Defining the Species Micromonospora saelicesensis and Micromonospora noduli Under the Framework of Genomics

Abstract

The type isolates of species Micromonospora saelicesensis and Micromonospora noduli are Gram-stain positive actinobacteria that were originally isolated from nitrogen fixing nodules of the legumes Lupinus angustifolius and Pisum sativum, respectively. These two species are very closely related and questions arise as to whether they should be merged into a single species. To better delineate the relationship of M. saelicesensis and M. noduli, 10 strains isolated from plant tissue (nodules and leaves) and identified by their 16S rRNA gene sequences as either M. saelicensesis or M. noduli, based on a cut-off value of ≥99.5% were selected for whole-genome sequencing and compared with the type strains of M. saelicesensis Lupac 09T and M. noduli GUI43T using overall genome relatedness indices (OGRI) which included ANI, OrthoANI and digital DNA-DNA hybridization. Whole- and core-genome phylogenomic analyses were also carried out. These results were compared with the topologies of the 16S rRNA and gyrB gene phylogenies. Good correlation was found between all trees except for the 16S rRNA gene. Overall results also supported the current classification of M. saelicesensis and M. noduli as separate species. Especially useful was the core-genome phylogenetic analyses based on 92 genes and the dDDH results which were highly correlated. The importance of using more than one strain for a better definition of a species was also shown. A series of in vitro phenotypic assays performed at different times were compared with in silico predictions based on genomic data. In vitro phenotypic tests showed discrepancies among the independent studies, confirming the lack of reproducibility even when tests were performed in the same laboratory. On the other hand, the use of in silico predictions proved useful for defining a stable phenotype profile among the strains analyzed. These results provide a working framework for defining Micromonospora species at the genomic and phenotypic level.

Genome-Based Analysis Reveals the Taxonomy and Diversity of the Family Idiomarinaceae

“…Presently, the integration of genomic information into microbial systematics, in addition to physiological and chemotaxonomic parameters as taxonomic criteria, is strongly recommended in the post-genomic era ( Chun and Rainey, 2014 ). Numerous genome-based approaches have been developed and applied for species delineation, for example pan-genome analysis ( Medini et al, 2005 ; Beukes et al, 2017 ), average nucleotide identity (ANI) analysis ( Konstantinidis and Tiedje, 2005 ; Riesco et al, 2018 ), and digital DNA–DNA hybridization (dDDH) analysis ( Meier-Kolthoff et al, 2013 ; Montero-Calasanz et al, 2017 ). The concept of the pan-genome was first introduced in 2005, and includes the core genome composed of genes shared by all strains, a dispensable genome made of genes present in a subset of the strains, and finally strain-specific genes ( Medini et al, 2005 ; Vernikos et al, 2015 ).…”

Six novel species of the obligate marine actinobacterium Salinispora, Salinispora cortesiana sp. nov., Salinispora fenicalii sp. nov., Salinispora goodfellowii sp. nov., Salinispora mooreana sp. nov., Salinispora oceanensis sp. nov. and Salinispora vitiensis sp. nov., and emended description of the genus Salinispora

“…However, a recent classification of the family Micromonosporaceae based on whole-genome sequencing provided support for the separation of the two genera [15]. Moreover, subsequent phylogenomic analyses using additional Micromonospora type strains and Salinispora [13] further supported the conclusions reached by Carro and colleagues and revealed that Micromonospora pattaloongensis and Micromonospra pisi , which clade outside of the Micromonospora / Salinispora lineage, may need to be reclassified as a third genus.…”

“…Within the family Micromonosporaceae , Salinispora is closely related to Micromonospora , a bacterial genus that has been reported from both terrestrial habitats [13] and marine samples [3]. While Salinispora fail to grow when seawater is replaced with deionized water in the growth medium, Micromonospora strains with this physiological trait have yet to be reported, although some strains can tolerate up to 7 % (w/v) NaCl [14].…”

Comparative proteomic and transcriptomic profiling of Micromonospora strains associated with legumes

“…Micromonospora has been isolated from plant tissues, mainly from nitrogen fixing nodules both actinorhizal and legume plants (Valdés et al, 2005;Trujillo et al, 2006Trujillo et al, , 2007Trujillo et al, , 2010Garcia et al, 2010;Carro et al, 2012aCarro et al, , 2013Trujillo et al, 2015;Riesco et al, 2018) and rarely from roots and leaves (Kirby and Meyers, 2010;Kittiwongwattana et al, 2015;Thawai, 2015;Kaewkla et al, 2017). This genus has been reported as a normal and widespread occupant of actinorhizal plants, including the angiosperm species Alnus viridis, Casuarina equisetifolia, Coriaria myrtifolia, Elaeagnus x ebbingei, Hippophae rhamnoides, Myrica gale, and Morella pensylvanica (Table 1) (Valdés et al, 2005;Trujillo et al, 2006;Carro et al, 2013).…”

“…Ornithopus sp., Pisum sativum, Phaseolus sp., Trifolium sp., and Vicia sp. (Table 1) (Cerda, 2008;Rodríguez, 2008;Carro, 2009;Alonso de la Vega, 2010;Trujillo et al, 2010;Martínez-Hidalgo et al, 2014;Riesco et al, 2018). Several works have reported that the distribution of Micromonospora strains in the nitrogen-fixing nodules in both legumes and actinorhizal plants is not homogeneous and varies from nodule to nodule and plant to plant Carro et al, 2012a).…”