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White RT, Taylor W, Klukowski N, Vaughan-Higgins R, Williams E, Petrovski S, Rose JJA, Sarker S. A discovery down under: decoding the draft genome sequence of Pantoea stewartii from Australia's Critically Endangered western ground parrot/kyloring ( Pezoporus flaviventris). Microb Genom 2023; 9:001101. [PMID: 37665208 PMCID: PMC10569725 DOI: 10.1099/mgen.0.001101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/13/2023] [Indexed: 09/05/2023] Open
Abstract
Pantoea stewartii, a plant pathogen, is primarily transmitted through contaminated seeds and insect vectors, with the corn flea beetle (Chaetocnema pulicaria) being the primary carrier. P. stewartii is a bacterium belonging to the order Enterobacterales and can lead to crop diseases that have a significant economic impact worldwide. Due to its high potential for spread, P. stewartii is classified as a quarantine organism in numerous countries. Despite its impact on agriculture, the limited genome sequences of P. stewartii hamper understanding of its pathogenicity and host specificity, and the development of effective control strategies. In this study, a P. stewartii strain (C10109_Jinnung) was discovered in the faecal matter of the Critically Endangered western ground parrot/kyloring (Pezoporus flaviventris) in Australia, which to our knowledge is the first reported P. stewartii genome from a bird source. Whole-genome sequencing and phylogenomic analysis of strain C10109_Jinnung, obtained from a captive psittacine, provides new insights into the genetic diversity and potential transmission route for the spread of P. stewartii beyond insects and plants, where P. stewartii is typically studied. Our findings provide new insights into the potential transmission route for spread of P. stewartii and expand the known transmission agents beyond insects and plants. Expanding the catalogue of P. stewartii genomes is fundamental to improving understanding of the pathogenicity, evolution and dissemination, and to develop effective control strategies to reduce the substantial economic losses associated with P. stewartii in various crops and the potential impact of endangered animal species.
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Affiliation(s)
- Rhys T. White
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - William Taylor
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Natalie Klukowski
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Victoria, Australia
| | | | - Ernest Williams
- Institute of Environmental Science and Research, Wallaceville, New Zealand
| | - Steve Petrovski
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Victoria, Australia
| | - Jayson J. A. Rose
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Victoria, Australia
| | - Subir Sarker
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Victoria, Australia
- Biomedical Sciences & Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
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Riesco R, Rose JJA, Batinovic S, Petrovski S, Sánchez-Juanes F, Seviour RJ, Goodfellow M, Trujillo ME. Gordonia pseudamarae sp. nov., a home for novel actinobacteria isolated from stable foams on activated sludge wastewater treatment plants. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The taxonomic status of two
Gordonia
strains, designated BEN371 and CON9T, isolated from stable foams on activated sludge plants was the subject of a polyphasic study which also included the type strains of
Gordonia
species and three authenticated
Gordonia amarae
strains recovered from such foams. Phylogenetic analyses of 16S rRNA gene sequences showed that these isolates formed a compact cluster suggesting a well-supported lineage together with a second branch containing the
G. amarae
strains. A phylogenomic tree based on sequences of 92 core genes extracted from whole genome sequences of the isolates, the
G. amarae
strains and
Gordonia
type strains confirmed the assignment of the isolates and the
G. amarae
strains to separate but closely associated lineages. Average nucleotide index (ANI) and digital DNA–DNA hybridisation (dDDH) similarities showed that BEN371 and CON9T belonged to the same species and had chemotaxonomic and morphological features consistent with their assignment to the genus
Gordonia
. The isolates and the
G. amarae
strains were distinguished using a range of phenotypic features and by low ANI and dDDH values of 84.2 and 27.0 %, respectively. These data supplemented with associated genome characteristics show that BEN371 and CON9T represent a novel species of the genus
Gordonia
. The name proposed for members of this taxon is Gordonia pseudamarae sp. nov. with isolate CON9T (=DSM 43602T=JCM 35249T) as the type strain.
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Affiliation(s)
- Raúl Riesco
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
| | - Jayson J. A. Rose
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Steven Batinovic
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Steve Petrovski
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Fernando Sánchez-Juanes
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, CSIC, Salamanca, Spain
- Department of Biochemistry and Molecular Biology, University of Salamanca, Salamanca, Spain
| | - Robert J. Seviour
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
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Batinovic S, Rose JJA, Ratcliffe J, Seviour RJ, Petrovski S. Cocultivation of an ultrasmall environmental parasitic bacterium with lytic ability against bacteria associated with wastewater foams. Nat Microbiol 2021; 6:703-711. [PMID: 33927381 DOI: 10.1038/s41564-021-00892-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 03/22/2021] [Indexed: 02/02/2023]
Abstract
Many wastewater treatment plants around the world suffer from the operational problem of foaming. This is characterized by a persistent stable foam that forms on the aeration basin, which reduces effluent quality. The foam is often stabilized by a highly hydrophobic group of Actinobacteria known as the Mycolata1. Gordonia amarae is one of the most frequently reported foaming members1. With no currently reliable method for treating foams, phage biocontrol has been suggested as an attractive treatment strategy2. Phages isolated from related foaming bacteria can destabilize foams at the laboratory scale3,4; however, no phage has been isolated that lyses G. amarae. Here, we assemble the complete genomes of G. amarae and a previously undescribed species, Gordonia pseudoamarae, to examine mechanisms that encourage stable foam production. We show that both of these species are recalcitrant to phage infection via a number of antiviral mechanisms including restriction, CRISPR-Cas and bacteriophage exclusion. Instead, we isolate and cocultivate an environmental ultrasmall epiparasitic bacterium from the phylum Saccharibacteria that lyses G. amarae and G. pseudoamarae and several other Mycolata commonly associated with wastewater foams. The application of this parasitic bacterium, 'Candidatus Mycosynbacter amalyticus', may represent a promising strategy for the biocontrol of bacteria responsible for stabilizing wastewater foams.
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Affiliation(s)
- Steven Batinovic
- Department of Physiology, Anatomy, and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Jayson J A Rose
- Department of Physiology, Anatomy, and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Julian Ratcliffe
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Robert J Seviour
- Department of Physiology, Anatomy, and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Steve Petrovski
- Department of Physiology, Anatomy, and Microbiology, La Trobe University, Melbourne, Victoria, Australia.
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