Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small-subunit-ribosomal RNA sequences

Abstract

The small‐subunit rRNA sequences of 51 species of Bacillus were determined by reverse transcription to elucidate the phylogenetic structure of the genus. Comparative analysis of the sequence data revealed five phylogenetically distinct clusters. Group 1 (Bacillus sensu stricto) included B. subtilis the type species of the genus and 27 other species. Group 2 consisted of B. sphaericus and five other bacilli and Sporosarcina ureae clustered within the confines of this group. Group 3 consisted of a phylogenetically coherent group of 10 species whereas groups 4 and 5 comprised two and three species respectively. It is evident that the genus Bacillus in genetically extremely heterogeneous and requires extensive taxonomic revision. The rRNA structures defined in the present study will provide a firm basis for the division of Bacillus into several phylogenetically distinct genera.

Phylogenetic Analyses of the Genus Hymenobacter and Description of Siccationidurans gen. nov., and Parahymenobacter gen. nov

“…The main impediment is the lack of diagnostic phenotypic differences. However, Stackebrandt et al [5], Ash et al [3], Reddy and Garcia-Pichel [4] and Ivanova et al [31] created the genera, families and orders based only on the presence of unique signatures in 16S rRNA gene sequences, further implicating that the phylogenetic evidence alone is sufficient to create a higher taxonomic rank. However, polyphasic taxonomy emphasizes the significance of consensus between phenotypic and genotypic characteristics [35][36][37][38], in delineation of taxa.…”

“…In this context, it is worth mentioning that, based on 16S rRNA gene sequence analyses, five distinct phylogenetic groups within the genus Bacillus [3], two novel orders, Solirubrobacterales and Thermoleophilales [4], and a new hierarchic classification structure for the actinomycete line of descent [5] were proposed and the phylogenetic affiliation of the genus pseudomonads was assessed [6]. In congruence with these, to take few examples, several novel genera, such as Solibacillus [7] and Planomicrobium [8], were created on the basis of their 16S rRNA gene sequence.…”

Paenibacillus yonginensis sp. nov., a potential plant growth promoting bacterium isolated from humus soil of Yongin forest

“…Many new species from the genus Paenibacillus have been reported, along with more research ongoing. The genus Paenibacillus was first proposed by Ash et al (1991) and later its description was emended by Shida et al (1997). Members of this genus are ubiquitous in nature and species have been isolated from various environments such as petroleum-hydrocarbon-contaminated sediment (Montes et al 2004), warm springs (Saha et al 2005), alkaline soils (Yoon et al 2005), rice fields (Sánchez et al 2005), a spacecraft assembly facility (Osman et al 2006), ginseng field soil (Park et al 2007), poultry litter compost (Vaz-Moreira et al 2007), phyllosphere (Valverde et al 2008), gut (Park et al 2009), rhizosphere (Beneduzi et al 2010), a subsurface molybdenum mine (Benardini et al 2011), tidal flat (Wang et al 2012), nodules (Carro et al 2013) and gamma-irradiated Antarctic soil (Dsouza et al 2014).…”

“…At the time of writing, there are nearly 150 species of the genus Paenibacillus with validly published names (http://www.bacterio.net/paenibacillus.html). Members of the genus Paenibacillus are Gram-positive or Gram-variable, rod-shaped bacteria, and strictly aerobic or facultatively anaerobic (Ash et al 1991). The major fatty acid is anteiso-C 15:0 , the predominant isoprenoid quinone is unsaturated menaquinone with seven units (MK-7) and meso-diaminopimelic acid is commonly found in the peptidoglycan (Priest 2009).…”

Virgibacillus arcticus sp. nov., a moderately halophilic, endospore-forming bacterium from permafrost in the Canadian high Arctic

“…Therefore, it was concluded that the peptidoglycan type of strain Hal 1 T was A1a (L-Lys direct, type A11 according to the DSMZ catalogue of strains). The presence of peptidoglycan type A1a is typically characteristic of genera of the Bacillus rRNA group 2 (Ash et al, 1991;Rheims et al, 1999;Stackebrandt et al, 1987) within the Bacillales; for example, the recently described Marinibacillus (Yoon et al, 2004a) and Jeotgabacillus (Yoon et al, 2001); however, peptidoglycan type A1a has also been detected for Bacillus seohaeanensis (Lee et al, 2006b) and the genera Sedimentibacter within the Clostridales (Breitenstein et al, 2002). Although the presence of cell-wall peptidoglycan type A1a differs from recognized Virgibacillus species (Table 1), we recommend that strain Hal 1 T is included within the genus Virgibacillus based on the results of other genotypic and phenotypic tests.…”