Francesco Dal Dal Grande
  • Post-Doc, Senckenberg Gesellschaft fuer Naturforschung
Research fields
  • Plant science
A Microbial Bioassay for Direct Contact Assessment of Soil Toxicity Based on Oxygen Consumption of Sulfur Oxidizing Bacteria
Authors:  Ebenezer Ashun, Umair Ali Toor, Heonseop Eom and Sang-Eun Oh, date: 01/05/2020, view: 3538, Q&A: 0
A new direct contact assessment of soil toxicity using sulfur oxidizing bacteria (SOB) is proposed for analyzing the toxicity of soils. The proposed method is based on the ability of SOB to oxidize elemental sulfur to sulfuric acid in the presence of oxygen. Since sulfate ions are produced from sulfur by SOB oxidation activity, changes in electrical conductivity (EC) serve as a proxy to assess toxicity in water. However, in soil medium, EC values are not reliable due to the adsorption of SO42- ions by soils. Here, we suggest a new parameter which measures oxygen consumption by SOB for 6 hours to assess soil toxicity by using a lubricated glass syringe method. The proposed method is rapid, simple, cost- effective as well as sensitive and capable of assessing direct contact soil toxicity.
Extraction and 16S rRNA Sequence Analysis of Microbiomes Associated with Rice Roots
Authors:  Joseph Edwards, Christian Santos-Medellín and Venkatesan Sundaresan, date: 06/20/2018, view: 16550, Q&A: 0
Plant roots associate with a wide diversity of bacteria and archaea across the root-soil spectrum. The rhizosphere microbiota, the communities of microbes in the soil adjacent to the root, can contain up to 10 billion bacterial cells per gram of soil (Raynaud and Nunan, 2014) and can play important roles for the fitness of the host plant. Subsets of the rhizospheric microbiota can colonize the root surface (rhizoplane) and the root interior (endosphere), forming an intimate relationship with the host plant. Compositional analysis of these communities is important to develop tools in order to manipulate root-associated microbiota for increased crop productivity. Due to the reduced cost and increasing throughput of next-generation sequencing, major advances in deciphering these communities have recently been achieved, mainly through the use of amplicon sequencing of the 16S rRNA gene. Here we first present a protocol for dissecting the microbiota from various root compartments, developed using rice as a model. We next present a method for amplifying fragments of the 16S rRNA gene using a dual index approach. Finally, we present a simple workflow for analyzing the resulting sequencing data to make ecological inferences.
Affymetrix Genome-wide Human SNP Assay
Author:  Alexis Bosman, date: 05/20/2016, view: 7708, Q&A: 0
To assess genomic variation, it is possible to identify the single nucleotide polymorphisms (SNP) which an individual carries. Using the Affymetrix Genome-wide Human SNP Assay, it is possible to assess 906,600 SNPs on a single array. This protocol, the next iteration of the GeneChip Mapping 500K array set, is based directly on the manufacturers’ protocol and shows steps which are highly similar to that which is found here: http://media.affymetrix.com/support/downloads/manuals/genomewidesnp6_manual.pdf.
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