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

Abstract

A Gram-stain negative, facultatively anaerobic, non-sporulating, non-motile and rod-shaped bacterium, designated CF3, was isolated from a tea plantation soil sample and its taxonomic position was determined using polyphasic taxonomy. Strain CF3 displayed optimum growth at 25 °C, pH 5.0 and in the presence of 0-1 % NaCl. Comparative phylogenetic analysis of the 16S rRNA, recA and gyrB gene sequences showed that the isolate belongs to the genus Paraburkholderia, showing high levels of similarity with respect to Paraburkholderia oxyphila OX-01 (98.3, 95 and 93 %, respectively) and Paraburkholderia sacchari IPT101 (98.2, 95 and 95 %, respectively). The predominant ubiquinone was determined to be Q-8, and the polar lipids are phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified amino-phospholipid, three unidentified amino-lipids and three unidentified polar lipids. The major fatty acids were found to be C16:0, C17:0 cyclo, summed feature 8 (C18:1 ω7c and/or C18:1 ω6c) and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The DNA G+C content was found to be 63.8 mol% and the DNA-DNA relatedness values between strain CF3 and its two close relatives P. oxyphila OX-01 and P. sacchari IPT101 was 41 and 40 %, respectively. Based on phylogenetic analysis, phenotypic and genotypic data, it is concluded that the isolate represents a novel species of the genus Paraburkholderia, for which the name Paraburkholderia caffeinitolerans sp. nov. is proposed. The type strain is CF3 (= LMG 28688 = CGMCC 1.15105).

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

“…Species were considered heterotypic synonyms if the genomes of both type strains possessed ANI values > 97%. Synonyms included “ Paraburkholderia caffeinitolerans ” ( Gao et al, 2016 ) and “Paraburkholderia dokdonella ” ( Jung et al, 2019 ); with a 99.9% pairwise ANI value, and were subsequently merged into the earlier synonym “ P. caffeinitolerans ” ( Figure 2 ). Paraburkholderia insulsa ( Dobritsa and Samadpour, 2016 ) type strain possessed an ANI value of 98.4% compared to Paraburkholderia fungorum ( Coenye et al, 2001a ; Sawana et al, 2014 ), and was subsequently merged into the earlier synonym P. fungorum ( Figure 2 ).…”

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

“…Our phylogenomic and ANI analyses ( Figures 1 and S2 ) indicated that, at least from a genomic standpoint, the species “ P. atlantica ”, “ P. bonniea ”, “ P. caffeinitolerans ”, and “ P. hayleyella ” represent new species ( Gao et al, 2016 ; Brock et al, 2020 ; Paulitsch et al, 2020a ). Despite displaying near-cutoff ANI values, not only Paraburkholderia dioscoreae and Paraburkholderia xenovorans but also Paraburkholderia youngii and “P.…”

“…“ Paraburkholderia caffeinitolerans ” was isolated from a Chinese tea plantation soil and showed caffeine degrading abilities ( Gao et al, 2016 ). Years later, a Korean strain isolated from the rhizosphere of Campanula takesimana was described as the new species “ Paraburkholderia dokdonella ” ( Jung et al, 2019 ).…”

“…Phylogenomics and genome metrics indicate that "Paraburkholderia atlantica" , "Paraburkholderia caffeinitolerans" , "Paraburkholderia bonniea" , and "Paraburkholderia hayleyella" indeed represent new species Our phylogenomic and ANI analyses (Figures 1 and S2) indicated that, at least from a genomic standpoint, the species "P. atlantica", "P. bonniea", "P. caffeinitolerans", and "P. hayleyella" represent new species (Gao et al, 2016;Brock et al, 2020;Paulitsch et al, 2020a). Despite displaying near-cutoff ANI values, not only Paraburkholderia dioscoreae and Paraburkholderia xenovorans but also Paraburkholderia youngii and "P. atlantica" could be differentiated by dDDH.…”