Encyclopedia
Please note this is an old version of this entry, which may differ significantly from the current revision.
Subjects:
Microbiology
Bacillales (later heterotypic synonyms of Caryophanales) is the most productive order of the phylum Firmicutes. The enormous diversity of the order, which includes numerous genera and species. The Order Bacillales, the type order of the class Bacilli, was approved in the list of bacterial names in 1980.
- Bacillales
- Caryophanales
- taxonomy
- biotechnology
1. Introduction
Bacillales (later heterotypic synonyms of Caryophanales) is the most productive order of the phylum Firmicutes. The enormous diversity of the order, which includes numerous genera and species, resulted in scanty detailed studies of the diverse taxa. Based on 16S rRNA gene sequencing analysis, phylogenomics, and other approaches, Bacillales is delineated to include ten validly published families [1]. Of these, the family Bacillaceae comprises certain strains capable of surviving under various conditions, which, from an anthropogenic perspective, are considered extreme, including high or low temperatures and pH ranges and high salt concentrations. In addition to these extremes individually, some members of Bacillaceae can survive under multiple combinations of the above extremes and, hence, are considered polyextremophiles [2]. The ability to withstand harsh conditions placed members of the order Bacillales at the center of interest for various industrial applications, and [3] up to now, additional biotechnologically relevant insights are being gained, even among the well-known species and strains.
2. Order Bacillales
2.1. Taxonomy
In the revised roadmap of the phylum Firmicutes, Ludwig et al. 2009 delineated the Bacillales Prévot 1953 (Approved Lists 1980), the type order of the class Bacilli, to include eight families [9,10]. This followed the removal of two families, including Caryophanaceae Peshkoff 1939 (Approved Lists 1980) and the reassignment of its type genus, Caryophanon, to Planococcaceae Krasilnikov 1949 (Approved Lists 1980), despite the priority of the former family [9,11]. Of note, the authors also questioned the descriptive validity of the name Caryophanaceae, thereby virtually promoting the propagation of the name Bacillales Prévot 1953 (Approved Lists 1980). The Approved Lists 1980 included the above families and the orders Caryophanales Peshkoff 1939 and Bacillales Prévot 1953 [11]. As highlighted recently by Tindall 2019, the list did not provide a clear recommendation for the assignment of taxa above the genus level and, since only one name could correctly represent the order, considering appropriate rules of the International Code of Nomenclature of Prokaryotes. Considering the priority of Caryophanales Peshkoff 1939 over Bacillales Prévot 1953 and the inclusion of the nomenclatural types of both, Caryophanon Peshkoff 1939 and Bacillus Cohn 1872, respectively, in the same order, the correct name of the order is Caryophanales Peshkoff 1939 [12,13]. Thus, Bacillales Prévot 1953 (Approved Lists 1980) represents the later heterotypic synonyms of Caryophanales Peshkoff 1939 [11,13].
The Order Bacillales, the type order of the class Bacilli, was approved in the list of bacterial names in 1980 [2,14]. Bergey’s Manual of Systematic Bacteriology has completely described this order completely based on 16S rRNA gene sequencing analysis and other polyphasic approaches such as chemotaxonomy and phenotypic methods [2,15]. Recently, based on the rules provided by The International Code of Nomenclature of Prokaryotes (ICNP), the name Caryophanales should be used instead of the name Bacillales. Since these names are heterotypic synonyms, however, the name approved first has the priority to be used. In this case, the name Caryophanales Peshkoff 1933 was approved prior to the name Bacillales Prévot 1953. Hence, the name Caryophanales Peshkoff 1933 is the correct name for the order Bacillales [13].
As with other taxa, the previous classification of the order Bacillales relied heavily on 16S rRNA gene sequences, resulting in noticeable anomalies. For example, several spores- and non-spore-forming families and genera group together, suggesting that a single gene marker does not provide sufficient resolving power for delineating the order Bacillales [16]. Recent phylogenomic approaches, notably the work of de Maayer et al. 2019, attempted to resolve the evolutionary relationship among strains affiliated to the order based on comparative genomics [16,17].
Despite referencing the later heterotypic synonym, Bacillales, the authors proposed eleven distinct families in the order Bacillales and an unplaced group (Table 1).
The allocation of the Incertae sedis families agrees with the phylogenetic outline in volume 3 of Bergey’s Manual of Systematic Bacteriology [2,14]. Although Bacillaceae is the most imposing and well-known family, Listeriaceae consisting of Listeria and Brochothrix is also noteworthy. Moreover, Pasteuriaceae, some genera of the family Paenibacillaceae such as Gorillibacterium or Brevibacillus, and Staphylococcus have clinical and pathological importance [2,8]. Based on a consensus phylogenomic strategy, de Maayer et al. resolved the observed anomalies in the family Bacillaceae. For instance, although the genus Staphylococcus comprises pathogenic strains previously grouped in the family Micrococcaceae, the phylogenetic and molecular analysis did not reveal any close relationships between them, resulting in the proposal for a new family Staphylococcaceae [16]. However, the precise identification of its members at the species level needs arduous efforts and may fail if based only on phenotypic approaches [4]. Another heterogeneous and polyphyletic family in this order is Planococcaceae, with many phylogenetic works focused on the history of its evolution, but its demarcation remains unresolved [16,18,19]. The classification in this family is based on 16S rRNA gene nucleotide signature, phenotypic characteristics, and observed branching in the drawn phylogenetic trees. However, these methods do not have enough resolving power at the genus and species level and cause significant overlap with other species of the families Bacillaceae and Incertae sedis 19 [16]. It is noteworthy that Planococcaceae represents the later heterotypic synonym of Caryophanaceae, as highlighted earlier by Tindal [13] and recently supported by Gupta and Patal [20].
Below the family level, the 16s rRNA gene-based classification of the genus Bacillus and especially the Cereus clade also represents some challenges [21]. This method remains the gold standard for assigning microbial strains to various taxa due to its low-cost and reproducibility between laboratories worldwide, providing people with an overview of the microbial strains for further research. At present, the Cereus clade comprises B. cereus, B. anthracis, Bacillus thuringiensis, Bacillus mycoides, Bacillus pseudomycoides, Bacillus cytotoxicus, and Bacillus toyonensis. Different phylogenomics approaches have clarified the interrelationship of the otherwise incoherent genus Bacillus [6,21,22]. Gupta et al. 2020 also showed that a subset of the core proteins of Bacillus species, including concatenated proteins GyrA_B-RpoB-C and PolA-UvrD, provide consistent clustering strain in the genus [4,23]. In addition to whole genome approaches, which provide consistent means of identifying and classifying Bacillales at different taxonomic ranks, relevant techniques for identifying industrially important strains may be pertinent toward effective industrial deployment [16,24,25].
| Family Name | Proposed by | IJSEM 1 Validation List No. (Year) | Type Genus | Involved Valid and Invalid Genera Until 2022 in LPSN 2 | Valid Genera with Correct Name until 2022 in LPSN |
|---|---|---|---|---|---|
| Alicyclobacillaceae | da Costa and Rainey 2010 | 132 (2010) | Alicyclobacillus | 5 | 5 |
| Bacillaceae | Fischer 1895 | (1980) | Bacillus | 134 | 117 |
| Caryophanaceae | Peshkoff 1939 | (1980) | Caryophanon | 26 | 19 |
| Desulfuribacillaceae | Sorokin et al. 2021 | 200 (2021) | Desulfuribacillus | 1 | 1 |
| Listeriaceae | Ludwig et al. 2010 | 132 (2010) | Listeria | 3 | 2 |
| Paenibacillaceae | De Vos et al. 2010 | 132 (2010) | Paenibacillus | 19 | 16 |
| Pasteuriaceae | Laurent 1890 | (1980) | Pasteuria | 1 | 1 |
| Sporolactobacillaceae | Ludwig et al. 2010 | 132 (2010) | Sporolactobacillus | 5 | 5 |
| Staphylococcaceae | Schleifer and Bell 2010 | 132 (2010) | Staphylococcus | 12 | 10 |
| Thermoactinomycetaceae | Matsuo et al. 2006 | (2007) | Thermoactinomyces | 25 | 24 |
| Incertae sedis 46 | - | - | - | 1 | 1 |
1 International Journal of Systematic and Evolutionary Microbiology. 2 List of Prokaryotic names with Standing in Nomenclature.
2.2. General Characteristics
General characteristics of bacteria include a wide range of features such as the shape and arrangement of the bacterial cells, cell wall chemical type, spore formation ability, motility, growth conditions, and resistance and tolerance to antibiotics. [8,28]. Interestingly, the genera of order Bacillales are phenotypically diverse. For example, cell shapes change from spherical to filamentous and may be motile by flagella. Oxygen requirement has a broad range from strictly aerobic, microaerophilic, facultative anaerobic, and aerotolerant to strictly anaerobic [2,29]. One of the most important characteristics of the order Bacillales is endospore formation, although some exceptions exist [2,3]. However, these exceptions remained to be clarified whether from one side lacking the genes for spore formation, or losing all or some of them during evolution, or alternatively, unfavorable physiological conditions cause unsuccessful spore formation [17]. Furthermore, the cell wall of order Bacillales stains Gram-positive for young cells, in general, but some genera react Gram-negatively, such as Aidingibacillus, Aquisalibacillus, Bhargavaea, Caldibacillus, Caryophanon, Exiguobacterium, Mammaliicoccus, Novibacillus, Sediminibacillus, and Thalassorhabdus [2,14,29,30]. Additionally, most of the genera allocated to this order have menaquinone 7 (MK-7) as their respiratory quinone, while various exceptions have been found [2].
This entry is adapted from the peer-reviewed paper 10.3390/microorganisms10122355
This entry is offline, you can click here to edit this entry!
