Academic literature on the topic 'Rhizosphere microbiota'
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Journal articles on the topic "Rhizosphere microbiota"
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Karpenko, V. P., S. P. Poltoretskyi, V. V. Liubych, D. M. Adamenko, I. S. Kravets, R. M. Prytuliak, V. S. Kravchenko, N. I. Patyka, and V. P. Patyka. "Microbiota in the Rhizosphere of Cereal Crops." Mikrobiolohichnyi Zhurnal 83, no. 1 (February 17, 2021): 21–31. http://dx.doi.org/10.15407/microbiolj83.01.021.
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Today, spelt wheat grain is used to produce high quality food. Intermediate wheatgrass is a promising crop for prairie restoration. One of the elements of biologization is the influence of growing crops on the microbiota of soil rhizosphere. The microbiota of spelt wheat and intermediate wheatgrass soil rhizosphere remains insufficiently studied. Aim. To study the number of individual groups of microbiota in dynamics in the rhizosphere of cereal crops (spelt wheat, intermediate wheatgrass) depending on the weather conditions and the phase of plants development. Methods. Classical microbiological, statistical methods were used in the work. In particular, the study of the number of microorganisms of different ecological and trophic groups (ammonifying, nitrifying, cellulolytic and nitrogen-fixing) was carried out according to generally accepted methods in soil microbiology. The reliability of the influence of factors was determined by the probability value «р» level which was calculated using STATISTICA 8 program. Results. The amount of ammonifying and cellulolytic microorganisms in the soil rhizosphere of spelt wheat is significantly higher compared to soft wheat. The rhizosphere microbiota amount of the intermediate wheatgrass on the 2–3 year of cultivation was more resistant to adverse environmental factors compared to soft wheat. The soil rhizosphere microbiota did not change a lot depending on the phase of plant development during the vegetation period of cereal crops (spelt wheat, intermediate wheatgrass). Conclusions. The formation of rhizosphere microbiota of spelt wheat and intermediate wheatgrass was first analyzed under the conditions of the Right-Bank forest-steppe of Ukraine. The conducted studies indicate the feasibility of growing and use of spelt wheat in breeding programs to create cultivars of soft wheat with higher activity of rhizosphere microbiota. The number of ammonifying, nitrifying and cellulolytic microorganisms of soil rhizosphere of intermediate wheatgrass was significantly higher compared to soft wheat during all growth stages. The conducted studies confirm the practical application of intermediate wheatgrass to preserve and increase soil fertility. Intermediate wheatgrass can be grown for up to three years in one field, as microbiological activity reaches its maximum development.
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Cheng, Zhiqiang, Shaonan Lei, Ye Li, Wei Huang, Rongqin Ma, Juan Xiong, Ting Zhang, et al. "Revealing the Variation and Stability of Bacterial Communities in Tomato Rhizosphere Microbiota." Microorganisms 8, no. 2 (January 25, 2020): 170. http://dx.doi.org/10.3390/microorganisms8020170.
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Microorganisms that colonize the plant rhizosphere can contribute to plant health, growth and productivity. Although the importance of the rhizosphere microbiome is known, we know little about the underlying mechanisms that drive microbiome assembly and composition. In this study, the variation, assembly and composition of rhizobacterial communities in 11 tomato cultivars, combined with one cultivar in seven different sources of soil and growing substrate, were systematically investigated. The tomato rhizosphere microbiota was dominated by bacteria from the phyla Proteobacteria, Bacteroidetes, and Acidobacteria, mainly comprising Rhizobiales, Xanthomonadales, Burkholderiales, Nitrosomonadales, Myxococcales, Sphingobacteriales, Cytophagales and Acidobacteria subgroups. The bacterial community in the rhizosphere microbiota of the samples in the cultivar experiment mostly overlapped with that of tomato cultivar MG, which was grown in five natural field soils, DM, JX, HQ, QS and XC. The results supported the hypothesis that tomato harbors largely conserved communities and compositions of rhizosphere microbiota that remains consistent in different cultivars of tomato and even in tomato cultivar grown in five natural field soils. However, significant differences in OTU richness (p < 0.0001) and bacterial diversity (p = 0.0014 < 0.01) were observed among the 7 different sources of soil and growing substrate. Two artificial commercial nutrient soils, HF and CF, resulted in a distinct tomato rhizosphere microbiota in terms of assembly and core community compared with that observed in natural field soils. PERMANOVA of beta diversity based on the combined data from the cultivar and soil experiments demonstrated that soil (growing substrate) and plant genotype (cultivar) had significant impacts on the rhizosphere microbial communities of tomato plants (soil, F = 22.29, R2 = 0.7399, p < 0.001; cultivar, F = 2.04, R2 = 0.3223, p = 0.008). Of these two factors, soil explained a larger proportion of the compositional variance in the tomato rhizosphere microbiota. The results demonstrated that the assembly process of rhizosphere bacterial communities was collectively influenced by soil, including the available bacterial sources and biochemical properties of the rhizosphere soils, and plant genotype.
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Zhang, Xiaoke, Huili Wang, Zhifei Li, Jun Xie, and Jiajia Ni. "Hydrological and soil physiochemical variables determine the rhizospheric microbiota in subtropical lakeshore areas." PeerJ 8 (September 29, 2020): e10078. http://dx.doi.org/10.7717/peerj.10078.
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Background Due to intensive sluice construction and other human disturbances, lakeshore vegetation has been destroyed and ecosystems greatly changed. Rhizospheric microbiota constitute a key part of a functioning rhizosphere ecosystem. Maintaining rhizosphere microbial diversity is a central, critical issue for sustaining these rhizospheric microbiota functions and associated ecosystem services. However, the community composition and abiotic factors influencing rhizospheric microbiota in lakeshore remain largely understudied. Methods The spatiotemporal composition of lakeshore rhizospheric microbiota and the factors shaping them were seasonally investigated in three subtropical floodplain lakes (Lake Chaohu, Lake Wuchang, and Lake Dahuchi) along the Yangtze River in China through 16S rRNA amplicon high-throughput sequencing. Results Our results showed that four archaeal and 21 bacterial phyla (97.04 ± 0.25% of total sequences) dominated the rhizospheric microbiota communities of three lakeshore areas. Moreover, we uncovered significant differences among rhizospheric microbiota among the lakes, seasons, and average submerged depths. The Acidobacteria, Actinobacteria, Bacteroidetes, Bathyarchaeota, Gemmatimonadetes, and Proteobacteria differed significantly among the three lakes, with more than half of these dominant phyla showing significant changes in abundance between seasons, while the DHVEG-6, Ignavibacteriae, Nitrospirae, Spirochaetes, and Zixibacteria varied considerably across the average submerged depths (n = 58 sites in total). Canonical correspondence analyses revealed that the fluctuation range of water level and pH were the most important factors influencing the microbial communities and their dominant microbiota, followed by total nitrogen, moisture, and total phosphorus in soil. These results suggest a suite of hydrological and soil physiochemical variables together governed the differential structuring of rhizospheric microbiota composition among different lakes, seasons, and sampling sites. This work thus provides valuable ecological information to better manage rhizospheric microbiota and protect the vegetation of subtropical lakeshore areas.
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Dries, Leonie, Maximilian Hendgen, Sylvia Schnell, Otmar Löhnertz, and Anne Vortkamp. "Rhizosphere engineering: leading towards a sustainable viticulture?" OENO One 55, no. 2 (June 11, 2021): 353–63. http://dx.doi.org/10.20870/oeno-one.2021.55.2.4534.
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Microorganisms are a substantial component of the rhizosphere, and the activity and composition of rhizosphere microbial populations markedly affect interactions between plants and the soil environment. In addition, the microbiota of the rhizosphere can positively influence plant development, growth and vitality. In vineyards, management practices influence both grapevine root growth directly and the rhizosphere microbiota, but the exact mode of action is largely unknown. Recently, however, two new research approaches are increasingly coming into focus to enhance grapevine growth and health: plant engineering and rhizosphere engineering. In plant engineering, knowledge about plant-microbiome interactions is used for plant breeding strategies. In rhizosphere engineering, microbial communities are modified by adding specific fertilisers, nutrients or by bio-inoculation with certain bacteria and/or fungi. Taken together, these new methods suggest a potential for reaching a more sustainable development of pesticide-reduced viticulture in the future.
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Han, Gil, Mohamed Mannaa, Hyoseong Jeon, Hyejung Jung, Jin-Cheol Kim, Ae Ran Park, and Young-Su Seo. "Dysbiosis in the Rhizosphere Microbiome of Standing Dead Korean Fir (Abies koreana)." Plants 11, no. 7 (April 5, 2022): 990. http://dx.doi.org/10.3390/plants11070990.
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The Korean fir (Abies koreana), a native coniferous tree species mainly found on Mt. Halla in Jeju, South Korea, is suffering from continuous population decline and has been declared an endangered species. Research efforts have focused on the possible abiotic causes behind this worrying decline. However, the potential link between tree vitality and the rhizosphere microbiome remains unclear. In this study, a comparative metagenomic 16S rRNA sequence analysis was used to investigate the composition of the rhizosphere microbiota of samples collected from healthy and die-back-affected trees on Mt. Halla. The results indicated a significant reduction in the richness and diversity of microbiota in the rhizosphere of die-back-affected trees. Moreover, the relative abundance of Proteobacteria, Actinobacteria, and Bacteroidetes were significantly higher in healthy trees than in standing dead trees. Many bacterial genera were significantly more abundant in the rhizosphere of healthy trees, including those known for promoting plant growth and tolerance to biotic and abiotic stresses (e.g., Bradyrhizobium, Rhizomicrobium, Caulobacter, Nitrosospira, Rhizobacter, Paraburkholderia, Rhizobium, Devosia, Caballeronia, Niveispirillum, Dyella, Herbaspirillum, Frankia, Streptomyces, Actinoallomurus, Lysobacter, Luteibacter, Mucilaginibacter, and Variovorax). To our knowledge, this is the first report on rhizosphere bacterial microbiome dysbiosis in die-back-affected Korean fir trees, suggesting that the influence of rhizosphere microbiota should be considered to save this endangered species by investigating possible intervention strategies in future work.
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Zhang, Zhen, Lu Chang, Xiuxiu Liu, Jing Wang, Xianhong Ge, Jiasen Cheng, Jiatao Xie, et al. "Rapeseed Domestication Affects the Diversity of Rhizosphere Microbiota." Microorganisms 11, no. 3 (March 11, 2023): 724. http://dx.doi.org/10.3390/microorganisms11030724.
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Rhizosphere microbiota is important for plant growth and health. Domestication is a process to select suitable plants to satisfy the needs of humans, which may have great impacts on the interaction between the host and its rhizosphere microbiota. Rapeseed (Brassica napus) is an important oilseed crop derived from the hybridization between Brassica rapa and Brassica oleracea ~7500 years ago. However, variations in rhizosphere microbiota along with rapeseed domestication remain poorly understood. Here, we characterized the composition and structure of the rhizosphere microbiota among diverse rapeseed accessions, including ten B. napus, two B. rapa, and three B. oleracea accessions through bacterial 16S rRNA gene sequencing. B. napus exhibited a higher Shannon index and different bacterial relative abundance compared with its wild relatives in rhizosphere microbiota. Moreover, artificial synthetic B. napus lines G3D001 and No.2127 showed significantly different rhizosphere microbiota diversity and composition from other B. napus accessions and their ancestors. The core rhizosphere microbiota of B. napus and its wild relatives was also described. FAPROTAX annotation predicted that the synthetic B. napus lines had more abundant pathways related to nitrogen metabolism, and the co-occurrence network results demonstrated that Rhodoplanes acted as hub nodes to promote nitrogen metabolism in the synthetic B. napus lines. This study provides new insights into the impacts of rapeseed domestication on the diversity and community structure of rhizosphere microbiota, which may highlight the contribution of rhizosphere microbiota to plant health.
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Zhatova, H. O., L. M. Bondarieva, and Y. V. Koplyk. "Features of the rhiospheric microbiota of medicinal plants." Bulletin of Sumy National Agrarian University. The series: Agronomy and Biology, no. 4(38) (December 25, 2019): 61–65. http://dx.doi.org/10.32845/agrobio.2019.4.9.
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Medicinal plants are the source of biologically active compounds that are in constant demand for the pharmacological industry. Active production of plant secondary metabolites is possible only under optimal conditions of plant growth and development. The state of medicinal plants is controlled not only by genotype and environmental conditions but by the qualitative and quantitative composition of their microbiota as well. The study of the structure and function of the rhizospheric communities of medicinal plants is important for obtaining of high quality medicinal raw materials. Microorganisms are the constant companions of higher plants, which can be used as a medicinal raw material. The rhizosphere microbiota is highly specific, even between different varieties of the same plant species. Each plant species has a specific microbiome of the rhizosphere, depending on the existing soil community. The rhizosphere of medicinal plants is marked by a special highly specific microbiome due to the specificity of root exudates. Active cell secretion of the roots provides nutrient substrates with microorganisms that form strong associations both inside the root tissues and on the root surface as well as in the soil around the roots. The purpose of the research was to study the effect of medicinal plants of different systematic groups on the composition of the microbial communities of the rhizosphere. The experiments were conducted in 2018–2019 at the nursery medicinal plant plot of the Department of ecology and botany of Sumy National Agrarian University.
Ecological-trophic groups of microorganisms associated with the roots of medicinal plants in the experiment were represented by ammonifying bacteria, nitrogen-fixing bacteria and bacterias that destroyed of plant residues (cellulose-destroying bacteria). In the analysis of the total number of microorganisms of the rhizosphere revealed differences in the quantitative and qualitative composition of microbiota, due to the specific features of a medicinal plant. Positive influence on the development of microflora in the area of the roots and individual ecological-trophic groups had Mentha longifolia (L)., and a negative effect was observed in plants of Bergenia crassifolia L. It has been established that the number of microorganisms and the diversity of ecological-trophic groups is due to the belonging of a medicinal plant to a particular taxon. The number of microorganisms and their diversity decreased in the direction of: Mentha longifolia – Lysimachia vulgaris – Aristolochia clematitis – Achillea submillefolium – Bergenia crassifolia.
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Sánchez-Salazar, Angela M., Jacquelinne J. Acuña, Michael J. Sadowsky, and Milko A. Jorquera. "Bacterial Community Composition and Presence of Plasmids in the Endosphere- and Rhizosphere-Associated Microbiota of Sea Fig (Carpobrotus aequilaterus)." Diversity 15, no. 11 (November 20, 2023): 1156. http://dx.doi.org/10.3390/d15111156.
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The plant microbiome is one of the most important environments for ecological interactions between bacteria that impact the plant and the ecosystem. However, studies on the diversity of mobile genetic elements (such as plasmids) associated with the plant microbiome are very scarce. Here, we determined the bacterial community composition and the occurrence of plasmids in the microbiota associated with sea fig, Carpobrotus aequilaterus (N.E. Br.), a succulent species widely used as an ornamental plant in Chile. The abundance and composition of the endophytic and rhizospheric bacterial communities were determined by quantitative PCR (qPCR) and DNA metabarcoding analysis. Plasmid diversity in the plant microbiome was determined by plasmid DNA extraction and screened by endpoint PCR of backbone genes for four different incompatibility groups (Inc). The results showed about 106 copies of the 16S rRNA gene in the endosphere and rhizosphere, showing significant differences according to the diversity index. Proteobacteria (Pseudomonadota; 43.4%), Actinobacteria (Actinomycetota; 25.7%), and Bacteroidetes (Bacteroidota; 17.4%) were the most dominant taxa in both plant compartments, and chemoheterotrophy (30%) was the main predicted function assigned to the microbiota. Plasmid diversity analysis showed the presence of transferable plasmids in the endosphere and rhizosphere of C. aequilaterus, particularly among environmental plasmids belonging to the IncP and IncN incompatibility groups.
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May-Mutul, Carla G., Miguel A. López-Garrido, Aileen O’Connor-Sánchez, Yuri J. Peña-Ramírez, Natalia Y. Labrín-Sotomayor, Héctor Estrada-Medina, and Miriam M. Ferrer. "Hidden Tenants: Microbiota of the Rhizosphere and Phyllosphere of Cordia dodecandra Trees in Mayan Forests and Homegardens." Plants 11, no. 22 (November 15, 2022): 3098. http://dx.doi.org/10.3390/plants11223098.
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During domestication, the selection of cultivated plants often reduces microbiota diversity compared with their wild ancestors. Microbiota in compartments such as the phyllosphere or rhizosphere can promote fruit tree health, growth, and development. Cordia dodecandra is a deciduous tree used by Maya people for its fruit and wood, growing, to date, in remnant forest fragments and homegardens (traditional agroforestry systems) in Yucatán. In this work, we evaluated the microbiota’s alpha and beta diversity per compartment (phyllosphere and rhizosphere) and per population (forest and homegarden) in the Northeast and Southwest Yucatán regions. Eight composite DNA samples (per compartment/population/region combination) were amplified for 16S-RNA (bacteria) and ITS1-2 (fungi) and sequenced by Illumina MiSeq. Bioinformatic analyses were performed with QIIME and phyloseq. For bacteria and fungi, from 107,947 and 128,786 assembled sequences, 618 and 1092 operating taxonomic units (OTUs) were assigned, respectively. The alpha diversity of bacteria and fungi was highly variable among samples and was similar among compartments and populations. A significant species turnover among populations and regions was observed in the rhizosphere. The core microbiota from the phyllosphere was similar among populations and regions. Forests and homegarden populations are reservoirs of the C. dodecandra phyllosphere core microbiome and significant rhizosphere biodiversity.
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Xu, Junhuan, Tyson Knight, Donchel Boone, Muhammad Saleem, Sheree J. Finley, Nicole Gauthier, Joseph A. Ayariga, et al. "Influence of Fungicide Application on Rhizosphere Microbiota Structure and Microbial Secreted Enzymes in Diverse Cannabinoid-Rich Hemp Cultivars." International Journal of Molecular Sciences 25, no. 11 (May 28, 2024): 5892. http://dx.doi.org/10.3390/ijms25115892.
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Microbes and enzymes play essential roles in soil and plant rhizosphere ecosystem functioning. However, fungicides and plant root secretions may impact the diversity and abundance of microbiota structure and enzymatic activities in the plant rhizosphere. In this study, we analyzed soil samples from the rhizosphere of four cannabinoid-rich hemp (Cannabis sativa) cultivars (Otto II, BaOx, Cherry Citrus, and Wife) subjected to three different treatments (natural infection, fungal inoculation, and fungicide treatment). DNA was extracted from the soil samples, 16S rDNA was sequenced, and data were analyzed for diversity and abundance among different fungicide treatments and hemp cultivars. Fungicide treatment significantly impacted the diversity and abundance of the hemp rhizosphere microbiota structure, and it substantially increased the abundance of the phyla Archaea and Rokubacteria. However, the abundances of the phyla Pseudomonadota and Gemmatimonadetes were substantially decreased in treatments with fungicides compared to those without fungicides in the four hemp cultivars. In addition, the diversity and abundance of the rhizosphere microbiota structure were influenced by hemp cultivars. The influence of Cherry Citrus on the diversity and abundance of the hemp rhizosphere microbiota structure was less compared to the other three hemp cultivars (Otto II, BaOx, and Wife). Moreover, fungicide treatment affected enzymatic activities in the hemp rhizosphere. The application of fungicides significantly decreased enzyme abundance in the rhizosphere of all four hemp cultivars. Enzymes such as dehydrogenase, dioxygenase, hydrolase, transferase, oxidase, carboxylase, and peptidase significantly decreased in all the four hemp rhizosphere treated with fungicides compared to those not treated. These enzymes may be involved in the function of metabolizing organic matter and degrading xenobiotics. The ecological significance of these findings lies in the recognition that fungicides impact enzymes, microbiota structure, and the overall ecosystem within the hemp rhizosphere.
Dissertations / Theses on the topic "Rhizosphere microbiota"
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Alegria, Terrazas Rodrigo. "Defining the host genetic control of the barley rhizosphere microbiota." Thesis, University of Dundee, 2019. https://discovery.dundee.ac.uk/en/studentTheses/4ca9658f-c69d-4c23-b1b2-46d0ef40339d.
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Limiting environmentally harmful consequences of crop production while increasing productivity amid climatic modifications is one of the major challenges facing agriculture in the XXIst century. Crucially, over the course of the next 30 years, innovative strategies are required to tackle this challenge and ensure a sustainable and safe access to food resources to a global population of over 9 billion people in 2050. One of these strategies proposes to exploit the microbial communities thriving in association with plant roots, collectively referred to as the rhizosphere microbiota, to uncouple profitable crop yield from the input of synthetic compounds in the agroecosystem. In the last decade technical advances have allowed scientists to gain unprecedented insights into plant-microbiota interactions in the rhizosphere. However, a precise understanding of how plants can shape these communities is still missing. This is information will be crucial to assist breeders in developing crops capable of maximising the mutualistic relationships with soil microbes. To fill this knowledge gap, in this thesis I use Barley (Hordeum vulgare), a global crop and an excellent experimental model, and will capitalise on state-of-the art sequencing and computational approaches to gain fundamentally novel insights into the host genetic control of the rhizosphere microbiota. The overarching hypothesis of my work is that the host genotype has the capacity to shape the rhizosphere microbiota to sustain plant growth in given soil conditions. I further hypothesize that this capacity impacts both the taxonomic and functional compositions of the rhizosphere microbiota and can be ultimately traced to loci in the barley genome. To test these hypotheses, I developed three major experimental lines aimed at a) characterising the microbiota of wild and cultivated barley genotypes grown in agricultural soils and how this impacts on plant growth; b) assessing the modulation of structure and function of the rhizosphere microbiota by the plant host under different nitrogen regimes and c) identifying the barley genetic region(s) responsible for the microbiota recruitment using experimental segregating populations between wild and modern barley genotypes. These experiments will contribute to decipher the genetic relationships between a plant genome and its associated microbiota and, in the long term, they will be key to devise novel strategies to enhance nutrient uptake efficiency in cereals.
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Walter, Diana Joyce, and dianawalter@internode on net. "The Environmental Impact of Genetically Modified Crop Plants on the Microbiology of the Rhizosphere." Flinders University. Biotechnology, 2005. http://catalogue.flinders.edu.au./local/adt/public/adt-SFU20070301.161014.
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The effect of genetically modified crop plants on the microbiology of the rhizosphere was investigated using the single-gene Bt cotton as a case study. The project compared the rhizosphere microbiota of four Ingard® 1cotton plant varieties that were closely matched with their non-GM parental strains. The plants were grown in
three different Australian soils, ie, a vertisol from a cotton-growing region, and two soils, a fine sandy loam and a red sand from South Australia that had not been exposed to cotton.
At the time of the commencement of the project, the only commercially available genetically modified plants were cotton and carnations. The cotton industry in Australia is worth $1.5b annually, and care of the soil and the dynamics of its living microbial consortia needs to be understood for optimum management to enable
agricultural sustainability. The general outline of the thesis incorporated four main sections:
1. Experimental setup and analysis of the soils and plants to be used, quantification of the Cry1A(c) plant-produced Bt protein, and its
persistence in the soil environment.
2. Measurement of the selected microbial populations of bacteria, fungi, AMfungi,
protozoans and nematodes, by counting and estimation by dilution and most-probable number methods.
3. Assessment of selected metabolic pathways to determine the effects on the soil microbial community by chemical and other biochemical methods
4. An overall analysis between different group ratios of expression of each of the variables tested, and the summary of the risk analysis and conclusion.
The outcome of this work was the acquisition of scientific data to produce an environmental impact report. The findings of this study showed that generally the microbial populations and the products of major metabolic pathways correlated more closely within the non-GM and GM plant rhizospheres of the paired trials than those
of separate trials, indicating that soil and plant cultivar had a stronger environmental effect. The results obtained from the paired trials did not show that there were consistent effects on the rhizosphere soil microbiota that could be attributed to the presence of the Cry1A(c) Bt plant protein on the selected strains of cotton plants.
The results from the tests of the paired trials correlate highly with previously published work that the risk factors of genetically modified cotton plants on the microbiology of the rhizosphere soil were found be negligible and not consistent across trials.
1 ® Monsanto Co. St Louis, MO.
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Chiaramonte, Josiane Barros. "The rhizosphere microbiome of common bean (Phaseolus vulgaris L.) and the effects on phosphorus uptake." Universidade de São Paulo, 2018. http://www.teses.usp.br/teses/disponiveis/11/11138/tde-17012019-161756/.
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The current population growth will demand a higher productive agriculture to full the food requirement. To supply this need and preserve the environment, many resources are applied to promote sustainable agriculture. Phosphorus depletion is the main factor that limits crops yields in tropical soils, where the pH and clay content rapid fixate this nutrient. Plant breeders aim to solve this issue by changing the plant requirements for phosphorus and adapting them to low P availability. However, with these approaches the demand for phosphorus fertilizers will continue and so the depletion of the natural deposits. In this study is proposed that plants with contrasting phosphorus uptake efficiency, i.e. P-efficient and P-inefficient, recruits distinct rhizosphere microbiome specialized in phosphorus mobilization. This hypothesis was tested growing plants in a gradient of two sources of P, triple superphosphate or rock phosphate Bayovar. Thebean rhizosphere microbiome was assessed with culture dependent and independent approaches, enzymatic assays, predictive metagenomics and networks analysis. A differential enrichment of several OTUs in the rhizosphere of the P-inefficient common bean genotype, and the enrichment of bacterial chemotaxis functions and functions involved in phosphorus mobilization suggest that this genotype has superior communication with the rhizosphere microbiome and is highly dependent on it for phosphorus mobilization. As a proof of concept, the P-efficientefficient genotype was sown in soil previously cultivated with P-inefficientinefficient genotype. The results showed that P-efficientefficient genotype positively responded to the modified rhizosphere in early stages, that is, the microbiome selected and enriched by the P-inefficient genotype improved the P uptake in the genotype cultivated afterwards in the same soil. Taken collectively, these results suggest that plants partly rely on the rhizosphere microbiome for P uptake and that the exploration of these interactions during plant breeding would allow the selection of even more efficient genotypes, leading to a sustainable agriculture by exploring soil residual P.O atual aumento populacional irá demandar uma maior produção agrícola para completar a necessidade de alimento. Para suprir essa necessidade e preservar o meio ambiente, muitos recursos serão aplicados para promover a agricultura sustentável. A depleção de fósforo é um dos principais fatores que limita a produção agrícola em solos tropicais, onde o pH e o conteúdo de argila fixam rapidamente esse nutriente. Os melhoristas de plantas visam solucionar esse problema alterando a necessidade de fósforo das plantas e adaptando-as as baixas disponibilidade de fósforo. No entanto, com essas estratégias a demanda por fertilizantes fosfatados irá continuar assim como a exploração das reservas naturais de fósforo. Nesse estudo foi proposto que as plantas contrastantes em relação a eficiência na absorção de fósforo, i.e. P-eficiente e P-ineficiente, recrutariam um microbioma rizosférico distinto em relação a mobilização de fósforo. Essa hipótese foi testada cultivando plantas em um gradiente usando duas fontes distintas de P, triplo fosfato ou fosfato de rocha Bayovar. O microbioma da rizosfera de feijão foi então avaliado por técnicas dependentes e independentes de cultivo, análise enzimática, predição metagenômica e análises de network. Um enriquecimento diferencial de várias OTUs observado na rizosfera do genótipo de feijão P-ineficiente, e o enriquecimento de funções de quimiotaxia bacteriana e envolvidas na mobilização de fósforo sugerem que esse genótipo tem uma maior comunicação com o microbioma rizosférico e é altamente dependente deste para a mobilização de fósforo. Como prova de conceito, o genótipo P-eficiente foi plantado em solo previamente cultivadocom o genótipo P-ineficiente. Os resultados mostraram que o genótipo P-eficiente responde positivamente à rizosfera modificada nos estádios iniciais de crescimento, ou seja, o microbioma selecionado e enriquecido pelo genótipo P-ineficiente melhorou a absorção de fósforo no genótipo cultivado posteriormente no mesmo solo. Coletivamente, esses resultados sugerem que as plantas dependem parcialmente do microbioma da rizosfera para a absorção de P e que a exploraçãodestas interações durante o melhoramento vegetal permitiria a seleção de genótipos muito mais eficientes, conduzindo à uma agricultura sustentável explorando o fósforo residual do solo.
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Tkacz, Andrzej. "Plant genotype, immunity and soil composition control the rhizosphere microbiome." Thesis, University of East Anglia, 2013. https://ueaeprints.uea.ac.uk/48113/.
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Three model plant and three crop plant species were grown for three generations in sand and compost. Pots were inoculated with 10 % soil initially, and with 10% of growth medium from the previous generation in generations 2 and 3, keeping replicates separate for all three generations. The microbiome community structure of the plant rhizosphere in each generation was characterised using ARISA DNA fingerprinting and 454 sequencing. Rhizosphere bacterial and fungal communities are different from those in bulk soil and there are also differences in the microbial community between different plant species. Plants both select and suppress specific bacteria and fungi in the rhizosphere microbiome, presumably via composition of their root exudates. Two out of three most abundant bacteria selected in the rhizosphere were isolated. These isolates proved to possess plant growth promotion properties. Plants are able to “farm” the soil in order to enrich it with plant growth promoting rhizobacteria (PGPR) species. However, in some plant species rhizospheres, invasions of opportunists and pathogens take place, mimicking events in plant monocultures. Other experiments using this multi-replicate system allowed for statistical analysis of the influence of Arabidopsis and Medicago mutants on the rhizosphere microbiome. Three groups of Arabidopsis mutants were tested: plants unable to produce aliphatic glucosinolates, plants impaired in the PAMP-triggered immune response and plants unable and over-expressed in methyl halides production and one group of Medicago mutants which are impaired in the mycorrhization ability. All these plant genotypes, except those for methyl-halide production and one genotype involved in PAMP response, significantly altered the rhizosphere microbiome.
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Turner, Thomas. "Metatranscriptomic analysis of community structure and metabolism of the rhizosphere microbiome." Thesis, University of East Anglia, 2013. https://ueaeprints.uea.ac.uk/49600/.
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Plant-microbe interactions in the rhizosphere, the region of soil influenced by plant roots, are integral to biogeochemical cycling, and maintenance of plant health and productivity. Interactions between model plants and microbes are well understood, but relatively little is about the plant microbiome. Here, comparative metatranscriptomics was used to determine taxonomic compositions and metabolic responses of microbes in soil and the rhizospheres of wheat, oat and pea. Additionally a wild-type oat was compared to a mutant (sad1) deficient in production of antifungal avenacins. Analyses of taxonomic compositions and functions based on rRNA and protein coding genes agreed that rhizosphere microbiomes differed from soil and between plant species. Pea had a stronger effect than wheat and oat, suggesting distinct cereal and legume microbiomes. Proportions of eukaryotic rRNA in the oat and pea rhizospheres were more than fivefold higher than in the wheat rhizosphere or soil. Nematodes and bacterivorous protozoa were enriched in all rhizospheres, while the pea rhizosphere was highly enriched for fungi. Only the eukaryotic community was distinct from wild-type oat in the sad1 mutant, suggesting avenacins have a broader role than protecting from fungal pathogens. The addition of an internal RNA standard allowed quantitative determination of global transcriptional activity in each environment. This was generally higher in the rhizospheres, particularly pea, than in soil. Taxa known to possess metabolic traits potentially important for rhizosphere colonisation, plant growth promotion and pathogenesis were selected by plants. Such traits included cellulose and other plant polymer degradation, nitrogen fixation, hydrogen oxidation, methylotrophy and antibiotic production. These functions were also more highly expressed in rhizospheres than soil. Microbes also induced functions involved in chemotaxis, motility, attachment, pathogenesis, responses to oxidative stress, cycling of nitrogen and sulphur, acquisition of phosphorous, iron and other metals, as well as metabolism of a variety of sugars, aromatics, organic and amino acids, many plant species specific. Profiling microbial communities with metatranscriptomics allowed comparison of relative and quantitative abundance of microbes and their metabolism, from multiple samples, across all domains of life, without PCR bias. This revealed profound differences in the taxonomic composition and metabolic functions of rhizosphere microbiomes between crop plants and soil.
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Guyonnet, Julien. "Effet de la stratégie de gestion des ressources des plantes sur l’investissement dans l’exsudation racinaire, et les conséquences sur les communautés bactériennes." Thesis, Lyon, 2017. http://www.theses.fr/2017LYSE1008.
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L'exsudation racinaire est connue pour avoir une influence sur le fonctionnement des communautés microbiennes, en particulier celles impliquées dans le cycle de l'azote (Haichar et al, 2012). Elle est liée à la physiologie de la plante, cette dernière pouvant être évaluée via les traits fonctionnels végétaux, permettant une classification des plantes en fonction de leur performance dans leur environnement. Ainsi, nous pouvons distinguer d'une part les espèces exploitatrices, avec une efficience de la photosynthèse élevée et une acquisition rapide de l'azote dans les sols, et d'autre part les plantes conservatrices, possédant des caractéristiques contraires (Aerts & Chapin, 1999) et des plantes intermédiaires dont les caractéristiques sont intermediaires.L'objectif de ces travaux de thèse est de déterminer l'influence de la stratégie de gestion des ressources de 6 poacées, réparties le long d'un gradient de stratégie de gestion des ressources, allant de stratégies conservatrices (Sesleria caerulea et Festuca paniculata), intermédiaires (Antoxanthum odoratum, Bromus erectus) à des stratégies exploitatrices (Dactylis glomerata et Trisetum flavescens), sur la diversité et le fonctionnement des communautés totales et dénitrifiantes. I) Dans un premier temps nous avons étudié le lien entre la stratégie de gestion de ressources des plantes et la quantité d'exsudats racinaires dans le sol adhérent aux racines (SAR). Nous avons ensuite déterminé l'influence de la quantité d'exsudats racinaire sur les activités microbiennes potentielles des communautés microbiennes du SAR (respiration et dénitrification potentielles), puis par une approche ADN-SIP (Stable Isotope Probing) couplée à du séquençage haut-débit, l'influence de l'exsudation racinaire sur la structure et la diversité des communautés bactérienne colonisant le SAR et le système racinaire. II) Dans un second temps, nous avons étudié le lien entre la stratégie de gestion des ressources des plantes et la nature des exsudats racinaires libérés au niveau du SAR et présents dans les extraits racinaires en analysant les profils des métabolites primaires chez Festuca paniculata, Bromus erectus et Dactylis glomerata, représentant respectivement des stratégies de gestion des ressources conservative, intermédiaire et exploitatriceRoot exudation is known to influence microbial communities functioning, in particular those involve in nitrogen cycle. (Haichar et al, 2012). It’s linked to plant physiology, which can be evaluated with functional traits, allowing a plant distribution in function of their performance in their environment. Thus, we can distinguish competitive species, with higher photosynthetic capacity and rapid rates of N acquisition, conservative species with the opposite characteristics (Aerts & Chapin, 1999) and intermediate plants, with intermediate characteristics.The objective of this work is to determinate the influence of nutrient management strategiy of 6 poaceae, along a strategies gradient from conservative strategy (Sesleria caerulea and Festuca paniculata), intermediate (Antoxanthum odoratum and Bromus erectus) to competitive strategy (Dactylis glomerata and Trisetum flavescens), on diversity and functioning of total and denitrifying communities.I) Firstly, we studied the link between the plant nutrient management strategy and the root exudates quantity in the root adhering soil (RAS). Then, we determined the influence of the rate of root exudation on potential microbial activities (respiration and denitrification), and with a DNA-SIP (Stable Isotope Probing) approach coupled to high-throughput sequencing, the influence of root exudation on the bacterial structure and diversity of communities colonizing the RAS and the root system. II) Secondly, we studied the link between the plant nutrient management strategy and the nature of molecules exuded in RAS and present in root extracts by analyzing primary metabolites profile to Festuca paniculata, Bromus erectus and Dactylis glomerata, respectively a conservative, an intermediate and a competitive plant. Then, we determined the influence of primary metabolites profile of each plant on semi-real denitrification of communities colonizing RAS of plants. III) Finally, an mRNA-SIP approach is in progress to determine the influence of exuded metabolites on active bacterial communities functioning and the expression of genes involved in denitrification process in RAS and root system. Our results show an influence of the nutrient management strategy on the rate of carbon exudation, the competitive plants exuding more than conservatives ones
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Ferreira, Clederson. "Dinâmica do microbioma da rizosfera de mandacaru na Caatinga." Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/11/11138/tde-21032014-104600/.
Full textAbstract:
O atual cenário mundial das mudanças climáticas, somado ao aquecimento global e ao aumento das áreas em processo de desertificação tem impactado diretamente nos padrões de produção agrícola. A Caatinga é um bioma que só ocorre no Brasil e possui um clima semiárido, quente e de baixa pluviosidade, sendo que na estação seca a temperatura do solo pode chegar até 60ºC. A Caatinga apresenta uma grande riqueza de ambientes e espécies, e boa parte dessa diversidade não é encontrada em nenhum outro bioma. Uma característica muito peculiar da Caatinga é a existência de duas estações bem contrastantes durante o ano, o inverno caracterizado por ser a estação da chuva e o verão a época da seca. A vegetação é composta por Euforbiáceas, Bromeliáceas e Cactáceas, dentre as quais destacam-se o Cereus jamacaru (mandacaru), Pilosocereus gounellei (xique-xique) e Melocactus sp. (cabeça-de-frade). O mandacaru planta que sobrevive às altas temperaturas e baixa disponibilidade de água da Caatinga possui adaptações morfológicas estruturais que contribuem para a sobrevivência da mesma. Além dessas adaptações a comunidade microbiana da rizosfera foi estudada para descobrir quais micro-organismos presentes nesse ambiente auxiliam na manutenção do hospedeiro frente a essas condições adversas. Assim como, quais grupos e funções são mais abundantes nessas condições. Nesse estudo foi feito o sequenciamento parcial do gene 16S rRNA e do DNA total da rizosfera de mandacaru. A comunidade bacteriana foi bem representada pelos filos Actinobacteria, Proteobacteria e Acidobacteria, sendo que o filo Actinobacteria foi mais abundante na seca de acordo com o sequenciamento metagenômico e o filo Acidobacteria foi mais abundante no período de chuva. Em geral o sequenciamento do gene 16S rRNA, indicou que Actinobacteria e Proteobacteria são os filos mais abundantes e os genes relacionados às funções de resistência a doenças foram mais abundantes na estação seca, enquanto genes relacionados ao metabolismo do nitrogênio foram mais abundantes durante o período chuvoso, revelando assim, um pouco do potencial que o microbioma da rizosfera de mandacaru possui para auxiliar a planta hospedeira.The present world scenario of climate change, global warming and the increase in areas undergoing desertification, have directly impacted on current patterns of agricultural crop production. The Caatinga is a specific Brazilian biome because of its semi-arid climate, hot and low rainfall, and the temperature that reaches the 60°C in the dry season. The Caatinga has a huge biodiversity and much of its diversity is not found in any other biome. A peculiar characteristic of the Caatinga biome is the occurrence of two very contrasting seasons during the year, the winter which is characterized by a rainy season and summer the dry season. The vegetation is composed by Euphorbiaceae , Bromeliaceae and Cactaceae, represented by Cereus jamacaru (Mandacaru) Pilosocereus gounellei (xique-xique) and Melocactus sp. (head-to-brother). Mandacaru is the plant that can survive through the specifics climate conditions of the Caatinga biome such as high temperatures and low water availability and this is probably due to some structural and morphological adaptations that contribute to its survival. Therefore, we assessed which microorganisms are associated with the plant rhizosphere, and which microbial groups contribute to the maintenance of the host throughout these adverse conditions. Also, we identified which are the most abundant microbial groups in these conditions and which microbial functions are more abundant in both evaluated seasons. Thus the present study assessed the mandacaru rhizosphere microbiome through a partial 16S rRNA gene sequencing and metagenomic sequencing. The bacterial community was well represented by the phyla Actinobacteria, Proteobacteria and Acidobacteria. The Actinobacteria was the most abundant microbial phyla in the dry season according to shotgun sequencing while the Acidobacteria was the most abundant microbial phyla in the rainy season. Overall, the 16S rRNA sequencing indicated that Actinobacteria and Proteobacteria were the most abundant groups and additionally, and genes related to disease resistance functions were more abundant in the dry season. Genes related to nitrogen metabolism were more abundant during the rainy season revealing some of the potential traits that the mandacaru can explore from its microbiome.
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Berdugo, Silvia Eugenia Barrera. "Redes ecológicas em comunidades bacterianas da filosfera, dermosfera e rizosfera de espécies arbóreas da Mata Atlântica." Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/11/11140/tde-09112016-155442/.
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A Mata Atlântica é uma floresta tropical úmida considerada um \"hotspot\" de biodiversidade e endemismo. É uma das florestas mais antigas do mundo e uma das maiores florestas da América, abrangendo aproximadamente 150 milhões de hectares em condições ambientais altamente heterogêneas. Estudos em diferentes ambientes da Mata Atlântica, nos núcleos de Picinguaba e Santa Virginia no Parque Estadual da Serra do Mar (PESM), têm sido realizados para determinar a diversidade de espécies e alterações da estrutura das comunidades de bactérias, tanto na filosfera, quanto na dermosfera e solo rizosférico. No entanto, pouco se sabe sobre as funções ecológicas dessas bactérias, e sobre as interações ecológicas entre as comunidades microbianas e os ambientes onde se desenvolvem. Assim o objetivo desse trabalho foi explorar as interações entre as comunidades microbianas da filosfera, dermosfera e solo coletado sobre a projeção da copa de duas espécies arbóreas da Mata Atlântica ao longo de um gradiente altitudinal, usando análises de co-ocorrência, a partir dos dados obtidos por pirosequenciamento da região V4 do gene rRNA 16S de bactérias, para determinar padrões de associações de bactérias em diferentes níveis taxonômicos em cada microambiente. Para esse estudo, foi proposta a hipótese de que mesmo que as condições ambientais sejam diferentes em cada tipo de floresta (gradiente altitudinal), pode existir grupos de bactérias específicos que co-ocorrem na filosfera, dermosfera ou solo das plantas, funcionando como taxons chaves na estruturação das comunidades bacterianas. Com base do sequenciamento dos genes rRNA 16S, as comunidades bacterianas associadas à filosfera e dermosfera de E. edulis e G. opposita nas diferentes florestas foram mais similares entre si do que as do solo. Actinobacteria, Firmicutes, Bacteroidetes e Proteobacteria foram mais abundantes em todos os microambientes estudados. Diferenças nas estruturas das comunidades bacterianas na filosfera, dermosfera e solo foram observadas ao longo do gradiente altitudinal, independente da espécie de planta. Na floresta de terras baixas, a comunidade bacteriana associada à filosfera foi mais similar entre E. edulis e G. opposita. No solo, a comunidade bacteriana foi mais similar dentro de cada tipo de floresta do que entre florestas, sugerindo um efeito da fisionomia da floresta nas comunidades de bactérias dos solos. Explorando as redes de co-ocorrência das comunidades bacterianas em cada microambiente observou-se que no nível de UTOs, cada microambiente têm diferentes táxons chaves que podem regular as interações ecológicas da comunidade. Embora táxons chaves não representam as UTOs mais abundantes em cada microambiente, eles pertencem, predominantemente às classes Alphaproteobacteria e Gammaproteobacteria, sugerindo que na filosfera, dermosfera e solo o core microbioma não pode ser definido ao nível de UTO, mas possivelmente a níveis taxonômicos mais elevados representando grandes grupos microbianos que apresentam funções redundantes.The Atlantic Forest is a rainforest considered a hotspot of biodiversity and endemism. It is one of the oldest forests in the world and one of the largest forests of America, covering approximately 150 million hectares in highly heterogeneous environmental conditions. Studies in different environments of the Atlantic forest, in the Picinguaba and Santa Virginia areas in the Serra do Mar State Park (PESM) have been conducted to determine the species diversity and changes in the structure of the bacterial communities in the phyllosphere, dermosphere and rhizosphere. However, little is known on the ecological functions of these bacteria, and on the ecological interactions between microbial communities and the environment in which they develop. The aim of this study was to explore the interactions between the microbial communities of the phyllosphere, dermosphere and rhizosphere of two tree species of the Atlantic Forest along an altitudinal gradient. Co-occurrence analysis based on data obtained by pyrosequencing of the 16S rRNA gene V4 region of bacteria to determine patterns of bacterial associations in different taxonomic levels in each microenvironment. For this study, the hypothesis that even if the environmental conditions are different in each type of forest (altitudinal gradient), there may be specific groups of bacteria that co-occur in the phyllosphere, dermosphere or rhizosphere, functioning as keystone taxa in the bacterial communities. Based on the sequencing of 16S rRNA genes, bacterial communities associated with the E. edulis and G. opposita phyllosphere and dermosphere in different forests were more similar to each other than the rhizosphere. Actinobacteria, Firmicutes, Proteobacteria and Bacteroidetes were the more abundant taxa in all studied microenvironments. Differences in the bacterial community structures in the phyllosphere, dermosphere and rhizosphere were observed along the altitudinal gradient, regardless of the plant species. In the lowland forest, the bacterial community associated with the phyllosphere was more similar between E. edulis and G. opposita. The rhizosphere bacterial community was more similar within each forest type than between forests, suggesting an effect of the forest physiognomy on the bacterial communities of the rhizosphere. Exploring the co-occurrence networks in the bacterial communities of each microenvironment it was observed that at the OTU level each microenvironment has different keystoine taxa that may regulate the ecological interactions in the community. Although the keystone taxa do not represent the most abundant OTUs in each microenvironment, they belong predominantly to Alphaproteobacteria and Gammaproteobacteria classes, suggesting that in the phyllosphere, dermosphere and rhizosphere the core microbiome cannot be determined at the OTU level, but possibly at higher taxonomic levels representing microbial groups having redundant functions.
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Xiao, Hua. "Exploring candidate genes and rhizosphere microbiome in relation to iron cycling in Andean potatoes." Diss., Virginia Tech, 2017. http://hdl.handle.net/10919/77917.
Full textAbstract:
Fe biofortification of potato is a promising strategy to prevent Fe deficiency worldwide either through traditional breeding or biotechnological approaches. These approaches require the identification of candidate genes to uptake, transport and store Fe in potato tubers. We employed multiple approaches including SNP genotyping, QTL analysis, identifying genes orthologous to Arabidopsis ferrome, yeast complementation assay and genetic transformation to avoid the limitation from a single approach. We revealed several candidate genes potentially associated with potato plant Fe acquisition, PGSC0003DMG400024976 (metal transporter), PGSC0003DMG400013297 (oligopeptide transporter), PGSC0003DMG400021155 (IRT1) and IRTunannotated (an ortholog to the IRT gene that is not annotated in the potato genome). The microorganisms in the rhizosphere react intensely with the various metabolites released by plant roots in a variety of ways such as positive, negative, and neutral. These interactions can influence the uptake and transport of micronutrients in the plant roots. Therefore, the contribution of soil microorganisms in the rhizosphere to improve Fe supply of plants may play a key role in Fe biofortification, especially under real world field-based soil scenarios. We thus investigated rhizosphere microbial community diversity in Andean potato landraces to understand the role of plant-microbial interaction in potato Fe nutrient cycling. From the analysis of the high-throughput Illumina sequences of 16S and ITS region of ribosomal RNA gene, we found that both potato landraces with low and high Fe content in tubers and a landrace on which low or high Fe content fertilizer was applied to the leaf surface had large impacts on the rhizosphere fungal community composition. Indicator species analysis (ISA) indicated that Operational Taxonomic Units (OTUs) contributing most to these impacts were closely related to Eurotiomycetes and Leotiomycetes in the phylum Ascomycota, Glomeromycetes in the phylum Glomeromycota and Microbotryomycetes in the phylum Basidiomycota. Lots of species from these groups have been shown to regulate plant mineral nutrient cycling. Our research revealed potential candidate genes and fungal taxa involved in the potato plant Fe nutrient dynamics, which provides new insights into crop management and breeding strategies for sustainable Fe fortification in agricultural production.Ph. D.
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Braga, Lucas Palma Perez. "Disentangling the influence of earthworms on microbial communities in sugarcane rhizosphere." Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/64/64133/tde-26052017-100757/.
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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, it was 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 the second chapter of this thesis it was demonstrate that 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 N2O. Shotgun sequencing (total DNA) revealed that around 70 microbial functions in bulk soil and rhizosphere differed between EW+ and EW- treatments. Overall, genes indicative of biosynthetic pathways and cell proliferation processes were enriched in EW+ treatments, suggesting a positive influence of worms. In EW+ rhizosphere, functions associated with plant-microbe symbiosis were enriched relative to EW- rhizosphere. Ecological networks inferred from the datasets revealed decreased niche diversification and increased keystone functions as an earthworm-derived effect. Plant biomass was improved in EW+ and worm population proliferated. Considering that earthworms contributed to with extra resources, it was evaluated in chapter three response of the soil resistome of sugarcane macrocosms under the influence of earthworms. Mechanisms of resistance against antimicrobial compounds appear to be an obligatory feature for the ecology and evolution of prokaryotic forms of life. However, most studies on resistance dynamics have been conducted in artificial conditions of anthropogenic inputs of antibiotics into very specific communities such as animal microbiomes. To resolve why and how resistance evolves, it is important to track antibiotics resistance genes (ARGs) (i.e., the resistome) in their natural hosts and understand their ecophysiological role in the environment. The results demonstrated that earthworms influenced changes of ARGs in bulk soil and rhizosphere. Negative correlations between ARGs and taxonomical changes were increased in EW+. Differential betweenness centrality (DBC=nBCEW+ - nBCEW-) values comparing the network models with and without earthworms showed earthworm presence changed the composition and the importance of the keystone members from the models. Redundancy analysis suggested that ARGs may be associated with microbial fitness, as the variance of relative abundance of members of the group Rhizobiales could be significantly explained by the variance of a specific gene responsible for one mechanism of tetracycline detoxificationAo longo dos últimos 150 anos muitos estudos têm demonstrado a importância das minhocas para o crescimento de plantas. Porém o exato mecanismo envolvido neste processo ainda é muito pouco compreendido. Muitas funções importantes necessárias para o crescimento de plantas podem ser realizadas pela comunidade microbiana da rizosfera. Para investigar a influência das minhocas na comunidade microbiana da rizosfera, foi desenvolvido um experimento de macrocosmo com cana-de-açúcar com e sem Pontoscolex corethrurus (EW+ e EW-, respectivamente) seguindo diversos procedimentos por 217 dias. No Segundo capítulo da tese é demonstrado que no tratamento EW+, as concentrações de N2O dentro do solo (15 cm profundidade) e a abundância relativa dos genes óxido nitroso redutase (nosZ) foram elevadas no solo e na rizosfera, sugerindo que microrganismos do solo foram capazes de consumir a emissão de N2O induzida pelas minhocas. O sequenciamento do DNA total revelou que aproximadamente 70 funções microbianas no solo e na rizosfera apresentaram diferenças entre os tratamentos EW+ e EW-. No geral, genes associados a biossíntese e proliferação de células foram enriquecidos em EW+, sugerindo uma influencia positiva por parte das minhocas. Na rizosfera EW+, funções associadas a simbiose entre planta e microrganismos foram relativamente enriquecidas comparado com rizosfera EW-. Modelos de rede de interação ecológica revelam menor número de diversificação de nichos e aumento de funções importantes como um efeito derivado da influência das minhocas. A biomassa das plantas foi aumentada no tratamento EW+ e a população de minhocas proliferou. Considerando que as minhocas contribuíram com o aumento de nutrientes, foi avaliado no capítulo três a resposta do resistoma presente nas comunidades microbianas dos solos do experimento. Mecanismos de resistência contra compostos antimicrobianos parecem ser características obrigatórias para a ecologia e evolução de procariotos. Entretanto, a maior parte dos estudos sobre genes de resistência tem sido conduzida em condições artificiais utilizando fontes antropogênicas de antibióticos em comunidades microbianas muito específicas como por exemplo o microbioma animal. Para resolver por que e como a resistência evolui, é importante estudar genes de resistência a antibióticos (GRA) (i.e., resistoma) no seu ambiente natural e entender seu papel ecofisiologico no ambiente. Os resultados demonstraram que minhocas influenciaram a mudança na composição de GRA no solo e na rizosfera. Tratamentos EW+ apresentaram maior número de correlações negativas entre ARG e grupos taxonômicos. A medida de centralidade diferencial (DBC=nBCEW+ - nBCEW-) comparando os modelos de rede de interações obtidos mostrou que a composição e o nível de importância dos indivíduos mais influentes é alterado nos tratamentos EW+ comparado com EW-. Além disso, por meio de uma análise de redundância (RDA) foi demonstrado que as alterações na abundancia relativa de GRA podem ser explicadas pelas alterações verificadas em grupos taxonômicos
Books on the topic "Rhizosphere microbiota"
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Asiegbu, Fred O., and Andriy Kovalchuk. Forest Microbiology : Volume 1 : Tree Microbiome: Phyllosphere, Endosphere and Rhizosphere. Elsevier Science & Technology, 2021.
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Asiegbu, Fred O., and Andriy Kovalchuk. Forest Microbiology : Volume 1 : Tree Microbiome: Phyllosphere, Endosphere and Rhizosphere. Elsevier Science & Technology Books, 2021.
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Gupta, Vijai Kumar, Dhananjaya Pratap Singh, and Ratna Prabha. Microbial Interventions in Agriculture and Environment : Volume 2: Rhizosphere, Microbiome and Agro-ecology. Springer, 2019.
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Gupta, Vijai Kumar, Dhananjaya Pratap Singh, and Ratna Prabha. Microbial Interventions in Agriculture and Environment : Volume 2: Rhizosphere, Microbiome and Agro-ecology. Springer, 2020.
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Gupta, Vijai Kumar, Dhananjaya Pratap Singh, and Ratna Prabha. Microbial Interventions in Agriculture and Environment : Volume 2: Rhizosphere, Microbiome and Agro-ecology. Springer, 2019.
Find full textBook chapters on the topic "Rhizosphere microbiota"
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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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Achouak, Wafa, and Feth el Zahar Haichar. "Stable Isotope Probing of Microbiota Structure and Function in the Plant Rhizosphere." In Methods in Molecular Biology, 233–43. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9721-3_18.
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Sharma, Mayur Mukut Murlidhar, Divya Kapoor, Rahul Rohilla, and Pankaj Sharma. "Nanomaterials and Their Toxicity to Beneficial Soil Microbiota and Fungi Associated Plants Rhizosphere." In Nanomaterials and Nanocomposites Exposures to Plants, 353–80. Singapore: Springer Nature Singapore, 2023. http://dx.doi.org/10.1007/978-981-99-2419-6_18.
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Afridi, Muhammad Siddique, Abdul Salam, and Flavio Henrique Vasconcelos De Medeiros. "Rhizosphere Microbiome Manipulation." In Advances in Plant Microbiome Research for Climate-Resilient Agriculture, 159–77. New York: Apple Academic Press, 2024. http://dx.doi.org/10.1201/9781003501893-8.
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Ashajyothi, Mushineni, K. Charishma, Asharani Patel, Surinder Paul, Y. N. Venkatesh, Ish Prakash, and Jyotsana Tilgam. "Rhizosphere Microbiome: Significance in Sustainable Crop Protection." In Rhizosphere Microbes, 283–309. Singapore: Springer Nature Singapore, 2022. http://dx.doi.org/10.1007/978-981-19-5872-4_14.
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Roy, Tina, Pooja Yadav, Anjali Chaudhary, Kanchan Yadav, and Kunal Singh. "Rhizosphere Microbiome-Assisted Approaches for Biotic Stress Management." In Rhizosphere Biology, 135–58. Singapore: Springer Nature Singapore, 2024. http://dx.doi.org/10.1007/978-981-97-4239-4_8.
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Raaijmakers, Jos M. "The Minimal Rhizosphere Microbiome." In Principles of Plant-Microbe Interactions, 411–17. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-08575-3_43.
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Gholap, Amol D., Sagar R. Pardeshi, Pankaj R. Khuspe, Sadikali F. Sayyad, Machindra Chavan, Navnath T. Hatvate, Md Faiyazuddin, and Md Jasim Uddin. "Manipulating the Rhizosphere Microbiome for Plant Health." In Microbiome Engineering, 175–93. Boca Raton: CRC Press, 2024. http://dx.doi.org/10.1201/9781003394662-13.
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Malviya, Deepti, Talat Ilyas, Rajan Chaurasia, Udai B. Singh, Mohammad Shahid, Shailesh K. Vishwakarma, Zaryab Shafi, Bavita Yadav, Sushil K. Sharma, and Harsh V. Singh. "Engineering the Plant Microbiome for Biotic Stress Tolerance: Biotechnological Advances." In Rhizosphere Microbes, 133–51. Singapore: Springer Nature Singapore, 2022. http://dx.doi.org/10.1007/978-981-19-5872-4_7.
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Bhuyan, Bhrigu, Sourav Debnath, and Piyush Pandey. "The Rhizosphere Microbiome and Its Role in Plant Growth in Stressed Conditions." In Rhizosphere Microbes, 503–29. Singapore: Springer Singapore, 2020. http://dx.doi.org/10.1007/978-981-15-9154-9_21.
Full textConference papers on the topic "Rhizosphere microbiota"
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Yin, Chuntao. "Disease-induced changes in the rhizosphere microbiome reduced root disease." In IS-MPMI Congress. IS-MPMI, 2023. http://dx.doi.org/10.1094/ismpmi-2023-5r.
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Rhizosphere microbiota, referred to as the second genome of plants, are crucial to plant health. Increasing evidence reveals that plants can change their rhizosphere microbiome and promote microbial activity to reduce plant disease. However, how plant and phytopathogens factor in combination to structure the rhizosphere microbiome and govern microbial selection for adaptation to disease stress remains incompletely understood. In this study, rhizosphere microbiota from successive wheat plantings under the pressure of the soilborne pathogen Rhizoctonia solani AG8 were characterized. Amplicon sequence analyses revealed that bacterial and fungal communities clustered by planting cycles. The addition of AG8 enhanced the separation of the rhizosphere microbiota. The alpha diversity of bacteria and fungi significantly decreased over planting cycles. Compared with rhizosphere bacterial communities, AG8 was a major driver structuring fungal communities. Pathogen-infected monocultures enriched a group of bacterial genera with potential antagonistic activities or abilities for plant growth promotion or nitrogen fixation. Further, eleven bacterial species exhibited antagonistic activities toward Rhizoctonia spp., and four of them displayed broad antagonism against multiple soilborne fungal pathogens. These findings support the potential to improve plant health through manipulating rhizosphere microbiota.
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Farkhudinov, R. G., A. S. Grigoriadi, and Yu M. Sotnikova. "The effect of oil pollution on the activity of physiological and biochemical processes in Triticum aestivum L. and the number of rhizospheric microbiota." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.069.
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The article presents the results of a study of the effect of oil pollution on the biochemical and morphometric parameters of the plant Triticum aestivum L., as well as a change in the number of rhizospheric microorganisms capable of degradation of petroleum hydrocarbons. It was shown that under the influence of pollution in plants increased the activity of redox enzymes. A significant increase in hydrocarbon-oxidizing bacteria and fungi was recorded in the rhizosphere.
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Egovtseva, A. Yu, and T. N. Melnichuk. "The influence of microbial preparations and farming systems on the structure of the microbocenosis of the rhizosphere of Triticum aestivum L." In РАЦИОНАЛЬНОЕ ИСПОЛЬЗОВАНИЕ ПРИРОДНЫХ РЕСУРСОВ В АГРОЦЕНОЗАХ. Federal State Budget Scientific Institution “Research Institute of Agriculture of Crimea”, 2020. http://dx.doi.org/10.33952/2542-0720-15.05.2020.09.
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Microorganisms are the most important bioindicators of the environment and ecological risk assessment. The impact of the no-till farming system in combination with microbial preparations needs to be studied and is an urgent task aimed at preserving fertility. The aim of our study was to determine the effect of pre-sowing inoculation with complex microbial preparations (CMP) and farming systems (no-till and conventional farming system) on the microbocenosis of the rhizosphere of Triticum aestivum L. in the Crimean Steppe. Microbiological analysis of the rhizosphere showed a significant increase in the number of actinobacteria (twice). The number of micromycetes, among which there are many pathogens of various plant diseases, decreased under direct sowing by 23 % as a result of inoculation and amounted to 21.5 thousand CFU/g of soil. The number of cellulose-destroying microorganisms that form soil fertility increased under the influence of microbial preparations by 23 % under conventional farming system (10.0 thousand CFU/g of soil); by 20 % under no-till (15.4 thousand CFU/g of soil). Thus, it was found that the use of microbial preparations under both farming techniques contributed to an increase in the number of microorganisms of most ecological-trophic groups that participate in the transformation of nitrogen in the rhizosphere, enhanced enzymatic processes, reduced the development of pathogenic microbiota and, consequently, contributed to improving the state of soil biocenosis.
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"Roots and rhizosphere microbiota diversity is influenced by rootstock and scion genotypes: can this be linked to the development of the grafted plant?" In Open-GPB. International Viticulture and Enology Society, 2024. http://dx.doi.org/10.58233/6oesc4ww.
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Glazunova, Darina, Polina Kuryntseva, Polina Galitskaya, and Svetlana Selivanovskaya. "ASSESSMENT OF THE DIVERSITY OF RHIZOSPHERIC CULTIVATED BACTERIA IN WHEAT PLANTS GROWN ON DIFFERENT SOIL TYPES." In 22nd SGEM International Multidisciplinary Scientific GeoConference 2022. STEF92 Technology, 2022. http://dx.doi.org/10.5593/sgem2022v/6.2/s25.11.
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Microbial communities associated with the plant rhizosphere play an important role in carbon sequestration, regulation of nutrient cycling, and the efficient functioning of the ecosystem as a whole. The diversity of microorganisms inhabiting the plant rhizosphere and their complex interactions with the host plant significantly affect the morphology, physiology, growth, development, and health of plants. At the same time, it is known that the soil microbiome diversity is affected by the type of soil, the type of cultivated crop, and the method of tillage. In this study, the abundance and diversity of cultivated bacteria of the rhizosphere microbiome of wheat was assessed. Rhizospheric soil samples were taken from 5 fields with different types of soils (Greyzem, Chernozem, Podzols, Podzoluvisols, Podzoluvisols). Cultivated bacteria from the rhizosphere soil were isolated on meat-peptone and soil agars, and their number was determined. It has been established that the cultivated bacterial rhizobiome was least diverse in wheat plants grown on medium podzolic soil. The MALDI-TOF method was used to identify isolated cultivated isolate species. The genera Achromobacter, Acinetobacter, Bacillus, Microbacterium, Paenibacillus, Pseudomonas, Stenotrophomonas predominated among the isolated bacteria.
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Egovtseva, A. Yu, T. N. Melnichuk, and S. F. Abdurashitov. "The influence of farming systems and microbial preparations on the structure of the microbocenosis of the rhizosphere of Triticum aestivum L." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.063.
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The use of microbial preparations contributed to a change in the taxonomic structure of winter wheat rhizosphere microbiome was established. A more significant effect of microbial preparations was noted under no-till technology on the structure of the microbiome than with the traditional farming system.
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Ramirez-Villacis, Dario. "Andean blueberry (Vaccinium floribundum) rhizosphere microbiome composition along the Ecuadorian Highlands." In ASPB PLANT BIOLOGY 2020. USA: ASPB, 2020. http://dx.doi.org/10.46678/pb.20.1382411.
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"Exploring wheat genotype influence on microbiome-mediated take-all disease suppression." In Plant Health 2024. American Phytopathological Society, 2024. http://dx.doi.org/10.1094/aps-ph24-027.
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Take-all disease caused by Gaeumannomyces tritici, a fungal root pathogen, significantly impacts wheat production globally. Effective biocontrol for take-all is the buildup of a 2,4-diacetylphloroglucinol-producing Pseudomonas spp, which both antagonizes the pathogen and induces plant disease resistance. Previous work found that wheat genotypes vary in accumulating Pseudomonas spp in the rhizosphere, with those hosting more Pseudomonas spp being more resistant to disease. Here, we aim to identify plant genetic markers associated with this variation. In a greenhouse experiment, we grew two recombinant inbred lines (RILs) known to be segregating for their ability to support disease-suppressive Pseudomonas spp. First, each RIL was grown for three weeks, after which above-ground tissue was removed and the same RIL was re-planted into the same soil for seven cycles. Following the final cycle, we infested the soil with the take-all pathogen to assess take-all severity. Our preliminary results will include disease data from this inoculation effort. We expect that soil from specific RILs will display better defense mechanisms against take-all. Next, we will collect rhizosphere soil samples to characterize bacterial and fungal symbionts, correlating microbial community profiles with disease data against quantitative trait locus (QTL) maps. Understanding how wheat genotypes accumulate protective populations of Pseudomonas and other soil microbes can provide new tools for managing an important disease of this staple food crop.
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"Antagonistic activity of rhizosphere bacterial community against corn pathogens." In Plant Health 2024. American Phytopathological Society, 2024. http://dx.doi.org/10.1094/aps-ph24-009.
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Worldwide, an estimated 20-40% of crop yield is lost to diseases. Growers often use agrochemicals to reduce yield loss. However, uncontrolled use of these chemicals is known to affect the soil fertility. One of the sustainable agriculture practices is to use biological controls. Single strain biological control are often not successful due to the lack of several traits that are collectively required to suppress the pathogens. Research has shown that the rhizosphere consortium plays a pivotal role in maintaining plant health and providing resistance against potential phytopathogens. Previous work with a microbial community representing corn rhizosphere microbiome showed biocontrol activity against Fusarium sp. We leveraged this work to add a plant growth-promoting rhizobacterium to this community. We challenged the predominant corn pathogen under the plate and pot assay and observed a 25-70% reduction growth of Pythium sp. and noticed similar results with individual strains against the same fungal pathogens. Some antimicrobial compounds produced by the community may be involved in the antagonistic activity. Subsequent tests, utilizing supernatants of the consortium and individual strains, confirmed the consistent inhibitory effect on pathogen growth. In future, we aim to isolate and identify the specific inhibitory compounds responsible for inhibiting the pathogen growth. This study highlights the potential of leveraging native microbiomes for sustainable disease management while elucidating the underlying mechanisms driving their biocontrol activity.
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Melnichuk, T., A. Egovtseva, S. Abdurashitov, E. Andronov, E. Abdurashitova, A. Radchenko, T. Ganotskaya, and L. Radchenko. "Changes in the taxonomic structure of the microbiome of chernozem southern of the rhizosphere Triticum aestivum L. under the influence of associative bacteria strains." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.167.
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The influence of strains associated with Triticum aestivum L. has been established on the taxonomic structure of the rhizosphere of the southern сhernozem of Crimean Steppe. Seventeen dominant families and 126 families with a minor share are defined in the prokaryotic biome.
Reports on the topic "Rhizosphere 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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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.
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Mendoza, Jonathan Alberto, Carolina Mazo, Lina Margarita Conn, Álvaro Rincón Castillo, Daniel Rojas Tapias, and Ruth Bonilla Buitrago. Evaluation of phosphate-solubilizing bacteria associated to pastures of Bracharia from acid soils. Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, 2015. http://dx.doi.org/10.21930/agrosavia.informe.2015.5.
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Rhizobia have been widely known by their capacity to form a symbiotic relationship with legumes and fix atmospheric nitrogen. Recently, however, rhizobia have shown to associate with plants in different botanical families. In this study, we aimed at elucidating the diversity of rhizobia associated to grasses, and determine their capabilities to solubilize phosphate in both lab and greenhouse experiments. Isolation of rhizobia was performed using rhizosphere from Brachiaria brizantha and B. decumbens and a promiscuous legume trap plant (i.e. Vigna unguiculata). Thirty days after inoculation of the trap plant, rhizobia were isolated from nodules using the conventional protocol, classified in basis on their phenotypic features, and molecularly grouped using Amplified Ribosomal DNA Restriction Analysis (ARDRA). Finally, phosphate solubilization assays and greenhouse experiments were carried out on representatives of each ARDRA cluster. The results showed that the diversity of rhizobia varied between both plant species, which suggests that plant exudates significantly determine the composition of the plant microbiome. Surprisingly, most of the isolated associated to B. brizantha rhizosphere exhibited typical attributes of slow-growing rhizobia, whereas rhizobia from B. decumbens displayed a mixed diversity including slow-, intermediate-, and fast-growing rhizobia. Sequencing of 16S rRNA of ARDRA representatives showed that most of the rhizobia isolated from B. brizantha belonged to the Mesorhizobium and Bradyrhizobium genera, while those isolated from B. decumbens were phylogenetically clustered into Rhizobium and Bradyrhizobium. The capability of the isolates to solubilize phosphate was studied using iron and calcium phosphate. We observed that overall Bradyrhizobium exhibited the highest ability to solubilize iron phosphate; by contrast, calcium phosphate was similarly solubilized within representatives of the three genera. In greenhouse experiments, we found that plants inoculated with isolated BT53, BD17 and BD21 exhibited a significantly higher content of phosphorus (p≤0.05). Additionally, dry weight was significantly higher in the treatment inoculated with BT16 isolate (p≤0.05). We conclude that 1) rhizobia is found associated with grasses, 2) plant genotype determines rhizobia diversity 3) rhizobia are able to solubilize phosphorus, and 4) they might be used to promote plant in different plant families. We further believe that further studies will reveal the true role of those old-known legume symbionts in development and growth of other important crops.
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Cytryn, E., Sean F. Brady, and O. Frenkel. Cutting edge culture independent pipeline for detection of novel anti-fungal plant protection compounds in suppressive soils. Israel: United States-Israel Binational Agricultural Research and Development Fund, 2022. http://dx.doi.org/10.32747/2022.8134142.bard.
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Fusarium oxysporum spp. causes Panama disease in bananas and crown and root rot in an array of vegetables and field crops, but increased regulations have restricted the use of many conventional chemical pesticides, and there are a limited number of commercially available products effective against them. The soil microbiome represents a largely untapped reservoir of secondary metabolites that can potentially antagonize fungal pathogens. However, most soil bacteria cannot be cultivated using conventional techniques and therefore most of these compounds remain unexplored. The overall goal of this two-year project was to extract and characterize novel secondary metabolites from "unculturable" soil microbiomes that antagonize Fusarium and other fungal plant pathogens. Initially, the Cytryn lab at the Volcani Institute (ARO) identified candidate biosynthetic gene clusters (BGCs) encoding for potentially novel antifungal compounds (specifically non-ribosomal peptides and polyketides) in soil and plant root microbiomes using cutting-edge metagenomic platforms. Next, the Brady lab at Rockefeller University (RU) screened archived soil metagenomic cosmid libraries for these BGCs, and heterologously expressed them in suitable hosts. Finally, the Frenkel and Cytryn labs at ARO assessed the capacity of these heterologous expressed strains to antagonize Fusarium and other fungal plant pathogens. Initially tomato and lettuce were analyzed, and subsequently roots of cucumbers grown in suppressive (biochar amended) soils were targeted. We found that the composition of tomato and lettuce root BGCs are similar to each other, but significantly different from adjacent bulk soil, indicating that root bacteria possess specific secondary metabolites that are potentially associated with rhizosphere competence. BGC linked to known metabolites included various antimicrobial, (e.g., streptazone E, sessilin), antifungal (heat-stable antifungal factor- HSAF, II and ECO-02301), and insecticidal (melingmycin, orfamide A) compounds. However, over 90% of the identified BGCs were moderately to significantly different from those encoding for characterized secondary metabolites, highlighting the profusion of potentially novel secondary metabolites in both root and soil environments. Novel BGCs that were abundant in roots and remotely resembled those of antifungal compounds were transferred to RU for subsequent screening and five were identified in RU soil metagenomic cosmid libraries. Two of these clusters (BARD-1711 BARD-B481) were heterologously-expressed in a Streptomyces albus J1074 strain, and transferred to ARO. The strain harboring BARAD-B481 was found to antagonize Fusarium significantly more than the host strain, indicating that this BGCs product has antifungal activity. Future studies will need to work on chemically characterizing the BARAD-B481 BGC and progress with the above described pipeline for other interesting BGCs.