenting lower diversity and distinct community structure compared to the bulk soil. The microbiome of the Fox-resistant bean cultivar presented a significantly higher expression of bacterial genes associated with nutrient...
Tipo: Separatas Palavras-chave: Rizosfera; Feijão; Microbiome; Rhizosphere; Beans; Breeding.
Ano: 2018 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1103238
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Characterization of Rhizobacteria from field grown Genetically Modified (GM) and non-GM maizes BABT
Bumunang,Emmanuel Wihkochombom; Babalola,Olubukola Oluranti.
This study was done to examine the rhizobacteria from field grown Genetically Modified (GM) maize and its non-GM counterpart. Rhizospheric soil samples were collected at 30 days after sowing (DAS) and at post-harvest from two experimental fields in Gauteng, South Africa. Total rhizobacteria (cfu/g) in GM and non-GM soil samples was not significantly different across the different media 30 DAS and at post-harvest. Rhizobacterial isolates obtained were biochemically characterized using the analytical profile index. Species of Pseudomonas, Aeromonas, Sphingomonas, Burkholderia, Stenotrophomonas, Achromobacter, Ewingella and Bacillus were screened in vitro for plant growth promoting traits such as, ammonia production, catalase activity, indole acetic acid...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Genetically modified maize; Plant growth promoting traits; Rhizosphere; Rhizobacteria.
Ano: 2014 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132014000100001
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Combined application of bio-organic phosphate and phosphorus solubilizing bacteria (Bacillus strain MWT 14) improve the performance of bread wheat with low fertilizer input under an arid climate BJM
Tahir,Muhammad; Khalid,Umaira; Ijaz,Muhammad; Shah,Ghulam Mustafa; Naeem,Muhammad Asif; Shahid,Muhammad; Mahmood,Khalid; Ahmad,Naveed; Kareem,Fazal.
Abstract This study was aimed to investigate the effect of bio-organic phosphate either alone or in combination with phosphorus solubilizing bacteria strain (Bacillus MWT-14) on the growth and productivity of two wheat cultivars (Galaxy-2013 and Punjab-2011) along with recommended (150–100 NP kg ha−1) and half dose (75–50 NP kg ha−1) of fertilizers. The combined application of bio-organic phosphate and the phosphorous solubilizing bacteria strain at either fertilizer level significantly improved the growth, yield parameters and productivity of both wheat cultivars compared to non-inoculated control treatments. The cultivar Punjab-2011 produced the higher chlorophyll contents, crop growth rate, and the straw yield at half dose of NP fertilizer; while...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Phosphorous; Phosphorous solubilizing bacteria; Bioavailability; Rhizosphere; Low fertilizer input.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822018000500015
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Construction and characterization of a metagenomic DNA library from the rhizosphere of wheat (Triticum aestivum) Phyton
Hernández-León,R; Martínez-Trujillo,M; Valencia-Cantero,E; Santoyo,G.
Rhizospheric soil of wheat plants contains a high diversity of microorganisms, and therefore, comprises a large reservoir for discovering genes with diverse agro-biotechnological applications. In this work, we constructed an E. coli metagenomic library based on bacterial artificial chromosome (BAC) clones with large genomic inserts from metagenomic DNA from the rhizosphere of wheat plants. The average of the DNA cloned segments varies from 5 to 80 kb, with an average size of 38 kb. Random clones were end-sequenced and homology results showed that the clonation of metagenomic DNA codes mainly for metabolic and catalytic functions (40%), including amidohydrolase, hydrolase, peptidase, serine protease, endonuclease and exonuclease. Another interesting...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Metagenomics; Rhizosphere; Wheat.
Ano: 2012 URL: http://www.scielo.org.ar/scielo.php?script=sci_arttext&pid=S1851-56572012000100018
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Cross-kingdom similarities in microbiome ecology and biocontrol of pathogens. Repositório Alice
BERG, G.; KRAUSE, R.; MENDES, R..
Abstract: The concept of "gut and root microbiota commonalities" was already presented by Ramírez-Puebla et al.(2013); they discussed a lot of similar functional traits, host-bacteria interactions as well as evolutionary trends but also several differences. Based on deeper insights obtained by omics technologies, Mendes and Raaijmakers (2015) recently presented their concept that the structure and function of rhizosphere and gut microbiomes showcross-kingdom similarities. In parallel, Hacquard et al. (2015) analyzed similarities of the microbiota composition across plant and animal kingdoms and found only little overlap comparing fish gut and plant root communities. They explained the differences by various start inoculants and abiotic, niche-specific...
Tipo: Separatas Palavras-chave: Ecological theories; Rizosfera; População microbiana; Bactéria; Controle biológico; Microbiome; Biological control agents; Rhizosphere; Pathogens.
Ano: 2015 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1032834
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Disentangling the influence of earthworms in sugarcane rhizosphere. Repositório Alice
BRAGA, L. P. P.; YOSHIURA, C. A.; BORGES, C. D.; HORN, M. A.; BROWN, G. G.; DRAKE, H. L.; TSAI, S. M..
For the last 150 years many studies have shown the importance of earthworms for plant growth, but the exact mechanisms involved in the process are still poorly understood. Many important functions required for plant growth can be performed by soil microbes in the rhizosphere. To investigate earthworm influence on the rhizosphere microbial community, we performed a macrocosm experiment with and without Pontoscolex corethrurus (EW+ and EW?, respectively) and followed various soil and rhizosphere processes for 217 days with sugarcane. In EW+ treatments, N2O concentrations belowground (15 cm depth) and relative abundances of nitrous oxide genes (nosZ) were higher in bulk soil and rhizosphere, suggesting that soil microbes were able to consume earthworm-induced...
Tipo: Artigo de periódico Palavras-chave: Crescimento de plantas; Minhoca; Solo; Rizosfera; Biologia do solo; Earthworms; Rhizosphere.
Ano: 2016 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1067637
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Disponibilização de K de rochas silicáticas para plantas de soja inoculadas com fungos micorrízicos arbusculares (FMA). Infoteca-e
ANDRADE, L. R. M. de; FALEIRO, A. S. G.; SANTOS SOBRINHO, D. A.; NASCIMENTO, M. T. DO; SOUZA, A. L. DE.
bitstream/item/75813/1/bolpd-303.pdf
Tipo: Boletim de Pesquisa e Desenvolvimento (INFOTECA-E) Palavras-chave: Fungo micorrízico arbuscular; Nutrientes; Arbuscular mycorrhizal fungus.; Rizosfera; Soja.; Nutrients; Soybeans.; Rhizosphere.
Ano: 2011 URL: http://www.infoteca.cnptia.embrapa.br/infoteca/handle/doc/931541
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Effect of Bacillus thuringiensis on microbial functional groups in sorghum rhizosphere PAB
Brasil,Carlos; Matsumoto,Leopoldo Sussumu; Nogueira,Marco Antonio; Spago,Flavia Regina; Rampazo,Luís Gustavo; Cruz,Marcio Ferreira; Andrade,Galdino.
The objective of this work was to assess the effect of two strains of Bacillus thuringiensis var. kurstaki on sorghum rhizosphere microorganisms. The strains were HD1, that produces the bioinsecticidal protein, and 407, that is a mutant non-producer. The strains do not influence microbial population, but reduce plant growth and improve mycorrhizal colonization and free living fixing N2 community.
Tipo: Info:eu-repo/semantics/report Palavras-chave: Bioinsecticide; Sorgum; Rhizosphere; Biocontrol.
Ano: 2006 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-204X2006000500022
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Effect of plant photosynthesis, carbon sources and ammonium availability on nitrogen fixation rates in the rhizosphere of Zostera noltii ArchiMer
Welsh, Dt; Bourgues, S; Dewit, R; Auby, Isabelle.
Rates of nitrogen fixation (measured as acetylene reduction) in the rhizosphere of the seagrass Zostera noltii were highly dependent upon plant photosynthetic activity being significantly stimulated at elevated CO2 concentrations and by light, both in the short-term and over diurnal cycles. Stimulation by light became insignificant when 5 mM sucrose was added to the sediment porewater, indicating that in the absence of added carbon sources, light stimulation was due to direct inputs of plant photosynthate to the rhizosphere. Addition of a range of carbon sources to the rhizosphere sediment stimulated rates of acetylene reduction, with this stimulation being significant for sucrose and lactate. Surprisingly, whilst low additions of ammonium to the sediment...
Tipo: Text Palavras-chave: Acetylene reduction; Nitrogen fixation; Rhizosphere; Zostera noltii; Plant photosynthesis; Root exudates; Carbon sources; Ammonium.
Ano: 1997 URL: http://archimer.ifremer.fr/doc/00151/26266/24350.pdf
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Efficient protocols for the extraction of microbial DNA from the rhizosphere of hydrophilic forests in Chile Ciencia e Investigación Agraria
Cáceres,Pablo; Cordero,Cecilia; González,Gloria; Quiroz,Karla; Bobadilla,Juan C; Bravo,Carmen; Caligari,Peter D.S; Carrasco,Basilio; García-Gonzales,Rolando.
A lysis buffer-based protocol (Protocol BA), a modified lysis buffer-based protocol (Protocol BA Mod) and a commercial extraction kit (Protocol PS Kit) (Power Soil, Mo bio Laboratories, CA USA) were each evaluated for their ability to produce high-quality DNA with yields sufficient to allow its use in biodiversity studies. Similarly, the effect of liquid nitrogen on the process of cell disruption in all of the protocols that were studied. DNA yields ranged from 12.4 ng g-1 of processed soil to 9620 ng g-1 using the modified lysis buffer and commercial extraction kit, respectively. The quality of the DNA was determined by the ability of the DNA to produce efficient and reproducible polymerase chain reaction (PCR) products, using primers for universal 16S...
Tipo: Journal article Palavras-chave: Hydrophilic forests; 16S ribosomal RNA; PCR; Rhizosphere; Soil DNA extraction.
Ano: 2012 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0718-16202012000300018
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Enhancement of clover growth by inoculation of P-solubilizing fungi and arbuscular mycorrhizal fungi Anais da ABC (AABC)
Souchie,Edson L.; Azcón,Rosario; Barea,Jose M.; Silva,Eliane M.R.; Saggin-Júnior,Orivaldo J..
This study evaluated the synergism between several P-solubilizing fungi isolates and arbuscular mycorrhizal fungi to improve clover ( Trifolium pratense) growth in the presence of Araxá apatite. Clover was sown directly in plastic pots with 300g of sterilized washed sand, vermiculite and sepiolite 1:1:1 (v:v:v) as substrate, and grown in a controlled environment chamber. The substrate was fertilized with 3 g L-1 of Araxá apatite. A completely randomized design, in 8×2 factorial scheme (eight P-solubilizing fungi treatments with or without arbuscular mycorrhizal fungi)and four replicates were used. The P-solubilizing fungi treatments consisted of five Brazilian P-solubilizing fungi isolates (PSF 7, 9, 20, 21 and 22), two Spanish isolates ( Aspergillus niger...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Araxá apatite; Phosphate solubilization; Co-inoculation; Plant growth promotion; Rhizosphere.
Ano: 2010 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0001-37652010000300023
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Exploring interactions of plant microbiomes Scientia Agricola
Andreote,Fernando Dini; Gumiere,Thiago; Durrer,Ademir.
A plethora of microbial cells is present in every gram of soil, and microbes are found extensively in plant and animal tissues. The mechanisms governed by microorganisms in the regulation of physiological processes of their hosts have been extensively studied in the light of recent findings on microbiomes. In plants, the components of these microbiomes may form distinct communities, such as those inhabiting the plant rhizosphere, the endosphere and the phyllosphere. In each of these niches, the "microbial tissue" is established by, and responds to, specific selective pressures. Although there is no clear picture of the overall role of the plant microbiome, there is substantial evidence that these communities are involved in disease control, enhance...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Microbial communities; Rhizosphere; Endophytes; Phyllosphere.
Ano: 2014 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-90162014000600013
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Extraction of bulk DNA from Thar Desert soils for optimization of PCR-DGGE based microbial community analysis Electron. J. Biotechnol.
Kumar Gothwal,Raj; Kumar Nigam,Vinod; Mohan,M. Krishna; Sasmal,Dinakar; Ghosh,Purnendu.
A reliable method for characterizing microbial communities on the basis of their differences in the 16S ribosomal RNA (rRNA) gene sequences in the hot arid zone sandy soils has been optimized. A desert plant (Calligonum polygonoides) was chosen to provide the rhizospheric soil samples, collected from three different agro-ecological locations. Total community DNA was efficiently extracted at small-scale level using direct lysis with hot sodium dodecyl sulphate (SDS), glass bead beating and finally subjecting the sandy soil to liquid nitrogen freeze-thaw cycles. To amplify V3 region of bacterial 16S rRNA gene, universal conserved primers were used. Second round polymerase chain reaction (PCR) was attempted to increase product concentration and to minimize...
Tipo: Journal article Palavras-chave: Arid soils; Microbial community; PCR-DGGE; Rhizosphere; Soil DNA extraction.
Ano: 2007 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582007000300007
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