Molecular methods as tools to control plant diseases caused by Dickeya and Pectobacterium spp: A minireview

Highlights

• Taxonomical position of Dickeya and Pectobacterium spp. underwent many fluctuations.

• Blackleg and soft rot are controlled only by preventive measures.

• Data-mining from NGS contributed to creation of new diagnostic tools.

• Successful implementation of modern methods enables limitation of bacterial spread.

Abstract

Dickeya spp. and Pectobacterium spp. are etiological agents of soft rot on crops, vegetables, and ornamentals. They also cause blackleg on potato. These pectinolytic phytopathogens are responsible for significant economic losses, mostly within the potato production sector. Importantly, there are no methods to eradicate these microorganisms once they have infected plant material. Solely preventive measures remain, including early detection and identification of the pathogens, monitoring of their spread in addition to planting certified seed material tested for latent infections. As proper identification of the causative agent allows for efficient limitation of disease spread, numerous detection and differentiation methods have been developed. Most commonly followed procedures involve: isolation of viable bacterial cells (alternatively post-enrichment) on semi-selective media, identification to species level by PCR (single, multiplex, Real time), serology or fatty acids profiling. Differentiation of the isolates is often accomplished by sequencing the housekeeping genes or molecular fingerprinting. In view of lowering total costs of next-generation sequencing (NGS), a huge amount of generated data reveals subtle differences between strains that have proven to be potentially useful for the establishment of specific novel detection pipelines. Successful implementation of molecular diagnostic methods is exemplified by 20-year studies on the populations of pectinolytic bacteria on potatoes in Poland. The presented work aims to gather the characteristics of Dickeya spp. and Pectobacterium spp. important for the identification process in addition to providing an overview of modern and newly developed specific, rapid, high-throughput and cost-effective screening methods for the detection and identification of these phytopathogens.

Introduction

Pectinolytic bacteria belonging to Dickeya spp. and Pectobacterium spp. (currently soft rot Pectobacteriaceae, SRP; formerly soft rot Enterobacteriaceae, SRE) are causative agents of soft rot on economically important plants, both vegetables and ornamentals. They are also responsible for blackleg symptoms on potato plants [1]. SRP might be shifted over long distances by infected seed material. They also spread locally by plant remains, soil, waterways, air, aerosols, alternative hosts or agricultural machines [2]. Despite the fact that the blackleg and soft rot are considered seed-borne diseases, Dickeya spp. and Pectobacterium spp. may invade neighboring plants through natural openings or mechanical injuries. Under environmental conditions favorable for the pathogen, infection latency state is disrupted and SRP secrete plant cell wall-degrading enzymes (PCWDEs) breaking down host macromolecules e.g. cellulose, pectins and proteins, in order to exploit plant protoplasts as rich sources of nutrients [3]. Once the disease symptoms develop, there are no control methods available. To limit the spread of these phytopathogens, solely preventive measures apply i.e. avoiding contamination of plant material, screening seed potatoes for latent infections, providing appropriate storage conditions, performing field inspections and monitoring the spread of pathogens [2], [4].

A strong demand exists for designing reliable and cost-effective methods intended for detection and identification of SRP in latently infected plant material. Until now, over thirty diverse procedures have been proposed [5] in order to identify distinct pectinolytic bacterial species, elucidate their origin and limit further spread. In this minireview we introduce crucial taxonomical and epidemiological aspects relevant to the proper understanding of considerable challenges related to an accurate identification of Dickeya spp. and Pectobacterium spp. Most of all, classical and molecular methods designated for the detection of pectinolytic bacteria are comprehensively summarized and discussed with particular focus on innovative and emerging techniques. Moreover, a case study that lasted over 20 years was included aiming to illustrate the successful utilization of molecular identification and differentiation methods to screen seed potato fields and waterways for Dickeya and Pectobacterium spp. under temperate climate in Poland.