Microbiota Nit Research PDF

Investigating Microbiota NITHYASRI MANIKANDA  Microbiota refers to the diverse community of Microbiota ? microorganisms, including bacteria, viruses, fungi, and archaea, that inhabit a particular environment. These microorganisms pla...

Investigating Microbiota NITHYASRI MANIKANDA  Microbiota refers to the diverse community of Microbiota ? microorganisms, including bacteria, viruses, fungi, and archaea, that inhabit a particular environment. These microorganisms play crucial roles in maintaining soil health and ecosystem functioning. Nutrient Cycling Soil Structure Nitrogen and Fixation Aggregatio n Detoxificati Water on Purification y should we understand soil microbiome? soil heal th we focus on the soil microbiome earn the protocol Weighing Soil Samples: 250mg Homogenization: vortex and centrifuge Lysis Buffer Addition: lysis buffer Bead Beating: disrupt the cells Incubation: facilitate cell lysis. Inhibitor Removal: Centrifuge the samples Binding DNA to Spin Columns: Transfer the supernatant to a spin column Washing: ethanol removes impurities DNA Elution: releases the PC purified DNA R What is PCR? Polymerase Chain Reaction enzymatic process that allows for the detection of specific genes from DNA sample target DNA DNA primers dNTPs water ( Amplicon)  Gel Electrophoresis of PCR Gel Electrophoresis of PCR Target Index Product Data Analysis QUBIT Protocol: 1. Take 198 µl of buffer with dye. 2. Add 2 µl of index sample in the buffer 3. Vortex the above mixture 4. Wait for 2 min (Keep the mixture in the dark) 5. Check the quantification. MARKER DATA PROFILING ? Microbiome Analyst MicrobiomeAnalyst is a web- based platform designed for the analysis of microbiome data, allowing users to perform various analyses,  This analysis provides taxonomic composition of VISUAL microbial communities by quantifying the relative EXPLORATION abundances of different taxa at various taxonomic levels (genus). Stacked bar/area plot Taxonomic Composition Analysis Taxonomic Composition Analysis Stacked Bar Plot T1 has more microorganisms present T2 has the least microorganisms present Pie Chart This chart shows the taxonomic compositions of microbial community. Rarefactio n Curve Rarefaction analysis involves randomly subsampling the reads from each sample to an equal sequencing depth and then calculating diversity metrics, such as alpha diversity This curve shows the species diversity. T0 has the least bacteria diversity  The heatmap displays the relative abundance or other quantitative measures of microbial taxa Heat Tree Comparing T1 and T0, proteobacteria, acidobacteria, actinobacteria and firmicutes are more abundant. Alpha Diversity This shows the diversity of species richness within the population. The Shannon index shows both richness and evenness. diversity present at the initial time  Beta diversity is a Beta measure of the dissimilarity between Diversity microbial communities in different samples Genus Bradyrhizobium This indicates that the microbial communities at different time points are relatively similar in composition, possibly due to the dominance of Bradyrhizobium. Core Microbiom e darker shade of red indicate lower abundance or prevalence Core microbiome analysis involves identifying these shared taxa and assessing their relative abundance and dynamics over time. darker shade of blue indicate This shows the higher abundance or prevalence of all prevalence the genus in the soil  search the specified patterns within the uploaded datasets. Pattern These algorithms may include statistical methods, or bioinformatics tools to microbiome Search analysis. About 25 genus correlated with the genus Bradyrhizobiu m. Rhizobium has the highest correlation. Research article Bradyrhizobi um A genus of gram- negative soil bacteria from the phylum of Pseudomonadota (proteobacteria) Most of the species are symbiotic and endophytic bacteria Source:Wiki Nitrogen Fixation Popularly known for fixing nitrogen in legumes. Bradyrhizobium decomposes organic matters and promotes nitrogen fixation in rice. (the Nitric oxide NO- producing strains could possible affect Source: rice growth) GFB Soil Fertility Bradyrhizobium improves soil fertility, promoting rice growth and eventually rice yield. Source:Greentumble Soil And Enviromental Pollution The use of Nitrogen fertilizers has contributed to nitrate contamination of soils and groundwater supplies, often leading to health hazards and environmental pollution. Biological fixation of nitrogen improves sustainable rice Source:BBC Resistance And Tolerance Bradyrhizobium has the ability to grow and nodulate Genisteae legumes in mercury-contaminated soils References Chaintreuil C, Giraud E, Prin Y, Lorquin J, Ba A, Gillis M, de Lajudie P, Dreyfus B. Photosynthetic bradyrhizobia are natural endophytes of the African wild rice Oryza breviligulata. Appl Environ Microbiol. 2000;66:5437–5447 Yanni Y G, Rizk R Y, Corich V, Squartini A, Ninke K, Philip-Hollingsworth S, Orgambide G, De Bruijn F, Stoltzfus J, Buckley D, Schmidt T M, Mateos P F, Ladha J K, Dazzo F B. Natural endophytic association between Rhizobium leguminosarum bv. trifolii and rice roots and assessment of its potential to promote rice growth. Plant Soil. 1997;194:99– 114. Heavy metals multi-tolerant Bradyrhizobium isolated from mercury mining region in Algeria. Authors Adouda Salmi, Farida Boulila. https://doi.org/10.1016/j.jenvman.2021.112547 Gu J, Guo F, Lin L, Zhang J, Sun W, Muhammad R, Liang H, Duan D, Deng X, Lin Z, Wang Y, Zhong Y, Xu Z. Microbiological mechanism for "production while remediating" in Cd-contaminated paddy fields: A field experiment. Sci Total Environ. 2023 Aug 10;885:163896. doi: 10.1016/j.scitotenv.2023.163896. Epub 2023 May 4. PMID: 37146825.