Academic literature on the topic 'Root microbiota'
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Journal articles on the topic "Root microbiota"
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Salas-González, Isai, Guilhem Reyt, Paulina Flis, Valéria Custódio, David Gopaulchan, Niokhor Bakhoum, Tristan P. Dew, et al. "Coordination between microbiota and root endodermis supports plant mineral nutrient homeostasis." Science 371, no. 6525 (November 19, 2020): eabd0695. http://dx.doi.org/10.1126/science.abd0695.
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Plant roots and animal guts have evolved specialized cell layers to control mineral nutrient homeostasis. These layers must tolerate the resident microbiota while keeping homeostatic integrity. Whether and how the root diffusion barriers in the endodermis, which are critical for the mineral nutrient balance of plants, coordinate with the microbiota is unknown. We demonstrate that genes controlling endodermal function in the model plant Arabidopsis thaliana contribute to the plant microbiome assembly. We characterized a regulatory mechanism of endodermal differentiation driven by the microbiota with profound effects on nutrient homeostasis. Furthermore, we demonstrate that this mechanism is linked to the microbiota’s capacity to repress responses to the phytohormone abscisic acid in the root. Our findings establish the endodermis as a regulatory hub coordinating microbiota assembly and homeostatic mechanisms.
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Fitzpatrick, Connor R., and Adam C. Schneider. "Unique bacterial assembly, composition, and interactions in a parasitic plant and its host." Journal of Experimental Botany 71, no. 6 (January 6, 2020): 2198–209. http://dx.doi.org/10.1093/jxb/erz572.
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Abstract How plant-associated microbiota are shaped by, and potentially contribute to, the unique ecology and heterotrophic life history of parasitic plants is relatively unknown. Here, we investigate the leaf and root bacterial communities of the root holoparasite Orobanche hederae and its host Hedera spp. from natural populations. Root bacteria inhabiting Orobanche were less diverse, had fewer co-associations, and displayed increased compositional similarity to leaf bacteria relative to Hedera. Overall, Orobanche bacteria exhibited significant congruency with Hedera root bacteria across sites, but not the surrounding soil. Infection had localized and systemic effects on Hedera bacteria, which included effects on the abundance of individual taxa and root network properties. Collectively, our results indicate that the parasitic plant microbiome is derived but distinct from the host plant microbiota, exhibits increased homogenization between shoot and root tissues, and displays far fewer co-associations among individual bacterial members. Host plant infection is accompanied by modest changes of associated microbiota at both local and systemic scales compared with uninfected individuals. Our results are a first step towards extending the growing insight into the assembly and function of the plant microbiome to include the ecologically unique but often overlooked guild of heterotrophic plants.
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Takenaka, Shoji, Naoki Edanami, Yasutaka Komatsu, Ryoko Nagata, Traithawit Naksagoon, Maki Sotozono, Takako Ida, and Yuichiro Noiri. "Periodontal Pathogens Inhabit Root Caries Lesions Extending beyond the Gingival Margin: A Next-Generation Sequencing Analysis." Microorganisms 9, no. 11 (November 13, 2021): 2349. http://dx.doi.org/10.3390/microorganisms9112349.
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We performed a comprehensive microbiome analysis of root caries lesions using 22 teeth extracted from patients with severe periodontitis. The carious lesions were mechanically collected and cryo-pulverized following tooth extraction. Differences in the microbiome were compared between independent lesions at the supragingival site (SG) and lesions extending beyond the gingival margin (GCB). DNA was extracted and the microbiome was characterized on the basis of the V3-V4 hypervariable region of the 16S rRNA gene using paired-end sequencing on an Illumina MiSeq device. The microbiota in root caries lesions showed compositionally distinct microbiota depending on the location. The most abundant OTUs in the SG group were Streptococcus (26.0%), Actinomyces (10.6%), and Prevotella (7.6%). GCB presented Prevotella (11.1%) as the most abundant genus, followed by Fusobacterium (9.6%) and Actinomyces (8.7%). The SG group showed a lack of uniformity in microbiota compared with the GCB group. The bacterial profiles of GCB varied considerably among patients, including periodontal pathogens such as Porphyromonas, Selenomonas, Filifactor, Peptococcus, and Tannerella. Periodontal pathogens inhabit root caries lesions that extend beyond the gingival margin. This study provides a new perspective for elucidating the microbial etiology of root caries.
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Ramírez-Puebla, Shamayim T., Luis E. Servín-Garcidueñas, Berenice Jiménez-Marín, Luis M. Bolaños, Mónica Rosenblueth, Julio Martínez, Marco Antonio Rogel, Ernesto Ormeño-Orrillo, and Esperanza Martínez-Romero. "Gut and Root Microbiota Commonalities." Applied and Environmental Microbiology 79, no. 1 (October 26, 2012): 2–9. http://dx.doi.org/10.1128/aem.02553-12.
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ABSTRACTAnimal guts and plant roots have absorption roles for nutrient uptake and converge in harboring large, complex, and dynamic groups of microbes that participate in degradation or modification of nutrients and other substances. Gut and root bacteria regulate host gene expression, provide metabolic capabilities, essential nutrients, and protection against pathogens, and seem to share evolutionary trends.
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Hines, Pamela J. "Mix of metabolites tunes root microbiota." Science 364, no. 6440 (May 9, 2019): 542.12–544. http://dx.doi.org/10.1126/science.364.6440.542-l.
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Mapelli, Francesca, Valentina Riva, Lorenzo Vergani, Redouane Choukrallah, and Sara Borin. "Unveiling the Microbiota Diversity of the Xerophyte Argania spinosa L. Skeels Root System and Residuesphere." Microbial Ecology 80, no. 4 (June 25, 2020): 822–36. http://dx.doi.org/10.1007/s00248-020-01543-4.
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Abstract The microbiota associated to xerophyte is a “black box” that might include microbes involved in plant adaptation to the extreme conditions that characterize their habitat, like water shortage. In this work, we studied the bacterial communities inhabiting the root system of Argania spinosa L. Skeels, a tree of high economic value and ecological relevance in Northern Africa. Illumina 16S rRNA gene sequencing and cultivation techniques were applied to unravel the bacterial microbiota’s structure in environmental niches associated to argan plants (i.e., root endosphere, rhizosphere, root-surrounding soil), not associated to the plant (i.e., bulk soil), and indirectly influenced by the plant being partially composed by its leafy residue and the associated microbes (i.e., residuesphere). Illumina dataset indicated that the root system portions of A. spinosa hosted different bacterial communities according to their degree of association with the plant, enriching for taxa typical of the plant microbiome. Similar alpha- and beta-diversity trends were observed for the total microbiota and its cultivable fraction, which included 371 isolates. In particular, the residuesphere was the niche with the highest bacterial diversity. The Plant Growth Promotion (PGP) potential of 219 isolates was investigated in vitro, assessing several traits related to biofertilization and biocontrol, besides the production of exopolysaccharides. Most of the multivalent isolates showing the higher PGP score were identified in the residuesphere, suggesting it as a habitat that favor their proliferation. We hypothesized that these bacteria can contribute, in partnership with the argan root system, to the litter effect played by this tree in its native arid lands.
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French, Elizabeth, Tri Tran, and Anjali S. Iyer-Pascuzzi. "Tomato Genotype Modulates Selection and Responses to Root Microbiota." Phytobiomes Journal 4, no. 4 (January 2020): 314–26. http://dx.doi.org/10.1094/pbiomes-02-20-0020-r.
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Using microbial inoculants to enhance plant health is promising for crop improvement. However, for success, knowledge of how different cultivars within a crop species select and respond to the root microbiome is critical. The aims of this study were to (i) determine the contribution of tomato genotype to the tomato root bacterial microbiome and (ii) investigate whether closely related tomato genotypes differ in their selection of and response to root endophytes. We used 16S ribosomal RNA amplicon sequencing to examine the root bacterial communities of six Solanum lycopersicum (domesticated tomato) and two S. pimpinellifolium (wild tomato) accessions. We found that, across accessions, both the root endosphere and rhizosphere were affected by genotype. Genotype accounted for 10% of the variation in root microbiota. Two bacterial families, Bacillaceae and Rhizobiaceae, were significantly enriched in the root endosphere in at least six of the eight tomato genotypes. To investigate whether closely related tomato genotypes differed in selection of these endosphere-enriched taxa, we profiled the root endosphere of 20 recombinant inbred lines (RILs) derived from two of the genotypes. The abundance of Bacillaceae and Rhizobiaceae isolates varied quantitatively in the root endosphere of the RILs. Inoculation of 16 RILs with a Bacillaceae isolate identified from the root endosphere of field-grown tomato showed that RIL responses, in terms of shoot and root growth, varied from less than 5% growth enhancement to more than 40%. Our data show that tomato genotypes have distinct but overlapping root bacterial microbiomes and respond differently to specific bacterial endophytes.
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Rovai, Emanuel da Silva, Felipe de Souza Matos, Warley David Kerbauy, Flávia Goulart da Rosa Cardoso, Frederico Canato Martinho, Luciane Dias de Oliveira, Marcia Carneiro Valera, and Cláudio Antonio Talge Carvalho. "Microbial Profile and Endotoxin Levels in Primary Periodontal Lesions with Secondary Endodontic Involvement." Brazilian Dental Journal 30, no. 4 (July 2019): 356–62. http://dx.doi.org/10.1590/0103-6440201902471.
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Abstract This study was carried out to investigate the microbial profile and endotoxin levels of endodontic-periodontal lesions of periodontal origin. Periodontal and endodontic samples were taken from periodontal pockets and necrotic root canals of 10 teeth with endodontic-periodontal lesions. Evidencing of 40 different bacterial species were determined in each endodontic and periodontal sample using the checkerboard DNA-DNA hybridization method and Kinetic chromogenic LAL assay was used for quantification of endotoxins. Fisher’s exact test correlated the bacterial species with the endodontic or periodontal microbiota. The endotoxin levels (EU/mL) found in samples of the root canal and periodontal pocket were compared by the Wilcoxon test (p<0.05). Bacteria and LPS units were found in 100% of the endodontic and periodontal samples. The species E. faecium, P. acnes, G. morbillorum, C. sputigena and L. buccalis were strongly correlated with the endodontic microbiota and P. nigrescens with the periodontal microbiota. P. intermedia, P. endodontalis and V. parvula were more prevalent in both endodontic and periodontal microbiots. The endotoxin levels in the periodontal pocket (89600 EU/mL) were significantly higher than in the root canal (2310 EU/mL). It was concluded that the microbiota present in the periodontal and endodontic tissues is similar, with a higher prevalence of species of the orange complex and a higher level of endotoxin in the periodontal pockets.
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Bodenhausen, Natacha, Vincent Somerville, Alessandro Desirò, Jean-Claude Walser, Lorenzo Borghi, Marcel G. A. van der Heijden, and Klaus Schlaeppi. "Petunia- and Arabidopsis-Specific Root Microbiota Responses to Phosphate Supplementation." Phytobiomes Journal 3, no. 2 (January 2019): 112–24. http://dx.doi.org/10.1094/pbiomes-12-18-0057-r.
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Phosphorus (P) is a limiting element for plant growth. Several root microbes, including arbuscular mycorrhizal fungi (AMF), have the capacity to improve plant nutrition and their abundance is known to depend on P fertility. However, how complex root-associated bacterial and fungal communities respond to various levels of P supplementation remains ill-defined. Here we investigated the responses of the root-associated bacteria and fungi to varying levels of P supply using 16S rRNA gene and internal transcribed spacer amplicon sequencing. We grew Petunia, which forms symbiosis with AMF, and the nonmycorrhizal model species Arabidopsis as a control in a soil that is limiting in plant-available P and we then supplemented the plants with complete fertilizer solutions that varied only in their phosphate concentrations. We searched for microbes, whose abundances varied by P fertilization, tested whether a core microbiota responding to the P treatments could be identified and asked whether bacterial and fungal co-occurrence patterns change in response to the varying P levels. Root microbiota composition varied substantially in response to the varying P application. A core microbiota was not identified as different bacterial and fungal groups responded to low-P conditions in Arabidopsis and Petunia. Microbes with P-dependent abundance patterns included Mortierellomycotina in Arabidopsis, while in Petunia, they included AMF and their symbiotic endobacteria. Of note, the P-dependent root colonization by AMF was reliably quantified by sequencing. The fact that the root microbiotas of the two plant species responded differently to low-P conditions suggests that plant species specificity would need to be considered for the eventual development of microbial products that improve plant P nutrition. [Formula: see text]Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
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Watanabe, Aya, Hiroyuki Sasaki, Hiroki Miyakawa, Yuki Nakayama, Yijin Lyu, and Shigenobu Shibata. "Effect of Dose and Timing of Burdock (Arctium lappa) Root Intake on Intestinal Microbiota of Mice." Microorganisms 8, no. 2 (February 6, 2020): 220. http://dx.doi.org/10.3390/microorganisms8020220.
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Water-soluble dietary fiber such as inulin improves the beta diversity of the intestinal microbiota of mice fed with a high-fat diet (HFD). The circadian clock is the system that regulates the internal daily rhythm, and it affects the pattern of beta diversity in mouse intestinal microbiota. Burdock (Arctium lappa) root contains a high concentration of inulin/fructan (approximately 50%) and is a very popular vegetable in Japan. Arctium lappa also contains functional substances that may affect intestinal microbiota, such as polyphenols. We compared the effects of inulin and A. lappa powder on the diversity of the intestinal microbiota of HFD-fed mice. 16S rDNA from the intestinal microbiota obtained from feces was analyzed by 16S Metagenomic Sequencing Library Preparation. It was found to have a stronger effect on microbiota than inulin alone, suggesting that inulin has an additive and/or synergic action with other molecules in A. lappa root. We examined the effects of intake timing (breakfast or dinner) of A. lappa on intestinal microbiota. The intake of A. lappa root in the evening had a stronger effect on microbiota diversity in comparison to morning intake. Therefore, it is suggested that habitual consumption of A. lappa root in the evening may aid the maintenance of healthy intestinal microbiota.
Dissertations / Theses on the topic "Root microbiota"
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Aleklett, Kristin Anna Eva. "Examining ecological determinants of community formation and stability in the root microbiota." Thesis, University of British Columbia, 2015. http://hdl.handle.net/2429/56741.
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The root system of a plant is known to host a wide diversity of microbes that can be beneficial or detrimental to the plant. Microbial ecologists have long struggled to understand the factors influencing the composition of these communities. One overlooked aspect of microbial community assembly in root systems is the potential for individual variation among plants, and the potential effect of early colonisation events such as microbial exposure of the seed inside the parent plant and during dispersal.
In this dissertation, I relate ecological theory of community assembly to the formation of the root microbiota. I explore the extent of variation between individuals in wild plant populations, and examine the effects of historical contingency in determining bacterial and fungal community assembly and stability in the root microbiota.
The main findings in my work showed that:
- Wild plants growing in close proximity, sharing environmental conditions will still host distinct bacterial communities in their root systems based on their species identity. We also documented individual variation in root microbiota within all species examined, even the clonal plant species Pilosella aurantiaca.
- Bacterial community composition varies significantly across the body of a plant, with different parts of the plant body hosting distinct communities.
- Plants are able to form new microbial associations throughout development, but the timing of microbial exposure affects the composition of the microbial community in mature plants.
- Microbial community stability fluctuates within weeks during early plant development, with one week-old plants hosting communities most likely to change in composition.Irving K. Barber School of Arts and Sciences (Okanagan)
Biology, Department of (Okanagan)
Graduate
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Yamashita, José Carlos. "Avaliação da microbiota e da reparação apical e periapical após preparo biomecânico de canais radiculares com diferentes soluções irrigadoras, em dentes de cães com reação periapical crônica /." Araraquara : [s.n.], 2004. http://hdl.handle.net/11449/101639.
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Orientador: Mário Tanomaru FilhoBanca: Mario Roberto Leonardo
Banca: Léa Assed Bezerra da Silva
Banca: Igor Prokopowitsch
Banca: Francisco José de Souza Filho
Resumo: O objetivo deste estudo foi avaliar a microbiota presente no sistema canais radiculares antes e após o preparo biomecânico; e as condições histopatológicas da reparação apical e periapical após preparo biomecânico dos canais radiculares de dentes com reação periapical crônica. Foram utilizados 78 canais radiculares de dentes de cães, os quais, após indução de lesão periapical, foram submetidos ao preparo biomecânico utilizando as seguintes soluções irrigadoras: solução de digluconato de clorexidina a 2%, de hipoclorito de sódio a 2,5% ou soro fisiológico. Um grupo controle não recebeu preparo biomecânico. Foram realizadas culturas microbiológicas antes e após 30 dias do preparo biomecânico. Após este período os animais foram mortos para processamento e análise histopatológica. O estudo microbiológico demonstrou que houve redução dos microrganismos nos grupos que utilizaram soluções antimicrobianas (p<0,05), com melhor resultado para a solução de clorexidina. Os grupos que utilizaram solução fisiológica controle apresentaram aumento de microrganismos. No estudo histopatológico, foi observado, de um modo geral, infiltrado inflamatório periapical severo e em grande extensão, severo espessamento do ligamento periodontal e grandes áreas de reabsorção óssea e apical em todos os grupos (p>0,05). Concluiu-se que o emprego de soluções irrigadoras antimicrobianas durante o preparo biomecânico promove redução da microbiota endodôntica, sem a sua eliminação do sistema de canais radiculares em dentes de cães com lesão periapical. A solução de clorexidina a 2% proporcionou maior redução da microbiota que a solução de hipoclorito de sódio a 2,5% (p<0,05). Porém, os resultados histopatológicos demonstram que somente o preparo biomecânico não foi capaz de criar condições para reparação dos tecidos apicais e periapicais.
Abstract: The aim of this study was to evaluate the microorganisms in the root canal system before and after biomechanical preparation and the apical and periapical repair after this biomechanical preparation. The study was performed in 78 root canals of dog's teeth with induced chronic periradicular lesion. There were used the following endodontic irrigating solutions: 2% chlorhexidine digluconate solution; 2.5% sodium hypochlorite solution, saline solution and a control group without biomechanical preparation. The microbiological sampling were performed before and 30 days after the biomechanical preparation. After this period the animals were killed to histological analysis. In the microbiologic study, the results showed that the antimicrobial solutions used reduced the number of microorganisms (p<0.05). The chlorhexidine solution showed better performance. The group that used saline solution and the control group presented an increased number of microorganisms. The histological results showed a severe periapical inflammation, severe thickness of periodontal ligament, apical and osseous resorption in all groups (p>0.05). It was concluded that the antimicrobial endodontic solution reduced but not eliminated the microorganisms present in root canals of dogþs teeth with necrosis and periapical lesion. The chlorhexidine solution was more effective in reducing the number of microorganisms than sodium hypochlorite solution (p<0.05). Although, the histopathological results showed that the biomechanical preparation alone was not capable to promote an adequate condition for the apical and periapical tissues repair.
Doutor
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Yamashita, José Carlos [UNESP]. "Avaliação da microbiota e da reparação apical e periapical após preparo biomecânico de canais radiculares com diferentes soluções irrigadoras, em dentes de cães com reação periapical crônica." Universidade Estadual Paulista (UNESP), 2004. http://hdl.handle.net/11449/101639.
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yamashita_jc_dr_arafo.pdf: 1654679 bytes, checksum: ea4cab55ba1e8890848c0a5afe9fc1d2 (MD5)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
O objetivo deste estudo foi avaliar a microbiota presente no sistema canais radiculares antes e após o preparo biomecânico; e as condições histopatológicas da reparação apical e periapical após preparo biomecânico dos canais radiculares de dentes com reação periapical crônica. Foram utilizados 78 canais radiculares de dentes de cães, os quais, após indução de lesão periapical, foram submetidos ao preparo biomecânico utilizando as seguintes soluções irrigadoras: solução de digluconato de clorexidina a 2%, de hipoclorito de sódio a 2,5% ou soro fisiológico. Um grupo controle não recebeu preparo biomecânico. Foram realizadas culturas microbiológicas antes e após 30 dias do preparo biomecânico. Após este período os animais foram mortos para processamento e análise histopatológica. O estudo microbiológico demonstrou que houve redução dos microrganismos nos grupos que utilizaram soluções antimicrobianas (p<0,05), com melhor resultado para a solução de clorexidina. Os grupos que utilizaram solução fisiológica controle apresentaram aumento de microrganismos. No estudo histopatológico, foi observado, de um modo geral, infiltrado inflamatório periapical severo e em grande extensão, severo espessamento do ligamento periodontal e grandes áreas de reabsorção óssea e apical em todos os grupos (p>0,05). Concluiu-se que o emprego de soluções irrigadoras antimicrobianas durante o preparo biomecânico promove redução da microbiota endodôntica, sem a sua eliminação do sistema de canais radiculares em dentes de cães com lesão periapical. A solução de clorexidina a 2% proporcionou maior redução da microbiota que a solução de hipoclorito de sódio a 2,5% (p<0,05). Porém, os resultados histopatológicos demonstram que somente o preparo biomecânico não foi capaz de criar condições para reparação dos tecidos apicais e periapicais.
The aim of this study was to evaluate the microorganisms in the root canal system before and after biomechanical preparation and the apical and periapical repair after this biomechanical preparation. The study was performed in 78 root canals of dog's teeth with induced chronic periradicular lesion. There were used the following endodontic irrigating solutions: 2% chlorhexidine digluconate solution; 2.5% sodium hypochlorite solution, saline solution and a control group without biomechanical preparation. The microbiological sampling were performed before and 30 days after the biomechanical preparation. After this period the animals were killed to histological analysis. In the microbiologic study, the results showed that the antimicrobial solutions used reduced the number of microorganisms (p<0.05). The chlorhexidine solution showed better performance. The group that used saline solution and the control group presented an increased number of microorganisms. The histological results showed a severe periapical inflammation, severe thickness of periodontal ligament, apical and osseous resorption in all groups (p>0.05). It was concluded that the antimicrobial endodontic solution reduced but not eliminated the microorganisms present in root canals of dogþs teeth with necrosis and periapical lesion. The chlorhexidine solution was more effective in reducing the number of microorganisms than sodium hypochlorite solution (p<0.05). Although, the histopathological results showed that the biomechanical preparation alone was not capable to promote an adequate condition for the apical and periapical tissues repair.
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Hou, Shiji [Verfasser], Paul [Gutachter] Schulze-Lefert, and Ute [Gutachter] Höcker. "Root microbiota functions in mitigating abiotic and biotic stresses in Arabidopsis / Shiji Hou ; Gutachter: Paul Schulze-Lefert, Ute Höcker." Köln : Universitäts- und Stadtbibliothek Köln, 2021. http://d-nb.info/1231992778/34.
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Dombrowski, Nina [Verfasser], Paul [Akademischer Betreuer] Schulze-Lefert, Alga [Akademischer Betreuer] Zuccaro, and George [Akademischer Betreuer] Coupland. "Structural and functional analysis of the bacterial root microbiota of Arabidopsis thaliana and relative species / Nina Dombrowski. Gutachter: Paul Schulze-Lefert ; Alga Zuccaro ; George Coupland." Köln : Universitäts- und Stadtbibliothek Köln, 2015. http://d-nb.info/1071369857/34.
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Lopes, Lucas Dantas. "From communities to genomes: a multifaceted approach to depict bacterial life in soils." Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/11/11140/tde-02012018-141554/.
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Unraveling soil microbial ecology is essential for improving sustainable agricultural productivity. Community-based studies revolutionized this field in the last decades, but much is yet to be disclosed. This thesis proposed an approach to increase the resolution of such studies by combining 16S rDNA high-throughput sequencing and population genomics, aiming to further explore the differences pointed by community analyses, as well as to overcome the limitations of using operational taxonomic units (OTUs) as ecological entities, and to introduce the evolutionary thinking in microbial ecology. Our main goal was to understand the features that make bacteria able to colonize sugarcane rhizosphere or live saprophytically in bulk soil. Rhizosphere and bulk soil are contrasting habitats for microbial life as they are highly distinct in its physical, chemical and consequently biological characteristics. Our results indicated that sugarcane shapes the rhizosphere microbiome and metabolism of D-galacturonic acid is a key function for colonizing this niche. Among the taxa prevailing in the rhizosphere, Pseudomonas genus was targeted for a more detailed study considering its known attributes for plant growth promotion. Seventy-six fluorescent Pseudomonas spp. were isolated and submitted to whole genome sequencing (WGS). A comparative genomic analysis was performed between populations from rhizosphere and bulk soil. Phylogenetic analyses classified the isolates in the P. fluorescens (57) or P. putida (19) groups. Twelve putative new species and two new proposed P. fluorescens subgroups were found in the prospected tropical soil. Comparative genomics revealed that phosphatases or xylose-utilization genes were significantly enriched in the rhizosphere and bulk soil populations of the P. fluorescens group, respectively. D-galactonate catabolism was higher in the rhizosphere population of the P. putida group based on both genotypic and phenotypic results. Growth in D-xylose was further explored using genetic modified strains and confirmed that this sugar is more used by members of the bulk soil than the rhizosphere population of the P. fluorescens group, a pattern also observed in the bulk soil microbiome. In summary, these findings constitute a step forward in understanding the ecology of rhizosphere and bulk soil bacteria, by overcoming some limitations of community-based analyses and showing genomic differences between bacterial populations of these habitats.Desvendar a ecologia microbiana do solo é essencial para aumentar a produtividade agrícola sustentável. Estudos baseados em comunidades revolucionaram esse campo nas últimas décadas, mas ainda há muito a ser revelado. Esta tese propôs uma abordagem para aumentar a resolução desses estudos, combinando sequenciamento em larga escala de rDNA 16S e genômica populacional, com o objetivo de explorar mais a fundo as diferenças apontadas por análises de comunidades, assim como superar as limitações do uso de unidades taxonômicas operacionais (UTOs) como entidades ecológicas e introduzir o pensamento evolutivo na ecologia microbiana. Nossa principal meta foi entender as características que tornam as bactérias hábeis em colonizar a rizosfera de cana-de-açúcar ou viver no solo saprofiticamente. Rizosfera e solo são hábitats contrastantes para a vida microbiana, já que são altamente distintos em suas características físicas, químicas e, consequentemente, biológicas. Nossos resultados indicaram que a cana-de-açúcar modifica o microbioma da rizosfera e o metabolismo do ácido D-galacturônico é uma função chave para colonizar este nicho. Dentre os táxons que prevalecem na rizosfera, o gênero Pseudomonas foi escolhido para um estudo mais detalhado, considerando os seus atributos de promoção de crescimento de plantas. Setenta e seis Pseudomonas spp. fluorescentes foram isoladas e submetidas ao sequenciamento do genoma. Uma análise de genômica comparativa foi realizada entre as populações obtidas do solo e rizosfera. As análises filogenéticas classificaram os isolados nos grupos P. fluorescens (57) ou P. putida (19). Doze prováveis novas espécies e dois novos subgrupos propostos de P. fluorescens foram encontrados no solo tropical prospectado. A genômica comparativa revelou que genes de fosfatases e de uso de xilose foram significativamente enriquecidos nas populações da rizosfera e solo do grupo P. fluorescens, respectivamente. O catabolismo do ácido D-galactônico foi maior na população da rizosfera do grupo P. putida, baseado tanto em resultados genotípicos quanto fenotípicos. O crescimento em D-xilose foi mais explorado usando linhagens geneticamente modificadas e confirmou que este açúcar é mais utilizado por membros da população do solo do que da rizosfera no grupo P. fluorescens, um padrão também observado no microbioma do solo. Em resumo, essas descobertas constituem um passo adiante no entendimento da ecologia bacteriana do solo e rizosfera, por superar algumas limitações de análises de comunidades e mostrar diferenças genômicas entre populações bacterianas destes hábitats.
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Achemedei, Bronwyn. "Potential risk factors associated with the microbiota of grass roots in the Kimberley region of Western Australia." Thesis, Achemedei, Bronwyn (2016) Potential risk factors associated with the microbiota of grass roots in the Kimberley region of Western Australia. Honours thesis, Murdoch University, 2016. https://researchrepository.murdoch.edu.au/id/eprint/35151/.
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The Kimberley region of Australia is a biological hotspot with highly diverse and often endemic flora and fauna. Much of the area has been understudied, although this has changed in recent years. The diversity of the microbiota of the region has remained relatively understudied, with the exception of a limited survey aimed at assessing the distribution of the pathogen Burkholderia pseudomallei. This study hypothesised that previously uncharacterised human pathogenic bacteria are present in the soils of the Kimberley region.
A total of 49 isolates were obtained from the rhizosphere, rhizoplane and bulk soil of 15 plant specimens. Of these, 18 isolates were identified as species that have been shown to cause disease in humans, and four isolates were selected to characterise further. The virulence of a Klebsiella pneumoniae, and three Burkholderia cepacia complex isolates were compared to clinical isolates. It was found that each isolate exhibited virulence factors, showing the ability to adhere to macrophage cells, form biofilms, and produce unique lipopolysaccharides. This study showed that the microbiota of the Kimberley region has the potential to cause disease in humans.
To further investigate the risk posed to the human population, these isolates should be studied further with improved virulence, and infection assays. Whole genome sequences should be analysed for the presence of specific virulence genes. The remaining uncharacterised isolates that have shown to be pathogenic in a clinical setting should be characterised further. Future studies should include a collection of more plant specimens, with more diversity in grass species collected, and from wider areas.
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Ourry, Morgane. "Contribution à l'analyse des interactions tripartites entre Brassica napus, Delia radicum et leur microbiote." Thesis, Rennes, Agrocampus Ouest, 2019. http://www.theses.fr/2019NSARA032.
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Les microorganismes exercent une forte influence sur les interactions plante-insecte. Nous avons étudié l’interaction entre le colza (Brassica napus), la mouche du chou (Delia radicum) et les communautés microbiennes qui leur sont associées. La diversité microbienne du sol a été manipulée par dilution jusqu’à extinction pour évaluer son effet sur la chimie de la plante et les traits d’histoire de vie de l’insecte. La différence de diversité a influencé le taux d’émergence et l’oviposition de la mouche, mais pas la chimie de la plante. A l’inverse, la phytophagie par D. radicum a drastiquement modifié la chimie des racines et les communautés microbiennes des racines et de la rhizosphère. Nous avons proposé le scénario selon lequel les plantes soumises à des attaques de phytophages produiraient des composes défensifs mais recruteraient aussi avec des composés chimiques attractifs, des microorganismes du sol qui permettraient à la plante de maintenir sesdéfenses. Les communautés bactériennes des mouches adultes, sans leur symbiote facultatif Wolbachia, ont été étudiées à l’aide d’un antibiotique. Nous avons montré que la tétracycline diminuait la diversité bactérienne des mouches sans les rendre stériles, modifiait la composition des communautés, et que les effets étaient durables sur plusieurs générations. Enfin, l’étude de la transmission des bactéries chez D. radicum a montré deux espèces partagées entre les femelles et les oeufs, et deux autres entre les larves et les racines et le sol. Cette étude montre qu’avoir une meilleure compréhension des interactions plantesinsecMicroorganisms have a strong influence on plant-insect interactions. We have studied the interaction between oilseed rape (Brassica napus), the cabbage root fly (Delia radicum) and their associated microbial communities. Soil microbial diversity was manipulated with the dilution to extinction approach to assess its effect on plant chemistry and insect life history traits. Diversity variation influenced the fly emergence rate and oviposition, but not plant chemistry. Conversely, herbivory by D. radicum strongly modified root chemistry and both root and rhizosphere microbial communities. We proposed a scenario that in the presence of herbivory, plants would produce defensive compounds but also would recruit, with attractive chemical compounds, soil microorganismsthat may maintain plant defenses. Bacterial communities of adult flies, free of their facultative symbiont Wolbachia, were studied using an antibiotic. We showed that tetracycline decreased fly bacterial diversity, without making them sterile, modified community composition, and that effect lasted over several generations. Lastly, studying bacterial transmission in D. radicum showed two species shared between females and eggs, and two others between larvae and both roots and rhizosphere. This study showed that having a better understanding of plant-insect interactions and how strongly microorganisms can influence their own host or other interacting organisms is a crucial step that could promote microbial applications in a context of insect biological control
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Lima, Bruna Roese de. "Detecção microbiana e de genes de resistência em ecossistemas da cavidade oral de pacientes infantis com necrose pulpar." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2015. http://hdl.handle.net/10183/128201.
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Alguns estudos caracterizaram a microbiota de canais radiculares de dentes decíduos com necrose pulpar como polimicrobiana, com predomínio de microrganismos anaeróbios. No entanto, nenhum estudo até o presente momento investigou a presença de genes de resistência a antimicrobianos em diferentes ecossistemas da cavidade oral de crianças. Este estudo tem por objetivo determinar a presença de espécies de Prevotella e do gene cfxa/cfxa2 associados à resistência à beta-lactâmicos, em diferentes ecossistemas orais de crianças com necrose pulpar. Vinte e sete crianças, que estavam sob cuidados odontológicos no Ambulatório de Clínica Infanto-Juvenil da Faculdade de Odontologia da UFRGS, e que apresentavam, pelo menos, um dente decíduo com necrose pulpar foram selecionados para este estudo. Foram coletadas amostras de saliva, biofilme supragengival, biofilme da câmara pulpar e do canal radicular de 32 dentes (27 posteriores e 5 anteriores). Após isolamento do DNA microbiano, a presença das bactérias Prevotella intermedia, Prevotella nigrescens, Prevotella tannerae e do gene cfxA/cfxA2 foi avaliada através do método de PCR. A amostra foi composta de pacientes com idade média de 5,5 anos (± 1,76). A taxa total de espécies de Prevotella foi de 29,1%, 25%, 21,8% e 32,29% em amostras de saliva, biofilme, câmara pulpar e canal radicular, respectivamente. As três espécies juntas não foram detectadas em todos os micro-ambientes do mesmo paciente, mas estavam presentes em 3,1% (n=1) de amostras do canal radicular. Prevotella nigrescens foi a bactéria mais frequentemente encontrada em todos os ecossistemas estudados. Foram observadas diferenças estatisticamente significativas em relação à presença de P. nigrescens em pelo menos um local e idade do paciente (teste t, p = 0,04). Também foi encontrada associação entre a presença desta bactéria, em pelo menos um local e uso de antimicrobianos (teste exato de Fisher, p = 0,014). A presença do gene de resistência à beta-lactâmicos, cfxA/cfxA2, foi testada em 12 pacientes da amostra, nos quatro micro-ambientes orais. Entre esses pacientes, 55,6% eram meninas, com idade média de 6 anos (± 2,5). Não foi detectada a presença deste gene em nenhuma amostra investigada. Os dados sugerem que a cavidade bucal de crianças com necrose pulpar apresenta presença diversificada de espécies de Prevotella em diferentes micro-ambientes orais. A ausência do gene cfxA/cfxA2 foi observada em todas as amostras investigadas. Estudos futuros, testando a presença de outros genes de resistência à beta-lactâmicos, são importantes para uma investigação abrangente.Some studies characterized the microbiota of root canals of primary teeth with pulp necrosis as polymicrobial, with a predominance of anaerobic microorganisms. However, no study to date has investigated the presence of antimicrobial resistance genes in different ecosystems of the oral cavity of children. This study aims to determine the presence of Prevotella species and genes associated with resistance to beta-lactams in different oral enviroments of children with pulp necrosis. Twenty-seven children who were under dental care at the Children and Youth Clinic (Dental School, UFRGS, Porto Alegre, Brazil), and who had at least one primary tooth with pulp necrosis were selected for this study. Saliva, supragingival biofilm, pulp chamber biofilm and root canal biofilm were collected of 32 teeth (27 posterior and 5 anterior). After isolation of microbial DNA, the presence of Prevotella intermedia, Prevotella nigrescens, Prevotella tannerae and cfxA/cfxA2 gene were evaluated using the PCR. The sample consisted of patients with a mean age of 5.5 years (± 1.76). The total rate of Prevotella species was 29.1%, 25%, 21.8% and 32.29% in saliva samples, biofilm, pulp chamber and root canal, respectively. The three strains were not detected in all enviroments of the same patient, but were present at 3.1% (n = 1) of the root canal samples. Prevotella nigrescens was the most common bacteria in all oral enviroments. Statistical significant differences were observed for the presence of P. nigrescens at least one oral enviroment and age of the patient (t-test, p = 0.04). Also an association was observed, among the presence of these bacteria in at least one enviroment and use of antimicrobials (Fisher's exact test, p = 0.014). The presence of the resistance gene to beta-lactams, cfxA/cfxA2, was tested on 12 patients of the sample at all four oral enviroments. Among these patients, 55.6% were girls with a mean age of 6 years (± 2.5). Absence of this gene in the sample investigated was detected. The absence of cfxA/cfxA2 gene was observed in all the investigated samples. Future studies testing the presence of other resistance genes to beta-lactams, are important for a comprehensive investigation.
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Pump, Judith [Verfasser], and Ralf [Akademischer Betreuer] Conrad. "Carbon translocation and methane emission in flooded rice microcosms with a manipulated root microbiome / Judith Pump. Betreuer: Ralf Conrad." Marburg : Philipps-Universität Marburg, 2013. http://d-nb.info/1035502224/34.
Full textBooks on the topic "Root microbiota"
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MD, Raphael Kellman. Microbiome Thyroid: Heal Your Gut and Discover the Root Cause of Hidden Thyroid Disease. Hachette Go, 2021.
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author, Biklé Anne, ed. The hidden half of nature: The microbial roots of life and health. W.W. Norton & Company, 2016.
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Krochmal, Robert. Nutritional Support and Addiction. Edited by Shahla J. Modir and George E. Muñoz. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780190275334.003.0017.
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Nutrition occupies a central position in the treatment of SUDs. Given the paradox that food can have apparently opposing effects in either causing addiction or in influencing its remedy, it is important to clarify this difference. Evidence is mounting that diseases such as obesity, heart disease, diabetes, and mental health disorders including addiction have a common root cause related to the increase in sugar and processed food consumption rather than fat consumption as has been commonly held. In addition to new integrative approach models encompassing a holistic perspective, new developments in genetics and epigenetics as well as the human microbiome and gut-brain health provide further evidence of the mechanisms by which a healthy approach to nutrition can change outcomes. Building upon the neurobiological theory of addiction and reward deficiency, these breakthroughs lead to new hope for a successful approach to recovery.
Book chapters on the topic "Root microbiota"
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Assad, Rezwana, Zafar Ahmad Reshi, and Irfan Rashid. "Root-Associated Ectomycorrhizal Mycobionts as Forest Biofertilizers: Standardized Molecular Methods for Characterization of Ectomycorrhizal Wood Wide Web." In Microbiota and Biofertilizers, 165–80. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-48771-3_10.
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Singh, Akanksha, Rupesh Chaubey, Stuti Srivastava, Sumit Kushwaha, and Rakesh Pandey. "Beneficial Root Microbiota: Transmogrifiers of Secondary Metabolism in Plants." In Emerging Trends in Plant Pathology, 343–65. Singapore: Springer Singapore, 2020. http://dx.doi.org/10.1007/978-981-15-6275-4_16.
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Schlaeppi, Klaus, Emiel Ver Loren van Themaat, Davide Bulgarelli, and Paul Schulze-Lefert. "Arabidopsis thalianaas Model for Studies on the Bacterial Root Microbiota." In Molecular Microbial Ecology of the Rhizosphere, 243–56. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118297674.ch23.
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Ghosh, Srayan, and Shraboni Ghosh. "Ally or Foe: Role of Soil Microbiota in Shaping Root Architecture." In Rhizobiology: Molecular Physiology of Plant Roots, 73–91. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-84985-6_6.
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Zolla, Gaston, Matthew G. Bakker, Dayakar V. Badri, Jacqueline M. Chaparro, Amy M. Sheflin, Daniel K. Manter, and Jorge Vivanco. "Understanding Root-Microbiome Interactions." In Molecular Microbial Ecology of the Rhizosphere, 743–54. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118297674.ch70.
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Pantigoso, Hugo A., Yanhui He, Michael J. DiLegge, and Jorge M. Vivanco. "Methods for Root Exudate Collection and Analysis." In The Plant Microbiome, 291–303. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-1040-4_22.
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Marappa, Narayanasamy, D. Dhanasekaran, and Thajuddin Nooruddin. "Root Nodule Microbiome from Actinorhizal Casuarina Plant." In Microbiome-Host Interactions, 295–305. First edition. | Boca Raton : CRC Press, 2021.: CRC Press, 2021. http://dx.doi.org/10.1201/9781003037521-22.
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Song, Yang, Corné M. J. Pieterse, Peter A. H. M. Bakker, and Roeland L. Berendsen. "Collection of Sterile Root Exudates from Foliar Pathogen-Inoculated Plants." In The Plant Microbiome, 305–17. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-1040-4_23.
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Robinson, Rebekah J., Vanessa N. Kavamura, Penny R. Hirsch, Ian M. Clark, and Tim H. Mauchline. "Culture-based Methods for Studying the Bacterial Root Microbiome of Wheat." In The Plant Microbiome, 53–60. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-1040-4_6.
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Weigh, Katherine V., Bruna D. Batista, and Paul G. Dennis. "A Bait-Trap Assay to Characterize Soil Microbes that Exhibit Chemotaxis to Root Exudates." In The Plant Microbiome, 283–89. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-1040-4_21.
Full textConference papers on the topic "Root microbiota"
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Akosah, Yaw Abaye, D. S. Pudova, S. G. Vologin, and A. M. Mardanova. "The influence of growth stage on the structure and formation of fungal microbiota in potato root." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.013.
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Melnyk, N., D. Popowski, L. Peeters, J. P. Piwowarski, and S. Granica. "Interaction of the extract from marigold flowers and comfrey root with human skin microbiota." In GA – 70th Annual Meeting 2022. Georg Thieme Verlag KG, 2022. http://dx.doi.org/10.1055/s-0042-1759303.
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Ramirez-Villacis, Dario. "Root Microbiome Modulates Plant Growth Promotion Induced by Low Doses of Glyphosate." In ASPB PLANT BIOLOGY 2020. USA: ASPB, 2020. http://dx.doi.org/10.46678/pb.20.1383160.
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Стратулат, Татьяна, Татьяна Щербакова, Штефан Кручан, and Андрей Лунгу. "Пораженность листвы древесных насаждений города Кишинева комплексом гнилей летом 2021 года." In VIIth International Scientific Conference “Genetics, Physiology and Plant Breeding”. Institute of Genetics, Physiology and Plant Protection, Republic of Moldova, 2021. http://dx.doi.org/10.53040/gppb7.2021.92.
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To determine the complex of fungi that cause rot on the leaves and needles of tree species in the green spaces of Chisinau, foliage was collected in four sectors of the city. It was determined by microbio-logical methods that the complex of pathogens on the leaves differs little in different sectors. The main leaf rot fungi present on the affected leaves and needles are Alternaria sp., Aspergillus sp., Fusarium sp., Penicillium sp. For the treatment of the green spaces of Chisinau against diseases, it is advisable to carry out phytosanitary measures with biological products.
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Murphy, Katherine. "Bioactive diterpeids impact the composition of the root-associated microbiome in maize (Zea mays)." In ASPB PLANT BIOLOGY 2020. USA: ASPB, 2020. http://dx.doi.org/10.46678/pb.20.989597.
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Hooshmand, K., EN Kudjordjie, R. Sapkota, M. Nicolaisen, and IS Fomsgaard. "How plant shape their root associated microbiome to acquire resilience against pathogen infection? What is the mechanism behind?" In 67th International Congress and Annual Meeting of the Society for Medicinal Plant and Natural Product Research (GA) in cooperation with the French Society of Pharmacognosy AFERP. © Georg Thieme Verlag KG, 2019. http://dx.doi.org/10.1055/s-0039-3399655.
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Liang, Bingbing, Wenyu Fan, Jing Ginger Han, Ning Chen, and Nan Zhao. "An implementation of infants' gut microbiome maturation analyses by 16s rRNA from stool samples in extraction solution of room temperature." In 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2017. http://dx.doi.org/10.1109/bibm.2017.8217778.
Full textReports on the topic "Root microbiota"
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Minz, Dror, Stefan J. Green, Noa Sela, Yitzhak Hadar, Janet Jansson, and Steven Lindow. Soil and rhizosphere microbiome response to treated waste water irrigation. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7598153.bard.
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Research objectives : Identify genetic potential and community structure of soil and rhizosphere microbial community structure as affected by treated wastewater (TWW) irrigation. This objective was achieved through the examination soil and rhizosphere microbial communities of plants irrigated with fresh water (FW) and TWW. Genomic DNA extracted from soil and rhizosphere samples (Minz laboratory) was processed for DNA-based shotgun metagenome sequencing (Green laboratory). High-throughput bioinformatics was performed to compare both taxonomic and functional gene (and pathway) differences between sample types (treatment and location). Identify metabolic pathways induced or repressed by TWW irrigation. To accomplish this objective, shotgun metatranscriptome (RNA-based) sequencing was performed. Expressed genes and pathways were compared to identify significantly differentially expressed features between rhizosphere communities of plants irrigated with FW and TWW. Identify microbial gene functions and pathways affected by TWW irrigation*. To accomplish this objective, we will perform a metaproteome comparison between rhizosphere communities of plants irrigated with FW and TWW and selected soil microbial activities. Integration and evaluation of microbial community function in relation to its structure and genetic potential, and to infer the in situ physiology and function of microbial communities in soil and rhizospere under FW and TWW irrigation regimes. This objective is ongoing due to the need for extensive bioinformatics analysis. As a result of the capabilities of the new PI, we have also been characterizing the transcriptome of the plant roots as affected by the TWW irrigation and comparing the function of the plants to that of the microbiome. *This original objective was not achieved in the course of this study due to technical issues, especially the need to replace the American PIs during the project. However, the fact we were able to analyze more than one plant system as a result of the abilities of the new American PI strengthened the power of the conclusions derived from studies for the 1ˢᵗ and 2ⁿᵈ objectives. Background: As the world population grows, more urban waste is discharged to the environment, and fresh water sources are being polluted. Developing and industrial countries are increasing the use of wastewater and treated wastewater (TWW) for agriculture practice, thus turning the waste product into a valuable resource. Wastewater supplies a year- round reliable source of nutrient-rich water. Despite continuing enhancements in TWW quality, TWW irrigation can still result in unexplained and undesirable effects on crops. In part, these undesirable effects may be attributed to, among other factors, to the effects of TWW on the plant microbiome. Previous studies, including our own, have presented the TWW effect on soil microbial activity and community composition. To the best of our knowledge, however, no comprehensive study yet has been conducted on the microbial population associated BARD Report - Project 4662 Page 2 of 16 BARD Report - Project 4662 Page 3 of 16 with plant roots irrigated with TWW – a critical information gap. In this work, we characterize the effect of TWW irrigation on root-associated microbial community structure and function by using the most innovative tools available in analyzing bacterial community- a combination of microbial marker gene amplicon sequencing, microbial shotunmetagenomics (DNA-based total community and gene content characterization), microbial metatranscriptomics (RNA-based total community and gene content characterization), and plant host transcriptome response. At the core of this research, a mesocosm experiment was conducted to study and characterize the effect of TWW irrigation on tomato and lettuce plants. A focus of this study was on the plant roots, their associated microbial communities, and on the functional activities of plant root-associated microbial communities. We have found that TWW irrigation changes both the soil and root microbial community composition, and that the shift in the plant root microbiome associated with different irrigation was as significant as the changes caused by the plant host or soil type. The change in microbial community structure was accompanied by changes in the microbial community-wide functional potential (i.e., gene content of the entire microbial community, as determined through shotgun metagenome sequencing). The relative abundance of many genes was significantly different in TWW irrigated root microbiome relative to FW-irrigated root microbial communities. For example, the relative abundance of genes encoding for transporters increased in TWW-irrigated roots increased relative to FW-irrigated roots. Similarly, the relative abundance of genes linked to potassium efflux, respiratory systems and nitrogen metabolism were elevated in TWW irrigated roots when compared to FW-irrigated roots. The increased relative abundance of denitrifying genes in TWW systems relative FW systems, suggests that TWW-irrigated roots are more anaerobic compare to FW irrigated root. These gene functional data are consistent with geochemical measurements made from these systems. Specifically, the TWW irrigated soils had higher pH, total organic compound (TOC), sodium, potassium and electric conductivity values in comparison to FW soils. Thus, the root microbiome genetic functional potential can be correlated with pH, TOC and EC values and these factors must take part in the shaping the root microbiome. The expressed functions, as found by the metatranscriptome analysis, revealed many genes that increase in TWW-irrigated plant root microbial population relative to those in the FW-irrigated plants. The most substantial (and significant) were sodium-proton antiporters and Na(+)-translocatingNADH-quinoneoxidoreductase (NQR). The latter protein uses the cell respiratory machinery to harness redox force and convert the energy for efflux of sodium. As the roots and their microbiomes are exposed to the same environmental conditions, it was previously hypothesized that understanding the soil and rhizospheremicrobiome response will shed light on natural processes in these niches. This study demonstrate how newly available tools can better define complex processes and their downstream consequences, such as irrigation with water from different qualities, and to identify primary cues sensed by the plant host irrigated with TWW. From an agricultural perspective, many common practices are complicated processes with many ‘moving parts’, and are hard to characterize and predict. Multiple edaphic and microbial factors are involved, and these can react to many environmental cues. These complex systems are in turn affected by plant growth and exudation, and associated features such as irrigation, fertilization and use of pesticides. However, the combination of shotgun metagenomics, microbial shotgun metatranscriptomics, plant transcriptomics, and physical measurement of soil characteristics provides a mechanism for integrating data from highly complex agricultural systems to eventually provide for plant physiological response prediction and monitoring. BARD Report
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Jung, Carina, Matthew Carr, Eric Fleischman, and Chandler Roesch. Response of the green June beetle and its gut microbiome to RDX and phenanthrene. Engineer Research and Development Center (U.S.), November 2020. http://dx.doi.org/10.21079/11681/38799.
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Green June beetles are a cosmopolitan pest in the United States. Adults are voracious consumers of tree and vine fruit, while their larvae can dam-age and inadvertently consume root systems, particularly those of grasses, as they move through the soil and forage for detritus. Larvae ingest and process large volumes of soil while in the process of feeding. Due to their intimate contact with the soil it was hypothesized that soil contaminants that are known animal toxins would perturb the larval and affect their overall health and survival. Studies of this kind are important contribu-tions to the development of new model organisms and our understanding of interactions between the environment, contaminants, gut microbiome, and animal development, health, and survival. It is important to continue to develop relevant model organisms for monitoring toxicity as regulations for working with vertebrates becomes more prohibitive. In this study green June beetle larvae were exposed to RDX and phenanthrene through-out their entire soil-bound development, starting within the first few days of hatching through to their emergence as adults. The overall findings included that even at high concentrations, RDX and phenanthrene (25 ppm) exerted no significant effect on body weight or survival. Also, there was lit-tle apparent effect of RDX and phenanthrene on the bacterial microbiome, and no statistical association with measurable health effects. Nevertheless, the green June beetle is an interesting model for soil toxicity experiments in the future as is it easy to collect, house, and handle.
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Crowley, David E., Dror Minz, and Yitzhak Hadar. Shaping Plant Beneficial Rhizosphere Communities. United States Department of Agriculture, July 2013. http://dx.doi.org/10.32747/2013.7594387.bard.
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PGPR bacteria include taxonomically diverse bacterial species that function for improving plant mineral nutrition, stress tolerance, and disease suppression. A number of PGPR are being developed and commercialized as soil and seed inoculants, but to date, their interactions with resident bacterial populations are still poorly understood, and-almost nothing is known about the effects of soil management practices on their population size and activities. To this end, the original objectives of this research project were: 1) To examine microbial community interactions with plant-growth-promoting rhizobacteria (PGPR) and their plant hosts. 2) To explore the factors that affect PGPR population size and activity on plant root surfaces. In our original proposal, we initially prqposed the use oflow-resolution methods mainly involving the use of PCR-DGGE and PLFA profiles of community structure. However, early in the project we recognized that the methods for studying soil microbial communities were undergoing an exponential leap forward to much more high resolution methods using high-throughput sequencing. The application of these methods for studies on rhizosphere ecology thus became a central theme in these research project. Other related research by the US team focused on identifying PGPR bacterial strains and examining their effective population si~es that are required to enhance plant growth and on developing a simulation model that examines the process of root colonization. As summarized in the following report, we characterized the rhizosphere microbiome of four host plant species to determine the impact of the host (host signature effect) on resident versus active communities. Results of our studies showed a distinct plant host specific signature among wheat, maize, tomato and cucumber, based on the following three parameters: (I) each plant promoted the activity of a unique suite of soil bacterial populations; (2) significant variations were observed in the number and the degree of dominance of active populations; and (3)the level of contribution of active (rRNA-based) populations to the resident (DNA-based) community profiles. In the rhizoplane of all four plants a significant reduction of diversity was observed, relative to the bulk soil. Moreover, an increase in DNA-RNA correspondence indicated higher representation of active bacterial populations in the residing rhizoplane community. This research demonstrates that the host plant determines the bacterial community composition in its immediate vicinity, especially with respect to the active populations. Based on the studies from the US team, we suggest that the effective population size PGPR should be maintained at approximately 105 cells per gram of rhizosphere soil in the zone of elongation to obtain plant growth promotion effects, but emphasize that it is critical to also consider differences in the activity based on DNA-RNA correspondence. The results ofthis research provide fundamental new insight into the composition ofthe bacterial communities associated with plant roots, and the factors that affect their abundance and activity on root surfaces. Virtually all PGPR are multifunctional and may be expected to have diverse levels of activity with respect to production of plant growth hormones (regulation of root growth and architecture), suppression of stress ethylene (increased tolerance to drought and salinity), production of siderophores and antibiotics (disease suppression), and solubilization of phosphorus. The application of transcriptome methods pioneered in our research will ultimately lead to better understanding of how management practices such as use of compost and soil inoculants can be used to improve plant yields, stress tolerance, and disease resistance. As we look to the future, the use of metagenomic techniques combined with quantitative methods including microarrays, and quantitative peR methods that target specific genes should allow us to better classify, monitor, and manage the plant rhizosphere to improve crop yields in agricultural ecosystems. In addition, expression of several genes in rhizospheres of both cucumber and whet roots were identified, including mostly housekeeping genes. Denitrification, chemotaxis and motility genes were preferentially expressed in wheat while in cucumber roots bacterial genes involved in catalase, a large set of polysaccharide degradation and assimilatory sulfate reduction genes were preferentially expressed.