Three new species,Xanthomonas hawaiiensissp. nov.,Stenotrophomonas aracearumsp. nov., andStenotrophomonas oahuensissp. nov., isolated from Araceae family

Chuang, Shu-Cheng; Dobhal, Shefali; Alvarez, Anne M.; Arif, Mohammad

doi:10.1101/2023.09.17.558166

Cited by 3 publications

(4 citation statements)

References 78 publications

(100 reference statements)

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“…nov. (A2111), X. citri pv. aracearum (A6252), X. sacchari (A5592), and X. sontii (A6237) 26 . Two control groups were included: one with healthy sugarcane and another with a non-template control.…”

Section: Resultsmentioning

confidence: 99%

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Loop-mediated Isothermal Amplification (LAMP) assay for reliable detection ofXanthomonas axonopodispv.vasculorum

Marabella,

Howard,

Bhandari

et al. 2024

Preprint

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Xanthomonas axonopodis pv. vasculorum (Xav), the causative agent of sugarcane gumming disease, represents a significant threat to global sugarcane production due to its systemic and destructive nature. Despite the economic implications, a field-deployable, Xav-specific diagnostic tool has not been developed. This resulted in a loop-mediated isothermal amplification (LAMP) assay targeting the pelL gene, unique to Xav strains, as a rapid and precise diagnostic assay. The selection of the pelL gene was informed by comprehensive in silico analyses of Xav genomes and related Xanthomonas species and other close relatives. Validation against the NCBI GenBank database and internally sequenced genomes confirmed the gene's exclusivity to Xav. Subsequent primers for both endpoint PCR and LAMP assays were designed using the pelL gene region. The LAMP assay underwent extensive testing against inclusivity and exclusivity panels. Use of exclusivity panel, comprising 81 strains from related species, other bacterial genera, and host genomes, demonstrated the assay's specificity with no false positives. The assay exhibited a detection limit of 1 pg, and its effectiveness was unimpeded by crude host lysate (sugarcane). Further validation through multi-device and multi-operator testing underscored the assay's 100% reproducibility and robustness. Application to infected plant samples resulted in the detection of all infected specimens without any false positives or negatives. This novel LAMP assay is accurate and reliable tool for Xav detection, with promising applications in routine diagnostics, biosecurity measures, microbial forensics, and epidemiological research.

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Section: Resultsmentioning

confidence: 99%

“…nov. (A2111), X. citri pv. aracearum (A6252), X. sacchari (A5592), and X. sontii (A6237) 26 . The plates were incubated for 2 days at 28 °C.…”

Section: Methodsmentioning

confidence: 99%

Loop-mediated Isothermal Amplification (LAMP) assay for reliable detection ofXanthomonas axonopodispv.vasculorum

Marabella,

Howard,

Bhandari

et al. 2024

Preprint

Self Cite

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“…However, the close relationship between X. sacchari, X. sontii, X. indica and a recently reported species, X. hawaiiensis, that form a clade, it is important to use the right and multiple approaches even when using genomic information to establish the species identity [43]. This is because, in literature, even the genome-based focussed studies have wrongly reported X. sontii strain(s) as X. sacchari [44,45].…”

Section: Frequent Misclassification Of X Sontii Isolates As X Saccharimentioning

confidence: 99%

“…With the new possibilities of complete 16S rRNA sequence metagenomic studies using long-read sequencing technologies and the advent of deep metagenomics and the genomic era can provide much-required resolution and confidence in diversity and culturomics studies. However, the close relationship between X. sacchari, X. sontii, X. indica and a recently reported species, X. hawaiiensis , that form a clade, it is important to use the right and multiple approaches even when using genomic information to establish the species identity [43]. This is because, in literature, even the genome-based focussed studies have wrongly reported X. sontii strain(s) as X. sacchari [44, 45].…”

Section: Introductionmentioning

confidence: 99%

Xanthomonas sontii, and notXanthomonas sacchari, is the dominant, vertically transmitted core rice seed endophyte

Rana,

Patil

2023

Preprint

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Seeds endophytes, particularly the abundant, core and vertically transmitted species, are major areas of focus in the host microbiome studies. Apart from being the first members to colonize, they accompany the plant throughout its development stages and also to the next generation. In a recently published study from china, a Xanthomonas species was reported as the keystone species that is core endophyte and vertically transmitted in rice with probiotic properties. However, the species status was wrongly reported as X. sacchari. Such report is misleading as Xanthomonas sacchari is a well-known and pathogenic species of sugarcane, and the study did not include the two-probiotic non-pathogenic Xanthomonas species from rice seeds, Xanthomonas sontii and Xanthomonas indica, that were discovered and investigated in details by our group, leading to the wrong inference. By including these species, we have correctly established the phylogenetic and taxonomic identity of keystone species as Xanthomonas sontii, a non-pathogen with plant protective functions. The course correction will enable researchers to use the correct reference or lab strain of X. sontii for further fundamental studies and translational research towards future agriculture.

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Xanthomonas protegenssp. nov., a rice seed-associated probiotic and taxonomic outlier species ofXanthomonas sontii

Rana,

Sharma,

Madhavan

et al. 2024

Preprint

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Rice seed microbiota play a vital role throughout their growth and developmental stages. Xanthomonas sontii is known as an abundant, core-vertically transmitted rice seed endophyte with probiotic properties. Studies reveal a less explored world of non-pathogenic Xanthomonas (NPX) species like X. sontii and X. indica that are associated with healthy rice seeds. The present study reports the isolation, biochemical characterization, and in-depth taxonogenomic evidence for a third NPX species, X. protegens, from rice seeds, a taxonomic outlier of X. sontii. It also highlights the importance of using multiple taxonogenomic indices to identify taxonomic outlier species. Similar to the other two NPX species, the new member species is also non-pathogenic and provides in vivo protection to rice plants from Xanthomonas oryzae pv. oryzae upon leaf clip inoculation. The pangenome investigation suggested a set of unique genes to the novel species that might be important in adaptation to rice plants and differentiate it from other NPX species. The study will allow the design of markers for the identification of these NPX members, targeted culturomics of a particular NPX species and in the discovery of other novel NPX species from healthy rice seed microbiome for further exploitation in rice health.

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Three new species,Xanthomonas hawaiiensissp. nov.,Stenotrophomonas aracearumsp. nov., andStenotrophomonas oahuensissp. nov., isolated from Araceae family

Cited by 3 publications

References 78 publications

Loop-mediated Isothermal Amplification (LAMP) assay for reliable detection ofXanthomonas axonopodispv.vasculorum

Loop-mediated Isothermal Amplification (LAMP) assay for reliable detection ofXanthomonas axonopodispv.vasculorum

Xanthomonas sontii, and notXanthomonas sacchari, is the dominant, vertically transmitted core rice seed endophyte

Xanthomonas protegenssp. nov., a rice seed-associated probiotic and taxonomic outlier species ofXanthomonas sontii

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