Metabarcoding Approach for Evaluation of Bacterial Diversity in Soft Rotting Potato Tubers and Corresponding Geocaulospheres

• Published in: Potato research Vol. 66; no. 3; pp. 793 - 810
• Main Authors: Markovic, Sanja, Popovic, Tatjana, Beric, Tanja, Dimkic, Ivica, Jelusic, Aleksandra, Ilicic, Renata, Stankovic, Slavisa
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01.09.2023; Springer; Springer Nature B.V
• Subjects: Agriculture; Analysis; Bacteria; Biological control; Biomedical and Life Sciences; Blackleg; DNA barcoding; Endophytes; Life Sciences; Microbial activity; Microorganisms; Next-generation sequencing; Pectobacterium; Pests; Plant Genetics and Genomics; Plant Sciences; Plant Systematics/Taxonomy/Biogeography; Potatoes; Proteobacteria; RNA; rRNA 16S; Signs and symptoms; Soft rot; Tubers; Microbial communities
• ISSN: 0014-3065; 1871-4528
• DOI: 10.1007/s11540-022-09601-9

Plant pathogenic bacteria from the genera Pectobacterium and Dickeya in association with potato cause blackleg and tuber soft rot disease. A metabarcoding was used to analyze the microbial communities of soft-rotted tubers and their geocaulospheres. In September 2018, samples collected from the blackleg-infected field (58 ha) in the Bačka region (Serbia) reached 45% disease incidence. Next-generation sequencing Illumina MiSeq platform was used to obtain 16S rRNA sequences from six tested tubers (with and without soft rot symptom) and the surrounding geocaulosphere. Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were present in all samples, with Proteobacteria being the most prevalent, especially in tubers without soft rot symptoms. In all tested samples, species of the Pectobacterium ( P. aroidearum , P. atrosepticum , P. carotovorum , and P. polaris ) were detected but were more represented in tubers without symptoms. However, the genus Dickeya was at the limit of detection or not detected at all. Acinetobacter was the most dominant in tubers with soft rot, while Pseudomonas and Enterobacter were the most abundant in tubers without symptoms. The genera Bacteroides and Dysgonomonas with starch-degradable features were almost exclusively present in soft rotted tubers and their corresponding geocaulospheres. The most represented genera in the geocaulosphere sample associated with no-symptom tubers were Gaiella , Sphingomonas , Sphingobium , Gemmatimonas , and Geminicoccus , which include species with confirmed biocontrol potential . This study indicates that the soft rot maceration process arises due to complex interactions between plant pathogens and other endophytic bacteria.