Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018

Agnieszka Klonowska; Julie Ardley; Lionel Moulin; Jaco Zandberg; Delphine Patrel; Margaret Gollagher; Dora Marinova; T B K Reddy; Neha Varghese; Marcel Huntemann; Tanja Woyke; Rekha Seshadri; Natalia Ivanova; Nikos Kyrpides; Wayne Reeve

doi:10.3389/fmicb.2023.1082107

Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018

Front Microbiol. 2023 Feb 28:14:1082107. doi: 10.3389/fmicb.2023.1082107. eCollection 2023.

Authors

Affiliations

¹ Université de Montpellier, IRD, CIRAD, INRAE, Institut AgroPHIM Plant Health Institute, Montpellier, France.
² Centre for Crop and Food Innovation, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia.
³ Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA, Australia.
⁴ Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.

Abstract

Integrated virus genomes (prophages) are commonly found in sequenced bacterial genomes but have rarely been described in detail for rhizobial genomes. Cupriavidus taiwanensis STM 6018 is a rhizobial Betaproteobacteria strain that was isolated in 2006 from a root nodule of a Mimosa pudica host in French Guiana, South America. Here we describe features of the genome of STM 6018, focusing on the characterization of two different types of prophages that have been identified in its genome. The draft genome of STM 6018 is 6,553,639 bp, and consists of 80 scaffolds, containing 5,864 protein-coding genes and 61 RNA genes. STM 6018 contains all the nodulation and nitrogen fixation gene clusters common to symbiotic Cupriavidus species; sharing >99.97% bp identity homology to the nod/nif/noeM gene clusters from C. taiwanensis LMG19424^T and "Cupriavidus neocalidonicus" STM 6070. The STM 6018 genome contains the genomes of two prophages: one complete Mu-like capsular phage and one filamentous phage, which integrates into a putative dif site. This is the first characterization of a filamentous phage found within the genome of a rhizobial strain. Further examination of sequenced rhizobial genomes identified filamentous prophage sequences in several Beta-rhizobial strains but not in any Alphaproteobacterial rhizobia.

Keywords: Betaproteobacteria; bacteriophage; filamentous phage; root-nodule bacteria; symbiosis.