Molecular-signature analyses support the establishment of the actinobacterial genus Sphaerimonospora (Mingma et al. 2016)

https://doi.org/10.1016/j.syapm.2017.07.009Get rights and content

Abstract

The genera Microbispora and Sphaerimonospora were examined for GyrB and RecA amino-acid signatures to determine whether molecular-signature analyses support the recent establishment of the genus Sphaerimonospora. The creation of Sphaerimonospora was based mainly upon morphological differences between Microbispora and Sphaerimonospora and the clustering of the type strains of the two genera in phylogenetic trees based on a multilocus sequence analysis. The molecular-signature analyses showed that all members of Sphaerimonospora can be distinguished from all members of Microbispora at 14 amino acid positions in the GyrB protein and at four positions in the shorter RecA protein. These amino acid differences can be used as signatures to differentiate the members of these genera from each other and thus provide support for the establishment of the genus Sphaerimonospora. This is the first demonstration of the use of molecular signatures to support the establishment of a new genus in the family Streptosporangiaceae. Following the transfer of Microbispora mesophila and Microbispora thailandensis from Microbispora to Sphaerimonospora, all species in the genus Microbispora are characterised by the insertion of a small, hydrophobic amino acid after position 208 in the GyrB protein. This insertion is absent from the GyrB protein of members of the genus Sphaerimonospora.

Introduction

The actinobacterial family Streptosporangiaceae (order Streptosporangiales) contains 14 genera (Acrocarpospora, Herbidospora, Microbispora, Microtetraspora, Nonomuraea, Planobispora, Planomonospora, Planotetraspora, Sphaerimonospora, Sphaerisporangium, Streptosporangium, Thermoactinospora, Thermocatellispora and Thermopolyspora; http://www.bacterio.net/-classifphyla.html; [10]).

Since its establishment, the genus Microbispora [12] has undergone several taxonomic revisions [11], [16], [1]. Microbispora currently contains seven species with validly-published names: Microbispora amethystogenes, Microbispora bryophytorum, Microbispora camponoti, Microbispora corallina, Microbispora hainanensis, Microbispora rosea (the type species) and Microbispora siamensis. M. rosea is represented by two subspecies: M. rosea subsp. rosea and M. rosea subsp. aerata (http://www.bacterio.net/microbispora.html).

The genus Sphaerimonospora was recently established with Sphaerimonospora cavernae as the type species [10]. In addition, Mingma et al. [10] proposed transferring Microbispora mesophila and Microbispora thailandensis to the new genus as Sphaerimonospora mesophila and Sphaerimonospora thailandensis, respectively. The establishment of the genus Sphaerimonospora was based primarily on morphology and a multilocus sequence analysis (MLSA). All members of the genus Sphaerimonospora produce single spores on aerial hyphae, whereas members of the genus Microbispora produce pairs of spores on aerial hyphae. The MLSA, using 5182-nt concatenated-gene sequences generated from partial sequences of the gyrB, rpoB, atpD, recA and 16S-rRNA genes, showed that the type strains of S. cavernae, M. mesophila and M. thailandensis clustered in the neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees with bootstrap values of 100%.

The chemotaxonomic characteristics of the genus Sphaerimonospora are very similar to those of the genus Microbispora. However, members of the genus Sphaerimonospora can be distinguished from members of the genus Microbispora by their fatty-acid profiles, with Sphaerimonospora strains containing large amounts of iso-C16:0 (>60%) and 10-methyl C17:0 (>9%)[10]. Sphaerimonospora strains also contain low amounts (<4%) of C16:0, C17:0 and anteiso-C17:0 fatty acids, which are usually present in higher proportions in Microbispora strains [10], [11]. The G + C contents of the genomic DNAs of members of the two genera are similar: 70–71% for Sphaerimonospora and 68–73% for Microbispora [10].

A phylogenetic analysis of gyrase subunit B gene sequences in the family Streptosporangiaceae identified the type strains of M. mesophila and M. thailandensis as being the deepest branching members of the genus Microbispora in the gyrB gene tree [7]. An analysis of Microbispora GyrB amino acid sequences showed that the type strains of M. mesophila and M. thailandensis could be distinguished from all other members of the genus Microbispora by the following GyrB amino acid signatures: R55; F69: S141; Q200; N210; A225; G240; G262; I318; A378; E484; A575 and L604 (all other members of the genus Microbispora have L55; M/L-69; K/Q-141; T/K/R-200; D/E-210; S225; N/S-240; A262; V318; S378; D484; L575 and V/I-604). Furthermore, the type strains of M. mesophila and M. thailandensis were identified as being the only members of the genus to lack an amino acid insertion after position 208 in the Microbispora GyrB protein [7].

The type strains of M. mesophila and M. thailandensis were also noted to be the deepest branching members of the genus Microbispora in the recA gene tree and to have unique RecA amino acids: T33; P35; S46 and Q266 (all other Microbispora strains have A33, A35, A46 and I/V/M266). The type strain of M. mesophila was shown to contain a large insertion in its recA gene, which was identified as an intein [8]. A large insertion was also identified in the recA gene of the type strain of S. cavernae [10], although this insertion was deleted from the sequence before being deposited in the GenBank/DDBJ/EMBL databases.

The establishment of the genus Sphaerimonospora in the family Streptosporangiaceae (and the transfer of two members of the genus Microbispora to the new genus Sphaerimonospora) provides an opportunity to assess whether GyrB and RecA molecular-signature analyses can be used to provide support for the separation of the genera Microbispora and Sphaerimonospora.

Section snippets

Bacterial strains, DNA isolation, PCR amplification and DNA sequencing

The type strains of all species with validly-published names in the genera Microbispora and Sphaerimonospora were studied. Non‐type strains from the genus Microbispora were included in the analyses. In addition, the gyrB and recA gene sequences from 103 strains from the other genera of the family Streptosporangiaceae with validly-published names were included in the phylogenetic analyses (Table S1; a total of 122 strains was used). Genomic DNA was isolated as described previously [7].

The PCR

Phylogenetic analyses

Fig. 1 shows the positions of the genera Microbispora and Sphaerimonospora within the family Streptosporangiaceae in a maximum-likelihood (ML) 16S-rRNA gene phylogenetic tree. The members of the genera Microbispora and Sphaerimonospora are more closely related to each other than to any other genera in the family Streptosporangiaceae and this association was supported by a moderate bootstrap value (77%). The members of the genus Microbispora formed a coherent cluster, but this association was

Conclusions

This study has shown that GyrB and RecA molecular-signature analyses support the separation of the genera Microbispora and Sphaerimonospora, as there are positions in both the GyrB and RecA proteins where the amino acid at that position is common to all members of the genus Microbispora, but is distinct from the amino acid at the corresponding position in the GyrB and RecA proteins of all members of the genus Sphaerimonospora. These amino-acid differences can be designated as molecular

Acknowledgements

Thanks to James Pelser for helpful comments on the manuscript. This work was supported by research grants to PRM from the National Research Foundation (Integrated Biodiversity Information Programme; grant number: 86955) and the University Research Committee (University of Cape Town).

References (16)

There are more references available in the full text version of this article.

Cited by (4)

  • Endophytic actinobacteria of Hymenachne amplexicaulis from the Brazilian Pantanal wetland produce compounds with antibacterial and antitumor activities

    2021, Microbiological Research
    Citation Excerpt :

    On the other hand, CMRP4859 isolate was grouped in another clade (Fig. 3) with high similarity with the species Microbispora siamensis (98.45 %) (Table S3). However, for the identification of these two isolates at the species level, additional sequencing of the gyrB and rpoB genes is required (Savi et al., 2016; Mingma et al., 2016; Meyers et al., 2017). Isolate CMRP4861 was identified as belonging to the genus Leifsonia.

  • Sphaerimonospora triticiradicis sp. nov., a novel actinomycete isolated from a root of wheat (Triticum aestivum L.)

    2019, Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

The GenBank accession numbers for the gyrB and recA gene sequences used in this study are shown in Table S1.

View full text