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

Summary

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

Abstract

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.

Introduction

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 communities^1,2. Siderophores can be broadly classified according to their active sites and structural features, creating four basic types: carboxylate, hydroxamate, catecholate, and mixed types^3,4. Many microorganisms are cap....

Protocol

NOTE: Location of Field Site: Washington State University, Plant Pathology Farm (46°46’38.0”N 117°04’57.4”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.

1. Preparation of modified M9 medium

1. Use Na₂PO₄∙7H₂O (12.8 g/200 mL), KH₂

Results

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 µM. Figure 1 shows the relationship between absorbance (420 nm) and starting concentration of pyoverdine (Log₁₀ molarity in µM). EDTA did not provide an adequate standard because samples exhibited greater absorbance measurements than were attainable.......

Discussion

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.......

Materials

Name	Company	Catalog Number	Comments
Agarose	Apex	LF451320014
Aluminum Baking Pan
Aluminum Foil
Ammonium chloride, granular	Fiesher Scientific	152315A
Autoclave and Sterilizer	Thermo Scientific
Calcium chloride dihydrate	Fiesher Scientific	171428
CAS (Chrome Azurol S)	Chem-Impex Int'l Inc)	000331-27168
Dextrose Monohydrate (glucose), crystalline powder	Fiesher Scientific	1521754
EDTA, disodium salt, dihydrate, Crystal	J.T.Baker	JI2476
Glycerol, Anhydrous	Baker Analyzed	C22634
HDTMA (Cetyltrimethylammomonium Bromide	Reagent World	FZ0941
Hydrochloride acid	ACROS Organic	B0756767
Infinite M200 PRO plate reader	TECAN
Iron (III) chloride hexahydrate, 99%	ACROS Organic	A0342179
Laboratory Fume Hood	Thermo Scientific
Laboratory Incubator	VWR Scientific
Magnesium Sulfate	Fiesher Scientific	27855
Niric Acid, (69-70)%	J.T.Baker	72287
PIPES buffer, 98.5%	ACROS Organic	A0338723
Potassium phosphate, dibaisc,powder	J.T.Baker	J48594
Pyoverdine	SIGMA-ALDRICH	078M4094V
Sand
SI-600R Shaker	Lab Companion
Sodium chloride, granular	Fiesher Scientific	136539
Sodium hydroxide, pellets	J.T.Baker	G48K53
Sodium phosphate, dibasic heptahydrate, 99%	ACROS Organic	A0371705