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

Abstract

The environment of plant rhizosphere soil differs from that of non-rhizosphere soil due to the secretion of mucilage polysaccharides from the roots. This environment is regarded as one of the preferential habitats for agar-degrading bacteria. In a previous study, agar-degrading Steroidobacter agariperforans KA5-B T was isolated from agar-enriched agricultural soil using diffusible metabolites from Rhizobiales bacteria. Based on the hypothesis that similar characteristic bacteria still exist in the rhizosphere, isolation was performed using rhizosphere soils. Agar-degrading SA29-B T and YU21-B were isolated from onion and soybean rhizosphere soils. The 16S rRNA genes of these strains showed ≥98.7% identities with the most closely related strain KA5-B T. However, differences were noted in polysaccharide utilization, and average nucleotide identities were <95-96% against strain KA5-B T , indicating that they are different species from S. agariperforans KA5-B T. To investigate the distribution of bacterial sequences affiliated with novel strains, a primer set was designed and a metaanalysis of the 16S rRNA gene was performed. Sequences were widely distributed in rhizospheres throughout Japan, but varied in plant-and region-dependent manners. Regarding phenotypic characterization, distinguishable features were observed in growth temperatures, pH, and dominant fatty acids. SA29-B T and YU21-B grew at 15-40°C and pH 6.0-12 and contained C 16:0 as the dominant cell fatty acid, whereas KA5-B T showed no growth at 40°C and pH 12 and contained a moderate amount of C 16:0. Based on these characteristics, SA29-B T (JCM 333368 T =KCTC 72223 T) and YU21-B (JCM 333367=KCTC 72222) represent novel species in the genus Steroidobacter, for which the name Steroidobacter agaridevorans sp. nov. is proposed.

Steroidobacter gossypii sp. nov., isolated from cotton field soil

“…S3c–f). This phenomenon was not consistent with previous studies [2, 6], showing that two isolates of the genus Steroidobacter displayed remarkably improved growth when cultivated with the metabolites produced by bacteria belonging to the order Rhizobiales . This suggested that strain S1-65 T survived in co-evolved microbial communities with structures distinct from where those two isolates were isolated, leading to different microbial interaction patterns.…”

“…ISP9 supplemented with 1 % glucose served as a positive control. Polysaccharide degradation capabilities were tested following the method described by Ikenaga et al [6]. Other physiological and biochemical properties of strains S1-65 T and KA5-B T were further tested using the API 20 NE systems (bioMérieux), according to the manufacturer’s instructions.…”

“…cummioxidans' 35Y (data adapted from [5]); 3，'S. agaridevorans' SA29-B (data adapted from [6]); 4, S. agariperforans KA5-B T (data adapted from [2]); 5, 'S. flavus' CPCC 100154 (data adapted from [4]); 6, S. soil JW-3 T (data adapted from [3]); 7, S. denitrifcans FS T (data adapted from [1]).…”

“…‘ Steroidobacter flavus ’ CPCC 100154 [4] and ‘ Steroidobacter cummioxidans ’ 35Y [5] have also been proposed, but not validly published. Recently, another novel species, ‘ Steroidobacter agaridevorans ’ SA29-B, was published by Ikenaga et al [6], where it was experimentally shown that diffusible metabolites from companion bacteria belonging to the order Rhizobiales remarkably enhanced the regular growth of the strain. S.…”

“…'Steroidobacter flavus' CPCC 100154 [4] and 'Steroidobacter cummioxidans' 35Y [5] have also been proposed, but not validly published. Recently, another novel species, 'Steroidobacter agaridevorans' SA29-B, was published by Ikenaga et al [6], where it was experimentally shown that diffusible metabolites from companion bacteria belonging to the order Rhizobiales remarkably enhanced the regular growth of the strain. S. agariperforans KA5-B T was also observed to show commensal interactions with bacteria belonging to the same order [2], suggesting potential ecological functions of species in this genus impacting and regulating micro-environments in plant rhizospheres.…”