Metabolic and taxonomic insights into the Gram-negative natural rubber degrading bacterium Steroidobacter cummioxidans sp. nov., strain 35Y

Abstract

The pathway of rubber (poly [cis-1,4-isoprene]) catabolism is well documented for Gram-positive rubber degraders but only little information exists for Gram-negative species. The first documented potent rubber degrading Gram-negative strain is Xanthomonas sp. strain 35Y that uses extracellular rubber oxygenases for the initial cleavage of the polyisoprene molecule. However, neither the exact phylogenetic position of Xanthomonas sp. strain 35Y nor the catabolic pathway of the primary polyisoprene cleavage products have been investigated. In this contribution, we started to address both these issues by a comprehensive taxonomic characterization and by the analysis of the draft genome sequence of strain 35Y. Evaluation of the 16S rRNA gene sequence pointed to a borderline taxonomic position of strain 35Y as a novel species of the genus Steroidobacter. Further, substantial differences in the genotypic properties of strain 35Y and the members of the genus Steroidobacter, including average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH), resolved the taxonomic position of strain 35Y and suggested its positioning as a novel species of the genus Steroidobacter. This was further confirmed by comparative analysis of physiological and biochemical features of strain 35Y with other members of the genus Steroidobacter. Thus, we conclude that strain 35Y represents a novel species of the genus Steroidobacter, for which we propose the designation Steroidobacter cummioxidans sp. nov., strain 35YT. A comprehensive analysis of the draft genome of S. cummioxidans strain 35Y revealed similarities but also substantial differences to rubber degrading Gram-positive counterparts. In particular, the putative transporters for the uptake of polyisoprene cleavage products differ from Gram-positive rubber degrading species. The draft genome sequence of S. cummioxidans strain 35Y will be useful for researchers to experimentally verify the predicted similarities and differences in the pathways of polyisoprene catabolism in Gram-positive and Gram-negative rubber degrading species.

Characterization and Distribution of Agar-degrading <i>Steroidobacter agaridevorans</i> sp. nov., Isolated from Rhizosphere Soils

“…1 2 3 4 5 6 7 8 Colony color pale yellow pale yellow pale yellow pale yellow yellow-brown yellow-orange light yellow, then turns to yellow light brown Motility non-motile non-motile non-motile motile motile by a single polar flagellum motile by 1 (or 2) polar flagellum motile by a single polar flagellum motile by a single polar flagellum Cell morphology Rod rod straight to slightly curved rod straight to slightly curved rod slightly curved rod rod rod rod Cell size width by length (μm) 0.4-0.6 by 1.5-2.5 0.4-0.7 by 1.3-2.0 0.4-0.6 by 1.0-2.1 0.3-0.5 by 1.0-3.1 0.3-0.5 by 0.6-1.6 0.4-0.6 by 2.0-5.0, occasionally longer (10 μm) 0.6-0.8 by 1.5-1.8 0.3-0.5 by 1.0-3. 6.0-12.0 (7.0-7.5) 6.0-12.0 (7.0) 4.5-9.0 (6.0-8.0) 6.0-9.0 (7.0) 6.1-7.8 (7.0) ND (ND) 6.0-8.0 (7.0-7.5) 6.5-9.0 (7.5 or 7.0) Growth range at different NaCl concentrations (optimum) (%) 0-2.0 (1.0) 0-3.0 (1.0) 0-2.0 (ND) 0-1.0 (0.5) ND (0.1) ND (ND) 0-3.0 (ND) 0-0.5 (0.1) Taxa: 1 strain SA29-B T ; 2 strain YU21-B; 3, Steroidobacter agariperforans KA5-B T (Suyama et al, 1993); 4, Steroidobacter soli JW-3 T (Huang et al, 2019); 5, Steroidobacter denitrificans FS T (Fahrbach et al, 2008); 6, "Steroidobacter cummioxidans" 35Y (Sharma et al, 2018); 7, "Steroidobacter flavus" CPCC 100154 (Gong et al, 2016); 8, Povalibacter uvarum Zumi 37 T (Nogi et al, 2014). Sum3, summed feature 3, is composed of C16:1ω7c and C16:1ω6c.…”

Rubber oxygenases

“…Gram-negative rubber-degrading bacteria seem to be less abundant and only one Gram-negative strain with clearly demonstrated rubber-degrading ability was known until recently. This strain is Steroidobacter cummioxidans 35Y (Sharma et al 2018) (previously Xanthomonas sp. 35Y (Tsuchii and Takeda 1990)) and meanwhile has become one of the best-studied rubber degraders (see below).…”

First report of cis-1,4-polyisoprene degradation by Gordonia paraffinivorans

“…Among the Gram-negatives, Steroidobacter cummioxidans 35Y (former Xanthomonas sp. strain Y35) [8][9][10] and Rhizobacter gummiphilus NS21 have been well characterized, as well as their enzymatic system (LatA1, RoxA, and RoxB), which are responsible for the first steps in rubber degradation [11]. Several Gram-positive rubber degraders are well known and most of them are Actinobacteria that belong to the Gordonia [12,13], Nocardia [14][15][16], Streptomyces [17,18], and Rhodococcus genera [19].…”