Bacillus

Bacillus (Latin "stick") is a genus of Gram-positive, rod-shaped bacteria, a member of the phylum Firmicutes, with 266 named species. The term is also used to describe the shape (rod) of certain bacteria; and the plural Bacilli is the name of the class of bacteria to which this genus belongs. Bacillus species can be either obligate aerobes: oxygen dependent; or facultative anaerobes: having the ability to be anaerobic in the absence of oxygen. Cultured Bacillus species test positive for the enzyme catalase if oxygen has been used or is present.[2]

This article is about the bacterial genus. For the bacterial class, see Bacilli. For rod-shaped bacteria in general, see Bacillus (shape). For the insect genus, see Bacillus (insect).

Bacillus
Bacillus subtilis, Gram stained
Scientific classification
Domain:	Bacteria
Phylum:	Firmicutes
Class:	Bacilli
Order:	Bacillales
Family:	Bacillaceae
Genus:	Bacillus Cohn, 1872[1]
Species
See text

Bacillus can reduce themselves to oval endospores and can remain in this dormant state for years. The endospore of one species from Morocco is reported to have survived being heated to 420 °C.[3] Endospore formation is usually triggered by a lack of nutrients: the bacterium divides within its cell wall, and one side then engulfs the other. They are not true spores (i.e., not an offspring).[4] Endospore formation originally defined the genus, but not all such species are closely related, and many species have been moved to other genera of the Firmicutes.[5] Only one endospore is formed per cell. The spores are resistant to heat, cold, radiation, desiccation, and disinfectants. Bacillus anthracis needs oxygen to sporulate; this constraint has important consequences for epidemiology and control. In vivo, B. anthracis produces a polypeptide (polyglutamic acid) capsule that protects it from phagocytosis. The genera Bacillus and Clostridium constitute the family Bacillaceae. Species are identified by using morphologic and biochemical criteria.[6] Because the spores of many Bacillus species are resistant to heat, radiation, disinfectants, and desiccation, they are difficult to eliminate from medical and pharmaceutical materials and are a frequent cause of contamination. Bacillus species are well known in the food industries as troublesome spoilage organisms.[6]

Ubiquitous in nature, Bacillus includes both free-living (nonparasitic) species, and two parasitic pathogenic species. These two Bacillus species are medically significant: B. anthracis causes anthrax; and B. cereus causes food poisoning.

Many species of Bacillus can produce copious amounts of enzymes, which are used in various industries, such as in the production of alpha amylase used in starch hydrolysis and the protease subtilisin used in detergents. B. subtilis is a valuable model for bacterial research. Some Bacillus species can synthesize and secrete lipopeptides, in particular surfactins and mycosubtilins.[7][8]

Structure

Cell wall

The cell wall of Bacillus is a structure on the outside of the cell that forms the second barrier between the bacterium and the environment, and at the same time maintains the rod shape and withstands the pressure generated by the cell's turgor. The cell wall is made of teichoic and teichuronic acids. B. subtilis is the first bacterium for which the role of an actin-like cytoskeleton in cell shape determination and peptidoglycan synthesis was identified and for which the entire set of peptidoglycan-synthesizing enzymes was localized. The role of the cytoskeleton in shape generation and maintenance is important.

Bacillus species are rod-shaped, endospore-forming aerobic or facultatively anaerobic, Gram-positive bacteria; in some species cultures may turn Gram-negative with age. The many species of the genus exhibit a wide range of physiologic abilities that allow them to live in every natural environment. Only one endospore is formed per cell. The spores are resistant to heat, cold, radiation, desiccation, and disinfectants.[6]

Origin of name

The genus Bacillus was named in 1835 by Christian Gottfried Ehrenberg, to contain rod-shaped (bacillus) bacteria. He had seven years earlier named the genus Bacterium. Bacillus was later amended by Ferdinand Cohn to further describe them as spore-forming, Gram-positive, aerobic or facultatively anaerobic bacteria.[1] Like other genera associated with the early history of microbiology, such as Pseudomonas and Vibrio, the 266 species of Bacillus are ubiquitous.[9] The genus has a very large ribosomal 16S diversity.

Isolation and identification

An easy way to isolate Bacillus species is by placing nonsterile soil in a test tube with water, shaking, placing in melted mannitol salt agar, and incubating at room temperature for at least a day. Cultured colonies are usually large, spreading, and irregularly shaped.

Under the microscope, the Bacillus cells appear as rods, and a substantial portion of the cells usually contain oval endospores at one end, making them bulge.

Phylogeny

Three proposals have been presented as representing the phylogeny of the genus Bacillus. The first proposal, presented in 2003, is a Bacillus-specific study, with the most diversity covered using 16S and the ITS regions. It divides the genus into 10 groups. This includes the nested genera Paenibacillus, Brevibacillus, Geobacillus, Marinibacillus and Virgibacillus.[10]

The second proposal, presented in 2008,[11] constructed a 16S (and 23S if available) tree of all validated species.[12][13] The genus Bacillus contains a very large number of nested taxa and majorly in both 16S and 23S. It is paraphyletic to the Lactobacillales (Lactobacillus, Streptococcus, Staphylococcus, Listeria, etc.), due to Bacillus coahuilensis and others.

A third proposal, presented in 2010, was a gene concatenation study, and found results similar to the 2008 proposal, but with a much more limited number of species in terms of groups.[14] (This scheme used Listeria as an outgroup, so in light of the ARB tree, it may be "inside-out").

One clade, formed by Bacillus anthracis, Bacillus cereus, Bacillus mycoides, Bacillus pseudomycoides, Bacillus thuringiensis, and Bacillus weihenstephanensis under the 2011 classification standards, should be a single species (within 97% 16S identity), but due to medical reasons, they are considered separate species[15]^:34–35 (an issue also present for four species of Shigella and Escherichia coli).[16]

Bacillus phylogenetics

Root "pathogenic"   Bacillus weihenstephanensis     Bacillus cereus/thuringiensis/anthracis       "soil"   Bacillus pumilus       Bacillus subtilis     Bacillus licheniformis         "benthic" Geobacillus kaustophilus     "aquatic"     Bacillus coahuilensis     Bacillus sp. m3-13       Bacillus sp. NRRLB-14911       "benthic" Oceanobacillus iheyensis   "halophiles"   Bacillus halodurans     Bacillus clausii

Phylogeny of the genus Bacillus according to [14]

Species

• B. acidiceler
• B. acidicola
• B. acidiproducens
• B. acidocaldarius
• B. acidoterrestris
• B. aeolius
• B. aerius
• B. aerophilus
• B. agaradhaerens
• B. agri
• B. aidingensis
• B. akibai
• B. alcalophilus
• B. algicola
• B. alginolyticus
• B. alkalidiazotrophicus
• B. alkalinitrilicus
• B. alkalisediminis
• B. alkalitelluris
• B. altitudinis
• B. alveayuensis
• B. alvei
• B. amyloliquefaciens
  • B. a. subsp. amyloliquefaciens
  • B. a. subsp. plantarum
• B. aminovorans[17]
• B. amylolyticus
• B. andreesenii
• B. aneurinilyticus
• B. anthracis
• B. aquimaris
• B. arenosi
• B. arseniciselenatis
• B. arsenicus
• B. aurantiacus
• B. arvi
• B. aryabhattai
• B. asahii
• B. atrophaeus
• B. axarquiensis
• B. azotofixans
• B. azotoformans
• B. badius
• B. barbaricus
• B. bataviensis
• B. beijingensis
• B. benzoevorans
• B. beringensis
• B. berkeleyi
• B. beveridgei
• B. bogoriensis
• B. boroniphilus
• B. borstelensis
• B. brevis Migula
• B. butanolivorans
• B. canaveralius
• B. carboniphilus
• B. cecembensis
• B. cellulosilyticus
• B. centrosporus
• B. cereus
• B. chagannorensis
• B. chitinolyticus
• B. chondroitinus
• B. choshinensis
• B. chungangensis
• B. cibi
• B. circulans
• B. clarkii
• B. clausii
• B. coagulans
• B. coahuilensis
• B. cohnii
• B. composti
• B. curdlanolyticus
• B. cycloheptanicus
• B. cytotoxicus
• B. daliensis
• B. decisifrondis
• B. decolorationis
• B. deserti
• B. dipsosauri
• B. drentensis
• B. edaphicus
• B. ehimensis
• B. eiseniae
• B. enclensis
• B. endophyticus
• B. endoradicis
• B. farraginis
• B. fastidiosus
• B. fengqiuensis
• B. firmus
• B. flexus
• B. foraminis
• B. fordii
• B. formosus
• B. fortis
• B. fumarioli
• B. funiculus
• B. fusiformis
• B. galactophilus
• B. galactosidilyticus
• B. galliciensis
• B. gelatini
• B. gibsonii
• B. ginsengi
• B. ginsengihumi
• B. ginsengisoli
• B. glucanolyticus
• B. gordonae
• B. gottheilii
• B. graminis
• B. halmapalus
• B. haloalkaliphilus
• B. halochares
• B. halodenitrificans
• B. halodurans
• B. halophilus
• B. halosaccharovorans
• B. hemicellulosilyticus
• B. hemicentroti
• B. herbersteinensis
• B. horikoshii
• B. horneckiae
• B. horti
• B. huizhouensis
• B. humi
• B. hwajinpoensis
• B. idriensis
• B. indicus
• B. infantis
• B. infernus
• B. insolitus
• B. invictae
• B. iranensis
• B. isabeliae
• B. isronensis
• B. jeotgali
• B. kaustophilus
• B. kobensis
• B. kochii
• B. kokeshiiformis
• B. koreensis
• B. korlensis
• B. kribbensis
• B. krulwichiae
• B. laevolacticus
• B. larvae
• B. laterosporus
• B. lautus
• B. lehensis
• B. lentimorbus
• B. lentus
• B. licheniformis
• B. ligniniphilus
• B. litoralis
• B. locisalis
• B. luciferensis
• B. luteolus
• B. luteus
• B. macauensis
• B. macerans
• B. macquariensis
• B. macyae
• B. malacitensis
• B. mannanilyticus
• B. marisflavi
• B. marismortui
• B. marmarensis
• B. massiliensis
• B. megaterium
• B. mesonae
• B. methanolicus
• B. methylotrophicus
• B. migulanus
• B. mojavensis
• B. mucilaginosus
• B. muralis
• B. murimartini
• B. mycoides
• B. naganoensis
• B. nanhaiensis
• B. nanhaiisediminis
• B. nealsonii
• B. neidei
• B. neizhouensis
• B. niabensis
• B. niacini
• B. novalis
• B. oceanisediminis
• B. odysseyi
• B. okhensis
• B. okuhidensis
• B. oleronius
• B. oryzaecorticis
• B. oshimensis
• B. pabuli
• B. pakistanensis
• B. pallidus
• B. pallidus
• B. panacisoli
• B. panaciterrae
• B. pantothenticus
• B. parabrevis
• B. paraflexus
• B. pasteurii
• B. patagoniensis
• B. peoriae
• B. persepolensis
• B. persicus
• B. pervagus
• B. plakortidis
• B. pocheonensis
• B. polygoni
• B. polymyxa
• B. popilliae
• B. pseudalcalophilus
• B. pseudofirmus
• B. pseudomycoides
• B. psychrodurans
• B. psychrophilus
• B. psychrosaccharolyticus
• B. psychrotolerans
• B. pulvifaciens
• B. pumilus
• B. purgationiresistens
• B. pycnus
• B. qingdaonensis
• B. qingshengii
• B. reuszeri
• B. rhizosphaerae
• B. rigui
• B. ruris
• B. safensis
• B. salarius
• B. salexigens
• B. saliphilus
• B. schlegelii
• B. sediminis
• B. selenatarsenatis
• B. selenitireducens
• B. seohaeanensis
• B. shacheensis
• B. shackletonii
• B. siamensis
• B. silvestris
• B. simplex
• B. siralis
• B. smithii
• B. soli
• B. solimangrovi
• B. solisalsi
• B. songklensis
• B. sonorensis
• B. sphaericus
• B. sporothermodurans
• B. stearothermophilus
• B. stratosphericus
• B. subterraneus
• B. subtilis
  • B. s. subsp. inaquosorum
  • B. s. subsp. spizizenii
  • B. s. subsp. subtilis
• B. taeanensis
• B. tequilensis
• B. thermantarcticus
• B. thermoaerophilus
• B. thermoamylovorans
• B. thermocatenulatus
• B. thermocloacae
• B. thermocopriae
• B. thermodenitrificans
• B. thermoglucosidasius
• B. thermolactis
• B. thermoleovorans
• B. thermophilus
• B. thermoruber
• B. thermosphaericus
• B. thiaminolyticus
• B. thioparans
• B. thuringiensis
• B. tianshenii
• B. trypoxylicola
• B. tusciae
• B. validus
• B. vallismortis
• B. vedderi
• B. velezensis
• B. vietnamensis
• B. vireti
• B. vulcani
• B. wakoensis
• B. xiamenensis
• B. xiaoxiensis
• B. zhanjiangensis

Ecological and clinical significance

Bacillus species are ubiquitous in nature, e.g. in soil. They can occur in extreme environments such as high pH (B. alcalophilus), high temperature (B. thermophilus), and high salt concentrations (B. halodurans). B. thuringiensis produces a toxin that can kill insects and thus has been used as insecticide.[18] B. siamensis has antimicrobial compounds that inhibit plant pathogens, such as the fungi Rhizoctonia solani and Botrytis cinerea, and they promote plant growth by volatile emissions.[19] Some species of Bacillus are naturally competent for DNA uptake by transformation.[20]

• Two Bacillus species are medically significant: B. anthracis, which causes anthrax; and B. cereus, which causes food poisoning, with symptoms similar to that caused by Staphylococcus.[21]
  • B. cereus produces toxins which cause 2 different set of symptoms
    • emetic toxin which can cause vomiting and nausea
    • diarrhea
• B. thuringiensis is an important insect pathogen, and is sometimes used to control insect pests.
• B. subtilis is an important model organism. It is also a notable food spoiler, causing ropiness in bread and related food.
  • B. subtilis can also produce and secrete antibiotics.
• Some environmental and commercial strains of B. coagulans may play a role in food spoilage of highly acidic, tomato-based products.

Industrial significance

Many Bacillus species are able to secrete large quantities of enzymes. Bacillus amyloliquefaciens is the source of a natural antibiotic protein barnase (a ribonuclease), alpha amylase used in starch hydrolysis, the protease subtilisin used with detergents, and the BamH1 restriction enzyme used in DNA research.

A portion of the Bacillus thuringiensis genome was incorporated into corn (and cotton) crops. The resulting GMOs are resistant to some insect pests. Bacillus species continue to be dominant bacterial workhorses in microbial fermentations. Bacillus subtilis (natto) is the key microbial participant in the ongoing production of the soya-based traditional natto fermentation, and some Bacillus species are on the Food and Drug Administration's GRAS (generally regarded as safe) list. The capacity of selected Bacillus strains to produce and secrete large quantities (20-25 g/L) of extracellular enzymes has placed them among the most important industrial enzyme producers. The ability of different species to ferment in the acid, neutral, and alkaline pH ranges, combined with the presence of thermophiles in the genus, has led to the development of a variety of new commercial enzyme products with the desired temperature, pH activity, and stability properties to address a variety of specific applications. Classical mutation and (or) selection techniques, together with advanced cloning and protein engineering strategies, have been exploited to develop these products. Efforts to produce and secrete high yields of foreign recombinant proteins in Bacillus hosts initially appeared to be hampered by the degradation of the products by the host proteases. Recent studies have revealed that the slow folding of heterologous proteins at the membrane-cell wall interface of Gram-positive bacteria renders them vulnerable to attack by wall-associated proteases. In addition, the presence of thiol-disulphide oxidoreductases in B. subtilis may be beneficial in the secretion of disulphide-bond-containing proteins. Such developments from our understanding of the complex protein translocation machinery of Gram-positive bacteria should allow the resolution of current secretion challenges and make Bacillus species preeminent hosts for heterologous protein production. Bacillus strains have also been developed and engineered as industrial producers of nucleotides, the vitamin riboflavin, the flavor agent ribose, and the supplement poly-gamma-glutamic acid. With the recent characterization of the genome of B. subtilis 168 and of some related strains, Bacillus species are poised to become the preferred hosts for the production of many new and improved products as we move through the genomic and proteomic era.[22]

Use as model organism

Colonies of the model species Bacillus subtilis on an agar plate.

Bacillus subtilis is one of the best understood prokaryotes, in terms of molecular and cellular biology. Its superb genetic amenability and relatively large size have provided the powerful tools required to investigate a bacterium from all possible aspects. Recent improvements in fluorescent microscopy techniques have provided novel insight into the dynamic structure of a single cell organism. Research on B. subtilis has been at the forefront of bacterial molecular biology and cytology, and the organism is a model for differentiation, gene/protein regulation, and cell cycle events in bacteria.[23]

See also

• Paenibacillus and Virgibacillus, genera of bacteria formerly included in Bacillus.[24][25]

References

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3. "Turn up the Heat: Bacterial Spores Can Take Temperatures in the Hundreds of Degrees".
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8. Favaro, Gabriella; Bogialli, Sara; Di Gangi, Iole Maria; Nigris, Sebastiano; Baldan, Enrico; Squartini, Andrea; Pastore, Paolo; Baldan, Barbara (2016). "Characterization of lipopeptides produced by Bacillus licheniformisusing liquid chromatography with accurate tandem mass spectrometry". Rapid Communications in Mass Spectrometry. 30 (20): 2237–2252. doi:10.1002/rcm.7705. PMID 27487987.
9. Bacillus entry in LPSN [Euzéby, J.P. (1997). "List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet". International Journal of Systematic and Evolutionary Microbiology. 47 (2): 590–2. doi:10.1099/00207713-47-2-590. PMID 9103655.]
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11. http://www.arb-silva.de/fileadmin/silva_databases/living_tree/LTP_release_104/LTPs104_SSU_tree.pdf
12. Yarza, P.; Richter, M.; Peplies, J. R.; Euzeby, J.; Amann, R.; Schleifer, K. H.; Ludwig, W.; Glöckner, F. O.; Rosselló-Móra, R. (2008). "The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains". Systematic and Applied Microbiology. 31 (4): 241–250. doi:10.1016/j.syapm.2008.07.001. hdl:10261/103580. PMID 18692976.
13. Yarza, P.; Ludwig, W.; Euzéby, J.; Amann, R.; Schleifer, K. H.; Glöckner, F. O.; Rosselló-Móra, R. (2010). "Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses". Systematic and Applied Microbiology. 33 (6): 291–299. doi:10.1016/j.syapm.2010.08.001. hdl:10261/54801. PMID 20817437.
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15. Ole Andreas Økstad and Anne-Brit Kolstø Chapter 2: "Genomics of Bacillus Species" in M. Wiedmann, W. Zhang (eds.), Genomics of Foodborne Bacterial Pathogens, 29 Food Microbiology and Food Safety. Springer Science+Business Media, LLC 2011 DOI 10.1007/978-1-4419-7686-4_2
16. Brenner (D.J.): Family I. Enterobacteriaceae Rahn 1937, Nom. fam. cons. Opin. 15, Jud. Com. 1958, 73; Ewing, Farmer, and Brenner 1980, 674; Judicial Commission 1981, 104. In: N.R. Krieg and J.G. Holt (eds), Bergey's Manual of Systematic Bacteriology, first edition, vol. 1, The Williams & Wilkins Co, Baltimore, 1984, pp. 408-420
17. Loshon, Charles A.; Beary, Katherine E.; Gouveia, Kristine; Grey, Elizabeth Z.; Santiago-Lara, Leticia M.; Setlow, Peter (March 1998). "Nucleotide sequence of the sspE genes coding for γ-type small, acid-soluble spore proteins from the round-spore-forming bacteria Bacillus aminovorans, Sporosarcina halophila and S. ureae". Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression. 1396 (2): 148–152. doi:10.1016/S0167-4781(97)00204-2. PMID 9540829.
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19. Jeong, Haeyoung; Jeong, Da-Eun; Kim, Sun Hong; Song, Geun Cheol; Park, Soo-Young; Ryu, Choong-Min; Park, Seung-Hwan; Choi, Soo-Keun (2012-08-01). "Draft Genome Sequence of the Plant Growth-Promoting Bacterium Bacillus siamensis KCTC 13613T". Journal of Bacteriology. 194 (15): 4148–4149. doi:10.1128/JB.00805-12. ISSN 0021-9193. PMC 3416560. PMID 22815459.
20. Keen, E; Bliskovsky, V; Adhya, S; Dantas, G (2017). "Draft genome sequence of the naturally competent Bacillus simplex strain WY10". Genome Announcements. 5 (46): e01295–17. doi:10.1128/genomeA.01295-17. PMC 5690344. PMID 29146837.
21. Ryan KJ; Ray CG, eds. (2004). Sherris Medical Microbiology (4th ed.). McGraw Hill. ISBN 978-0-8385-8529-0.
22. Schallmey, M.; Singh, A.; Ward, O. P. (2004). "Developments in the use of Bacillus species for industrial production". Canadian Journal of Microbiology. 50 (1): 1–17. doi:10.1139/w03-076. PMID 15052317.
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24. Ash, Carol; Priest, Fergus G.; Collins, M. David (1994). "Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test". Antonie van Leeuwenhoek. 64 (3–4): 253–260. doi:10.1007/BF00873085. PMID 8085788.
25. Heyndrickx, M.; Lebbe, L.; Kersters, K.; De Vos, P.; Forsyth, G.; Logan, N. A. (1 January 1998). "Virgibacillus: a new genus to accommodate Bacillus pantothenticus (Proom and Knight 1950). Emended description of Virgibacillus pantothenticus". International Journal of Systematic Bacteriology. 48 (1): 99–106. doi:10.1099/00207713-48-1-99.

External links

• Bacillus genomes and related information at PATRIC, a Bioinformatics Resource Center funded by NIAID