Paraburkholderia solitsugae sp. nov. and Paraburkholderia elongata sp. nov., phenolic acid-degrading bacteria isolated from forest soil and emended description of Paraburkholderia madseniana

Abstract

Two bacterial strains, 1NT and 5NT, were isolated from hemlock forest soil using a soluble organic matter enrichment. Cells of 1NT (0.65×1.85 µm) and 5NT (0.6×1.85 µm) are Gram-stain-negative, aerobic, motile, non-sporulating and exist as single rods, diplobacilli or in chains of varying length. During growth in dilute media (≤0.1× tryptic soy broth; TSB), cells are primarily motile with flagella. At higher concentrations (≥0.3× TSB), cells of both strains increasingly form non-motile chains, and cells of 5NT elongate (0.57×~7 µm) and form especially long filaments. Optimum growth of 1NT and 5NT occurred at 25–30 °C, pH 6.5–7.0 and <0.5% salinity. Results of comparative chemotaxonomic, genomic and phylogenetic analyses revealed that 1NT and 5NT were distinct from one another and their closest related type strains: Paraburkholderia madseniana RP11T, Paraburkholderia aspalathi LMG 27731T and Paraburkholderia caffeinilytica CF1T. The genomes of 1NT and 5NT had an average nucleotide identity (91.6 and 91.3%) and in silico DNA–DNA hybridization values (45.8%±2.6 and 45.5%±2.5) and differed in functional gene content from their closest related type strains. The composition of fatty acids and patterns of substrate use, including the catabolism of phenolic acids, also differentiated strains 1NT and 5NT from each other and their closest relatives. The only ubiquinone present in strains 1NT and 5NT was Q-8. The major cellular fatty acids were C16 : 0, 3OH-C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c and summed features 2 (3OH-C14 : 0 / C16 : 1 iso I), 3 (C16 : 1 ω6c/ω7c) and 8 (C18 : 1 ω7c/ω6c). A third bacterium, strain RL16-012-BIC-B, was isolated from soil associated with shallow roots and was determined to be a strain of P. madseniana (ANI, 98.8%; 16S rRNA gene similarity, 100%). Characterizations of strain RL16-012-BIC-B (DSM 110723=LMG 31706) led to proposed emendments to the species description of P. madseniana . Our polyphasic approach demonstrated that strains 1NT and 5NT represent novel species from the genus Paraburkholderia for which the names Paraburkholderia solitsugae sp. nov. (type strain 1NT=DSM 110721T=LMG 31704T) and Paraburkholderia elongata sp. nov. (type strain 5NT=DSM 110722T=LMG 31705T) are proposed.

Ecophysiological Study ofParaburkholderiasp. Strain 1N under Soil Solution Conditions: Dynamic Substrate Preferences and Characterization of Carbon Use Efficiency

“…Annotated ATP-binding cassette (ABC) transporters of interest include the presence of the branched-chain amino acid uptake systems (Liv, TC 3.A.1.4.1), an oligopeptide uptake system (Opp, TC 3.A.1.5.1), and a dipeptide system (Dpp, TC 3.A.1.5.2). Further characterization of this isolate can be found in the work of Wilhelm et al ( 42 ).…”

“…1N was isolated on soil-extracted solubilized organic matter (SESOM) and classified to the genus Paraburkholderia (see Fig. S2 in the supplemental material) ( 42 ). Draft genome size was measured to be 11.1 Mb, containing 353 contigs, with a GC content of 60.6%.…”

“…In this work, we utilized time-resolved exometabolomic footprinting to profile substrate preferences and CUE of the fast-growing soil bacterium Paraburkholderia sp. strain 1N ( 42 ). Paraburkholderia is a relatively newly defined genus created from the subdivision of Burkholderia and predominantly isolated from bulk soil and the rhizosphere or found as endophytes ( 43 – 45 ).…”

Corrigendum: Paraburkholderia madseniana sp. nov., a phenolic acid-degrading bacterium isolated from acidic forest soil

“…Discrepancies with the initially reported activities of P. madseniana RP11 T were identified in repeated Biolog GenIII, API ZYM and phenolic acid-degradation assays in preparation of [2]. The following were incorrectly reported as positive: 4-coumaric acid, acetic acid and alpha-keto-butyric acid metabolism and alkaline phosphatase activity.…”

“…All discrepancies resulted from marginally positive or negative values which were called based on a strict threshold. The discrepancy in 4-coumaric acid catabolism may have stemmed from denaturation caused by the use of autoclaving, which was not used in [2]. An updated table showing the phenotypic differences between P.…”