Genomic evidence that Ornithinicoccus soli Jiang et al. 2020 is a later heterotypic synonym of Segeticoccus rhizosphaerae Lee and Whang 2020

TL;DR

This study shows that two soil bacteria species, Ornithinicoccus soli and Segeticoccus rhizosphaerae, are actually the same species based on genomic and phylogenetic evidence.

Contribution

The paper provides genomic evidence to reclassify Ornithinicoccus soli as a later synonym of Segeticoccus rhizosphaerae.

Findings

Both strains share identical 16S rRNA gene sequences and similar genomic features.

Average nucleotide identity and digital DNA–DNA hybridization values confirm they are the same species.

Phylogenetic analysis shows they form a distinct cluster separate from other genera.

Abstract

The genus Segeticoccus includes only one species with validly published name, Segeticoccus rhizosphaerae. The type strain Segeticoccus rhizosphaerae YJ01T was isolated from soil in Korea, while Ornithinicoccus soli XNB-1T was isolated from soil in China. Both strains share similar phenotypic and chemotaxonomic characteristics, including predominant menaquinone MK-8(H4) and major polar lipids diphosphatidylglycerol and phosphatidylglycerol. Whole genome sequences revealed a DNA G+C content of 70.1 mol% for both strains and 100% similarity in their 16S rRNA gene sequences. Phylogenetic analysis showed they form a distinct cluster separate from other genera. Genomic comparisons showed average nucleotide identity and digital DNA–DNA hybridization values of 99.16 and 94.2%, respectively, indicating they represent a single species. Based on this genomic evidence, Ornithinicoccus soli Jiang et al. 2020 is proposed to be a later heterotypic synonym of Segeticoccus rhizosphaerae Lee and Whang 2020.

Figures

Full text

The genus Segeticoccus, was first described by Lee and Whang [1]. Currently, only one species within Segeticoccus is validly published, namely, Segeticoccus rhizosphaerae [2]. The type strain Segeticoccus rhizosphaerae YJ01^T^ (=KACC 19547^T^=NBRC 113173^T^), was isolated from a spinach farming field soil at Shinan in Korea. It was a Gram-stain-positive, aerobic, non-motile, non-spore-forming cocci, capable of growing at 10–37 °C (optimum, 28–30 °C) and 0–7.5 % (w/v) NaCl (optimum, 1.0% NaCl) [1]. Ornithinicoccus soli XNB-1^T^ (=CCTCC AB 2019099^T^=KCTC 49259^T^) was isolated from farmland soil in Taian, Shandong province, PR China [3]. It is a Gram-stain-positive, aerobic, non-motile, coccoid-shaped bacterium, capable of growing at 16–30 °C (optimum, 30 °C) and 0–7% (w/v) NaCl (optimum, 1.0%). Both strains contained MK-8(H_4_) as the predominant menaquinone, and diphosphatidylglycerol and phosphatidylglycerol as the major polar lipids. Both the names Segeticoccus rhizosphaerae Lee and Whang 2020 [1] and Ornithinicoccus soli Jiang et al. 2020 [3] were published in issue 3 of volume 70 in 2020. However, their relationship and taxonomic status need to further clarified.

Whole genome sequences of type strains in the genera Segeticoccus, Ornithinicoccus, Ornithinimicrobium, and related genera within family Intrasporangiaceae were obtained from the publicly available NCBI GenBank. Genome quality, genome completeness and contamination were evaluated using the CheckM program version 1.1.3 [4]. The genome sequences were annotated using Prokka v1.13 software [5]. The 16S rRNA gene phylogenetic trees were reconstructed by the neighbour-joining (NJ) [6] and maximum-likelihood (ML) [7] methods using the mega software version 5.2 [8]. The alignment was generated using mafft version 7.520 software [9]. The genetic distances for the NJ analysis were calculated by Kimura’s two parameter model [10]. The ML phylogenetic tree was generated with the best nucleotide substitution model of GTR+G+I [11]. The tree topologies were evaluated by bootstrap values based on 1000 resamplings [12]. The phylogenomic tree was reconstructed usingiq-tree version 2.0.7 [13] with model GTR+F+R5 based on 92 core genes extracted by UBCG program [14]. The digital DNA–DNA hybridization (dDDH) values were calculated using the TYGS as implemented on the DSMZ website [15]. The average nucleotide identity (ANI) values were determined using FastANI version 1.33 [16]. The average amino acid identity (AAI) values were calculated using the CompareM program (https://github.com/dparks1134/CompareM).

The genome information showed that the DNA G+C content of both strains was 70.1 mol% (Table 1). The complete 16S rRNA gene sequences of Segeticoccus rhizosphaerae YJ01^T^ (1519 bp) and Ornithinicoccus soli XNB-1^T^ (1519 bp) were retrieved from their genomic sequences, revealing 100% similarity, indicating a very close relationship. The 16S rRNA gene phylogenetic tree showed that Segeticoccus rhizosphaerae and Ornithinicoccus soli formed a distinct cluster, separated from Ornithinicoccus halotolerans and Ornithinicoccus hortensis (Figs 1 and S1, available in the online Supplementary Material).

A robust phylogenomic tree showed the very close relationship between Segeticoccus rhizosphaerae YJ01^T^ and Ornithinicoccus soli XNB-1^T^, indicating they may belong to the same species (Fig. 2). They formed an independent branch, separated from other genera such as Ornithinicoccus, Oryzihumus and Ornithinimicrobium. Therefore, strain XNB-1^T^ should be classified as belonging to the genus Segeticoccus rather than Ornithinicoccus. The ANI and dDDH values between the two strains were 99.1 and 94.2%, respectively, confirming that they represent a single species. The ANI values between Segeticoccus rhizosphaerae YJ01^T^, Ornithinicoccus soli XNB-1^T^ and other type strains of genus Ornithinicoccus were lower than 78% (Table 2). The AAI values between Segeticoccus rhizosphaerae YJ01^T^, Ornithinicoccus soli XNB-1^T^ and other members of Ornithinicoccus were lower than 63.7%, which were below the AAI threshold for bacterial genus delineation of 65–72% suggested by Konstantinidis and Tiedje [17]. Therefore, combined with the evidence provided by Lee and Whang [1], they should be classified into the genus Segeticoccus. Additionally, both strains shared similar phenotypic and chemotaxonomic characteristics, as shown in Table 3.

Collectively, based on the genomic evidence, including ANI, dDDH and AAI values, and phylogenetic characteristics, Ornithinicoccus soli is proposed to be a later heterotypic synonym of Segeticoccus rhizosphaerae.

supplementary material

10.1099/ijsem.0.006503Uncited Fig. S1.