Name: high-throughput siderophore screening from environmental samples: plant tissues, bulk soils, and rhizosphere soils
Uploaded: 2019-02-09T15:00:00
Description: Watch this Scientific Journal Video about High-throughput Siderophore Screening from Environmental Samples: Plant Tissues, Bulk Soils, and Rhizosphere Soils at JoVE.com

The authors wish to thank Kalyani Muhunthan for assistance in laboratory procedures, Lee Opdahl for wheat genotype harvesting, the Washington State Concord Grape Research Council, and the Washington State University Center for Sustaining Agriculture and Natural Resources for a BIOAg grant to support this work. Additional funding was provided by the USDA/NIFA through Hatch project 1014527.

NOTE: Location of Field Site: Washington State University, Plant Pathology Farm (46&#176;46&#8217;38.0&#8221;N 117&#176;04&#8217;57.4&#8221;W). Seeds were sown using a mechanical planter on October 19, 2017. Each wheat genotype was planted in headrows, approximately 1 meter apart to avoid overlapping of root system. Plant and soil samples were collected on August 9, 2018, when plants were ready for harvest. Samples were gathered from three replicates of four wheat genotypes: PI561727, PI561725, Madsen, Lewjain.
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<ol>
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The primary result of this work is the production of a new methodology that can be used to rapidly enrich for siderophore producing microbes while quantitatively measuring siderophore production/activity in the environmental sample. The methodology is quick, simple, and cost-effective, and the results show how it can be used to detect siderophore activity from complex and novel sample types (e.g., soil and plant tissue). The protocol also results in the production of glycerol stocks of the enrichment cultures, w...

Siderophores are important biomolecules involved primarily in iron-chelation for bioavailability, but with a wide array of additional purposes in terrestrial and aquatic ecosystems ranging from microbial quorum sensing, signaling to microbial plant-hosts, plant growth promotion, cooperation and competition within complex microbial communities1,2. Siderophores can be broadly classified according to their active sites and structural features, creating four basic types: carboxylate, hydroxamate, catecholate, and mixed types3,4. Many microorganisms are capable of excreting more than one type of siderophore5 and in complex communities, a vast majority of organisms biosynthesize the membrane receptors to allow the uptake of an even wider variety of siderophores1,6. Recent work indicates that siderophores are particularly important at the community level, and even in inter-kingdom communications and biogeochemical transfers7,8,9,10,11.
Chrome azurol sulphonate (CAS) has been used for over 30 years as a chelating agent to bind iron (Fe) in such a way that addition of ligands (i.e., siderophores) can result in dissociation of the CAS-Fe complex, creating an easily identifiable color change in the medium12. When the CAS is bound with Fe, the dye appears as a royal blue color, and as the CAS-Fe complex dissociates, the medium changes color according to the type of ligand used to scavenge the Fe13. The initial, liquid-based medium established by Schwyn and Neilands in 1987, has been modified in many ways to accommodate changing microbial targets14, growth habits and limitations15, as well as a variety of metals besides Fe, including aluminum, manganese, cobalt, cadmium nickel, lithium, zinc16, copper17, and even arsenic18.
Many human pathogens, as well as plant growth promoting microorganisms (PGPM) have been identified as siderophore-producing organisms3,19,20, and important rhizosphere and endophytic PGPM often test positive for siderophore-production4. The traditional Fe-based liquid method has been adapted to microtiter testing of isolates in cultivation for siderophore production21. However, these techniques fail to recognize the importance of the microbial community as a whole (the microbiome), in cooperation and potential regulation of siderophore production in soils and plant systems22. For that reason, we have developed a high-throughput community-level assessment of siderophore production from a given environment, based on the traditional CAS assay, but with replication, ease of measurement, reliability, and repeatability in a microplate assay.
In this study, a cost-effective, high-throughput CAS-Fe assay for detecting siderophore production is presented to assess the enrichment of siderophore production from complex samples (i.e., soil and plant tissue homogenates). Bulk, loosely-bound, and tightly-bound rhizosphere soil (in terms of how the soil was bound to the root) were obtained along with grain, shoot, and root tissues from four distinct wheat (Triticum aestivum L.) genotypes: Lewjain, Madsen, PI561725, and PI561727. It was hypothesized that fundamental differences in the wheat genotypes could result in differences in recruitment and selection of siderophore producing communities. Of particular interest is the difference between microbial communities associated with the PI561725 isogenic line, which is aluminum tolerant because it possesses ALMT1 (Aluminum-activated Malate Transporter 1), compared with the aluminum sensitive PI561727 isogenic line, which possesses a non-aluminum responsive form of the gene, almt123,24,25,26. The chief objective of the study was to develop a straightforward, rapid method of quantitatively assessing siderophore production in siderophore enrichment cultures of complex sample types while preserving the cultures for future work.

<table>
	<tbody>
		<tr>
			<td>Agarose</td>
			<td>Apex</td>
			<td>LF451320014</td>
			<td></td>
		</tr>
		<tr>
			<td>Aluminum Baking Pan</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Aluminum Foil</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Ammonium chloride, granular</td>
			<td>Fiesher Scientific</td>
			<td>152315A</td>
			<td></td>
		</tr>
		<tr>
			<td>Autoclave and Sterilizer</td>
			<td>Thermo Scientific</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Calcium chloride dihydrate</td>
			<td>Fiesher Scientific</td>
			<td>171428</td>
			<td></td>
		</tr>
		<tr>
			<td>CAS (Chrome Azurol S)</td>
			<td>Chem-Impex Int&#39;l Inc)</td>
			<td>000331-27168</td>
			<td></td>
		</tr>
		<tr>
			<td>Dextrose Monohydrate (glucose), crystalline powder</td>
			<td>Fiesher Scientific</td>
			<td>1521754</td>
			<td></td>
		</tr>
		<tr>
			<td>EDTA, disodium salt, dihydrate, Crystal</td>
			<td>J.T.Baker</td>
			<td>JI2476</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycerol, Anhydrous</td>
			<td>Baker Analyzed</td>
			<td>C22634</td>
			<td></td>
		</tr>
		<tr>
			<td>HDTMA (Cetyltrimethylammomonium Bromide</td>
			<td>Reagent World</td>
			<td>FZ0941</td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrochloride acid</td>
			<td>ACROS Organic</td>
			<td>B0756767</td>
			<td></td>
		</tr>
		<tr>
			<td>Infinite M200 PRO plate reader</td>
			<td>TECAN</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Iron (III) chloride hexahydrate, 99%</td>
			<td>ACROS Organic</td>
			<td>A0342179</td>
			<td></td>
		</tr>
		<tr>
			<td>Laboratory Fume Hood</td>
			<td>Thermo Scientific</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Laboratory Incubator</td>
			<td>VWR Scientific</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Magnesium Sulfate</td>
			<td>Fiesher Scientific</td>
			<td>27855</td>
			<td></td>
		</tr>
		<tr>
			<td>Niric Acid, (69-70)%</td>
			<td>J.T.Baker</td>
			<td>72287</td>
			<td></td>
		</tr>
		<tr>
			<td>PIPES buffer, 98.5%</td>
			<td>ACROS Organic</td>
			<td>A0338723</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium phosphate, dibaisc,powder</td>
			<td>J.T.Baker</td>
			<td>J48594</td>
			<td></td>
		</tr>
		<tr>
			<td>Pyoverdine</td>
			<td>SIGMA-ALDRICH</td>
			<td>078M4094V</td>
			<td></td>
		</tr>
		<tr>
			<td>Sand</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>SI-600R Shaker</td>
			<td>Lab Companion</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium chloride, granular</td>
			<td>Fiesher Scientific</td>
			<td>136539</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium hydroxide, pellets</td>
			<td>J.T.Baker</td>
			<td>G48K53</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium phosphate, dibasic heptahydrate, 99%</td>
			<td>ACROS Organic</td>
			<td>A0371705</td>
			<td></td>
		</tr>
	</tbody>
</table>

high-throughput siderophore screening from environmental samples: plant tissues, bulk soils, and rhizosphere soils

Siderophores (low-molecular weight metal chelating compounds) are important in various ecological phenomenon ranging from iron (Fe) biogeochemical cycling in soils, to pathogen competition, plant growth promotion, and cross-kingdom signaling. Furthermore, siderophores are also of commercial interest in bioleaching and bioweathering of metal-bearing minerals and ores. A rapid, cost effective, and robust means of quantitatively assessing siderophore production in complex samples is key to identifying important aspects of the ecological ramifications of siderophore activity, including, novel siderophore producing microbes. The method presented here was developed to assess siderophore activity of in-tact microbiome communities, in environmental samples, such as soil or plant tissues. The samples were homogenized and diluted in a modified M9 medium (without Fe), and enrichment cultures were incubated for 3 days. Siderophore production was assessed in samples at 24, 48, and 72 hours (h) using a novel 96-well microplate CAS (Chrome azurol sulphonate)-Fe agar assay, an adaptation of the traditionally tedious and time-consuming colorimetric method of assessing siderophore activity, performed on individual cultivated microbial isolates. We applied our method to 4 different genotypes/Lines of wheat (Triticum aestivum L.), including Lewjain, Madsen, and PI561725, and PI561727 commonly grown in the inland Pacific Northwest. Siderophore production was clearly impacted by the genotype of wheat, and in the specific types of plant tissues observed. We successfully used our method to rapidly screen for the influence of plant genotype on siderophore production, a key function in terrestrial and aquatic ecosystems. We produced many technical replicates, yielding very reliable statistical differences in soils and within plant tissues. Importantly, the results show the proposed method can be used to rapidly examine siderophore production in complex samples with a high degree of reliability, in a manner that allows communities to be preserved for later work to identify taxa and functional genes.

A pyoverdine mixture biosynthesized by Pseudomonas fluorescens was used as a standard to interpret and quantify absorbance (at 420 nm) of samples in terms of pyoverdine equivalents in &#181;M. Figure 1 shows the relationship between absorbance (420 nm) and starting concentration of pyoverdine (Log10 molarity in &#181;M). EDTA did not provide an adequate standard because samples exhibited greater absorbance measurements than were attainable...

Watch this Scientific Journal Video about High-throughput Siderophore Screening from Environmental Samples: Plant Tissues, Bulk Soils, and Rhizosphere Soils at JoVE.com

High-throughput Siderophore Screening from Environmental Samples: Plant Tissues, Bulk Soils, and Rhizosphere Soils (Video) | JoVE

We present a protocol for rapid screening of environmental samples for siderophore potential contributing to micronutrient bioavailability and turnover in terrestrial systems.

High-throughput Siderophore Screening from Environmental Samples: Plant Tissues, Bulk Soils, and Rhizosphere Soils

Siderophores (low-molecular weight metal chelating compounds) are important in various ecological phenomenon ranging from iron (Fe) biogeochemical cycling ...

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Determination of Microbial Extracellular Enzyme Activity in Waters, Soils, and Sediments using High Throughput Microplate Assays (Video) | JoVE

Much of the nutrient cycling and carbon  processing in natural environments occurs through the activity of extracellular  enzymes released by ...

Integrated Field Lysimetry and Porewater Sampling for Evaluation of Chemical Mobility in Soils and Established Vegetation

Integrated Field Lysimetry and Porewater Sampling for Evaluation of Chemical Mobility in Soils and Established Vegetation (Video) | JoVE

Potentially toxic chemicals are routinely applied to land to meet growing demands on waste management and food production, but the fate of these chemicals ...

Measurement of Greenhouse Gas Flux from Agricultural Soils Using Static Chambers

Measurement of Greenhouse Gas Flux from Agricultural Soils Using Static Chambers (Video) | JoVE

Measurement of greenhouse gas (GHG) fluxes between the soil and the atmosphere, in both managed and unmanaged ecosystems, is critical to understanding the ...

Automated Gel Size Selection to Improve the Quality of Next-generation Sequencing Libraries Prepared from Environmental Water Samples

Automated Gel Size Selection to Improve the Quality of Next-generation Sequencing Libraries Prepared from Environmental Water Samples (Video) | JoVE

Next-generation sequencing of environmental samples can be challenging because of the variable DNA quantity and quality in these samples. High quality DNA ...

Physical Isolation of Endospores from Environmental Samples by Targeted Lysis of Vegetative Cells

Physical Isolation of Endospores from Environmental Samples by Targeted Lysis of Vegetative Cells (Video) | JoVE

Endospore formation is a survival strategy found among some bacteria from the phylum Firmicutes. During endospore formation, these bacteria enter a ...

A Bending Test for Determining the Atterberg Plastic Limit in Soils

A Bending Test for Determining the Atterberg Plastic Limit in Soils (Video) | JoVE

The thread rolling test is the most commonly used method to determine the plastic limit (PL) in soils. It has been widely criticized, because a ...

Extraction and Analysis of Microbial Phospholipid Fatty Acids in Soils

Extraction and Analysis of Microbial Phospholipid Fatty Acids in Soils (Video) | JoVE

Phospholipid fatty acids (PLFAs) are key components of microbial cell membranes. The analysis of PLFAs extracted from soils can provide information about ...

Methods of Soil Resampling to Monitor Changes in the Chemical Concentrations of Forest Soils

Methods of Soil Resampling to Monitor Changes in the Chemical Concentrations of Forest Soils (Video) | JoVE

Recent soils research has shown that important chemical soil characteristics can change in less than a decade, often the result of broad environmental ...

A 3-dimensional (3D)-printed Template for High Throughput Zebrafish Embryo Arraying

A 3-dimensional 3D-printed Template for High Throughput Zebrafish Embryo Arraying (Video) | JoVE

The zebrafish is a globally recognized fresh water organism frequently used in developmental biology, environmental toxicology, and human disease related ...