Paraburkholderia caffeinitolerans sp. nov., a caffeine degrading species isolated from a tea plantation soil sample

Genome-based taxonomy of Burkholderia sensu lato: Distinguishing closely related species

The taxonomy of Burkholderia sensu lato (s.l.) has been revisited using genome-based tools, which have helped differentiate closely related species. Many species from this group are indistinguishable through phenotypic traits and 16S rRNA gene sequence analysis. Furthermore, they also exhibit whole-genome Average Nucleotide Identity (ANI) values in the twilight zone for species circumscription (95-96%), which may impair their correct classification. In this work, we provided an updated Burkholderia s.l. taxonomy focusing on closely related species and give other recommendations for those developing genome-based taxonomy studies. We showed that a combination of ANI and digital DNA-DNA hybridization (dDDH) applying the universal cutoff values of 95% and 70%, respectively, successfully discriminates Burkholderia s.l. species. Using genome metrics with this pragmatic criterion, we demonstrated that i) Paraburkholderia insulsa should be considered a later heterotypic synonym of Paraburkholderia fungorum; ii) Paraburkholderia steynii differs from P. terrae by harboring symbiotic genes; iii) some Paraburkholderia are indeed different species based on dDDH values, albeit sharing ANI values close to 95%; iv) some Burkholderia s.l. indeed represent new species from the genomic viewpoint; iv) some genome sequences should be evaluated with care due to quality concerns.

Genome-based Reclassification of Paraburkholderia insulsa as a Later Heterotypic Synonym of Paraburkholderia fungorum and Proposal of Paraburkholderia terrae subsp. terrae subsp. nov. and Paraburkholderia terrae subsp. steynii subsp. nov

Based on the 16S rRNA gene sequences similarity of > 99.8%, the phylogeny of 88 Paraburkholderia strains was reconstructed. Further, they were subjected to overall genome-related indices (OGRI), which resulted in the identification of distinct pairs of species that were closely related. A pair consist of the type strains of Paraburkholderia insulsa and Paraburkholderia fungorum possessed a dDDH value of 87.9%, correspondingly, and the average nucleotide identity (ANI) value was 98.5%. Based on the phylogenetic analysis, OGRI and phenotypical evidence, P. insulsa was proposed as a later heterotypic synonym of P. fungorum. Furthermore, a pair comprising type strains of Paraburkholderia terrae and Paraburkholderia steynii possessed dDDH and ANI values of 71.2% and 96.6%, respectively, and difference in phenotypic traits, which supports a subspecies proposal within these taxa. Thus, the recently described Paraburkholderia steynii was proposed into two subspecies namely Paraburkholderia terrae subsp terrae subsp. nov and as Paraburkholderia terrae subsp. steynii subsp. nov.

The Hidden Genomic Diversity, Specialized Metabolite Capacity, and Revised Taxonomy of Burkholderia Sensu Lato

Burkholderia sensu lato is a collection of closely related genera within the family Burkholderiaceae that includes species of environmental, industrial, biotechnological, and clinical importance. Multiple species within the complex are the source of diverse specialized metabolites, many of which have been identified through genome mining of their biosynthetic gene clusters (BGCs). However, the full, true genomic diversity of these species and genera, and their biosynthetic capacity have not been investigated. This study sought to cluster and classify over 4000 Burkholderia sensu lato genome assemblies into distinct genomic taxa representing named and uncharacterized species. We delineated 235 species groups by average nucleotide identity analyses that formed seven distinct phylogenomic clades, representing the genera of Burkholderia sensu lato: Burkholderia, Paraburkholderia, Trinickia, Caballeronia, Mycetohabitans, Robbsia, and Pararobbisa. A total of 137 genomic taxa aligned with named species possessing a sequenced type strain, while 93 uncharacterized species groups were demarcated. The 95% ANI threshold proved capable of delineating most genomic species and was only increased to resolve several closely related species. These analyses enabled the assessment of species classifications of over 4000 genomes, and the correction of over 400 genome taxonomic assignments in public databases into existing and uncharacterized genomic species groups. These species groups were genome mined for BGCs, their specialized metabolite capacity calculated per species and genus, and the number of distinct BGCs per species estimated through kmer-based de-replication. Mycetohabitans species dedicated a larger proportion of their relatively small genomes to specialized metabolite biosynthesis, while Burkholderia species harbored more BGCs on average per genome and possessed the most distinct BGCs per species compared to the remaining genera. Exploring the hidden genomic diversity of this important multi-genus complex contributes to our understanding of their taxonomy and evolutionary relationships, and supports future efforts toward natural product discovery.

Occurrence, fate, persistence and remediation of caffeine: a review

Pharmaceutical and personal care products (PPCPs) have gained attention in recent years due to their continuous discharge in natural waters. Their persistence in the environment has impacted flora, fauna and human being worldwide. One of the most common PPCPs is caffeine (1, 3, 7-trimethylxanthine) which acts as a stimulant to the central nervous system in humans and is found in nature in about 60 plant species, especially in coffee, tea and cacao plants. Here we discuss the evidence with respect to caffeine occurrence, its persistence and remediation in light of increasing knowledge and the impact of caffeine on the environment. Daily intake of caffeine around the world is found to increase due to the frequent introduction of new caffeinated beverages as well as increased consumption of coffee, tea and carbonated soft drinks, which has led to increase in its concentration in water bodies including agricultural soil. The caffeine concentration in different water system, studied by various authors is also described. Diverse effects of the use of caffeine on several organisms including humans are also briefly presented. Therefore, urgent attention for the removal of caffeine and its derivatives is the need of the hour. Various methods described in literature for caffeine degradation/removal is also presented. Another widely used technique in environmental remediation is molecular imprinting (MIP); however, only few MIPs have been demonstrated for caffeine which is also discussed. Regular monitoring can be useful to control toxic effects of caffeine. Graphical abstract.

Paraburkholderia panacisoli sp. nov., a potentially antagonistic bacterium against the root rot fungal pathogen Cylindrocarpon destructans, isolated from ginseng cultivation soil

A new bacterium, designated DCY113^T, was isolated from ginseng cultivation soil in Gochang-gun, South Korea, and its taxonomic position identified by the polyphasic approach. 16S rRNA gene sequence analysis determined that this isolate belongs to the genus Paraburkholderia, and was closest to P. dipogonis DL7^T (98.6%), P. phytofirmans PsJN^T (98.5%), P. kirstenboschensis Kb15^T (98.4%) and P. aromaticivorans BN^T (98.1%). Strain DCY113^T is Gram-reaction negative, strictly aerobic, rod-shaped, non-motile, and catalase and oxidase positive. The predominant isoprenoid quinone of DCY113^T was ubiquinone Q-8. The major cellular fatty acids were C_16:0, cyclo-C_17:0 and the Summed feature 8 (C_18:1ω7c and/or C_18:1ω6c). The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), and an unknown amino lipid (AL1). The G+C content of the genomic DNA was 62.2 mol%. Average nucleotide identity (ANI) between strain DCY113^T and the related Paraburkholderia type strains were below the threshold value for species delineation. This low DNA relatedness in combination with phylogenetic and phenotypic tests indicates that strain DCY113^T cannot be assigned to any recognized species. Strain DCY113^T was also found to have antifungal activity against the pathogenic fungi Cylindrocarpon destructans. In conclusion, this study found DCY113^T to be a novel species within the genus Paraburkholderia, for which the name P. panacisoli is proposed. The type strain is DCY113^T (= KCTC 52951^T = JCM 32098^T).