Bacillus safensis

Bacillus safensis
Scientific classification
Kingdom: Bacteria
Division: Firmicutes
Class: Bacilli
Order: Bacillales
Family: Bacillaceae
Genus: Bacillus
Species: B. safensis
Binomial name
Bacillus safensis
Satomi et al. 2006 [1]

Bacillus safensis is a Gram-positive, spore-forming, and rod bacterium, originally isolated from a spacecraft in Florida and California.[2] Bacillus safensis could have possibly been transported to the planet Mars on spacecraft Opportunity and Spirit in 2004.[2] There are several known strains of this bacterium, all of which belong to the Firmicutes phylum of Bacteria.[2] This bacterium also belongs to the large, pervasive genus Bacillus. Bacillus safensis is an aerobic chemoheterotroph and is highly resistant to salt,[3] UV radiation, and gamma radiation.[4] Because of these features, Bacillus safensis is a powerful plant hormone producer. The bacteria is also a plant growth-promoting rhizobacteria, which enhances plant growth after root colonization.[3] Strain B. safensis JPL-MERTA-8-2 is (so far) the only bacterial strain shown to grow noticeably faster in micro-gravity environments than on the Earth surface.[5]

Discovery & importance

Thirteen strains of the novel bacterium, Bacillus safensis, were first isolated from spacecraft surfaces and assembly-facility surfaces at the Kennedy Space Center in Florida as well as the NASA Jet Propulsion Laboratory in California. The bacteria get its name from the Spacecraft Assembly Facility (SAF).[2] Researchers used customary swabbing techniques to detect and collect the bacteria from cleanrooms where the spacecraft were put together in the Jet Propulsion Laboratory.[2] The bacterium was accidentally brought to Mars during space travel missions due to contamination of clean rooms. Contamination of clean rooms during space travel is an area of concern as it can threaten microbial experimentation and give false positives of other microbial life forms on other planets.[6]

V.V. Kothari and his colleagues from Saurashtra University in Gujarat, India first isolated another strain, Bacillus safensis VK.[3] Strain VK was collected from Cuminum cyminum, a cumin plant in the desert area of Gujarat, India.[3] Specifically, the bacteria were collected from the rhizosphere of the cumin plant.[3]

Ram S. Singh and colleagues discovered one of the strains, AS-08 in soil samples of root tubers of asparagus plants in a botanical garden at Punjabi University in India.[7] Bacillus safensis AS-08 was found to have inulase activity, which is used for the production of fructooligosaccharides and high-fructose corn syrup.[7] Fructooligosaccharides are used as artificial sweeteners and can be found in many commercial food products. Corn syrup is also found in many processed foods.[7]

Davender Kumar and colleagues from Kurukshetra University in India isolated strain DVL-43 from soil samples.[4] This strain was found to possess lipase, which is an important enzyme for fat digestion. Lipases are a class of chemicals that are abundant in nature amongst plants, animals and microorganisms that are widely used in industry for production of food, paper products, detergents and biodiesel fuel.[4]

P Ravikumar Government Arts College (A) (Bharathiar University) in India isolated strain PR 2 from explosive laden soil samples.[8] This strain was identified by its 16S rDNA sequence by sanger dideoxy sequenceing method and deposited in the GenBank Maryland USA with accession number KP 261381 with 885bp linear DNA with base count 175 a 295 c 199 g 216 t[8]

Physical characteristics & metabolism

Bacillus safensis is a Gram-positive, spore-forming rod bacterium. Bacillus safensis is also an aerobic, chemoheterotroph. Cell size ranges from 0.5-0.7 μm in diameter and 1.0-1.2 μm in length.[2] Bacteria are motile, and use polar flagella for locomotion. Cells are considered mesophillic, as they can grow in temperatures ranging between 10-50 °C.[2] Bacillus safensis FO-036b has an optimal temperature range from 30-37 °C, and cannot grow at 4 or 55 °C.[2] Bacillus safensis FO-036b prefers 0-10% salt, and a pH of 5.6. This strain was also found to produce spores that are resistant to hydrogen peroxide and UV radiation.[9]

Strain VK of Bacillus safensis is a salt-tolerant microbe, and can grow beyond the 0-10% salt range for the general microbial species.[3] This strain can grow in 14% NaCl, with a pH ranging from 4 to 8.[3] Strain VK also contains genes that encode for 1-aminocyclopropane-1-carboxylate deaminase enzyme.[3] This enzyme is able to generate 2-oxobutanoate and ammonia (NH3) by cleaving the precursor of plant hormone, ethylene 1-aminocyclopropane-1-carboxylate.[3] This enables the plant to tolerate salt, heavy metals, and polyaromatic hydrocarbons.[3] Because of these features, Bacillus safensis VK is a powerful plant hormone producer.

Genomics

The genome of Bacillus safensis strain FO-036b shows a GC content of 41.0-41.4 mol%.[2]

The Bacillus safensis VK genomic DNA was obtained from a 24-hr-old nutrient broth culture. Isolation of this strain was performed using a GenElute commercial DNA isolation kit, and whole-genome shotgun sequencing was carried out. Thirty-nine contigs, overlapping DNA fragments, greater in size than 200 base pairs were observed in strain VK.[3] This strain displays a G+C content of 46.1% in a circular chromosome of 3.68 Mb. 3,928 protein-coding sequences were identified, and 1,822 protein-coding sequences were appointed to one of the 457 RAST subsystems.[3] RAST, Rapid Annotation using Subsystem Technology, is a server that generates bacterial and archaeal genome annotations.[10] The genome also displays 73 tRNA genes.[3]Bacillus safensis VK genome sequence can be found in GenBank under the accession number AUPF00000000.[3] Another strain, DVL-43, can also be found in GenBank under the accession number KC156603.[4] Another strain, PR-2 can also be found in GenBank under the accession number KP261381.[8]

Strains

Listed below are currently identified Bacillus safensis strains, including where they were discovered, and the year discovered (if available).[11]

Differentiation between related species

Several isolates of the genus Bacillus are nearly identical to Bacillus pumilus. The group of isolates related to B. pumilus contains five related species: B. pumilus, B. safensis, B. stratosphericus, B. altitudinis, and B. aerophilus. These species are difficult to distinguish due to their 99.5% similarity in their 16S rRNA gene sequence. Recently, scientists have discovered an alternate way to differentiate between these closely related species, especially B. pumilus and B. safensis.[12]

DNA gyrase is an important enzyme that introduces a negative supercoil to the DNA and is responsible for the biological processes in DNA replication and transcription.[12] DNA gyrase is made of two subunits, A and B. These subunits are denoted as gyrA and gyrB. The gyrB gene, subunit B protein, is a type II topoisomerase that is essential for DNA replication.[12] This gene is conserved among bacterial species. The rate of evolution at the molecular level deduced from gyrB related gene sequences can be determined at more accelerated rate compared to the 16S rRNA gene sequences.[12] These subunits have provided a way to phylogenetically distinguish between the diversity of species related to B. pumilus, which includes B. safensis. Strain B. safensis DSM19292 shares 90.2% gyrA sequence similarity with B. pumilus strain DSM 27.[12]

In 1952, a strain of B. pumilus was discovered in the DSMZ culture and labeled as strain DSM 354.[12] The strain was identified before B. safensis was discovered. In 2012, a gyrA sequence similarity was tested between the B. pumilus strain DSM 354 B. pumilus strain DSM 27, as well as against B. safensis strain DSM 19292.[12] Strain DSM 354 showed a 90.4% and 98% sequence similarity with B. pumilus strain DSM 27 and B. safensis strain DSM 19292, respectively.[12] These results indicated that DSM 354 may in fact be a B. safensis strain, instead of a B. pumilus strain. These results supported that gyrA sequences could be used to differentiate between closely related bacteria.[12]

References

  1. ↑ Page Bacillus on bacterio.net
  2. 1 2 3 4 5 6 7 8 9 Satomi, Masataka; La Duc, Myron T.; Venkateswaran, Kasthuri (2006). "Bacillus safensis sp. nov., isolated from spacecraft and assembly-facility surfaces" (PDF). International Journal of Systematic and Evolutionary Microbiology. 56 (8): 1735–1740. doi:10.1099/ijs.0.64189-0. ISSN 1466-5026.
  3. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Kothari, V.V.; R. K. Kothari; C. R. Kothari; V. D. Bhatt; N. M. Nathani; P. G. Koringa; C. G. Joshi; B. R. M. Vyas (September 2013). "Genome Sequence of Salt-Tolerant Bacillus safensis Strain VK, Isolated from Saline Desert Area of Gujarat, India" (PDF). Genome Announcements. 1 (5). doi:10.1128/genomeA.00671-13.
  4. 1 2 3 4 5 Kumar, Davender; Rajinder Parshadb; Vijay Kumar Gupta (February 2014). "Application of a statistically enhanced, novel, organic solvent stable lipase from Bacillus safensis DVL-43" (PDF). International Journal of Biological Macromolecules. 66: 97–107. doi:10.1016/j.ijbiomac.2014.02.015.
  5. ↑ Coil, David; Neches, Russell; et al. (2016). "Growth of 48 built environment bacterial isolates on board the International Space Station (ISS)". PeerJ. 4: e1842. doi:10.7717/peerj.1842.
  6. ↑ Probst, Alexander; Rainer Facius; Reinhard Wirth; Marco Wolf; Christine Moissl-Eichinger (March 2011). "Recovery of Bacillus Spore Contaminants from Rough Surfaces: a Challenge to Space Mission Cleanliness Control" (PDF). Applied And Environmental Microbiology. 77 (5). doi:10.1128/AEM.02037-10.
  7. 1 2 3 4 Singh, Ram S.; Rupinder P. Singh; Mukesh Yadav (2013). "Molecular and biochemical characterization of a new endoinulinase producing bacterial strain of Bacillus safensis AS-08*" (PDF). Biologia. 68 (6): 1028–1033. doi:10.2478/s11756-013-0259-2.
  8. 1 2 3 ⟨cite journal⟩>
  9. ↑ Tirumalai, Madhan R.; Rajat Rastogi; Nader Zamani; Elisha O'Bryant Williams; Shamail Allen; Fatma Diouf; Sharon Kwende; George M. Weinstock; Kasthuri J. Venkateswaran; George E. Fox (June 2013). "Candidate Genes That May Be Responsible for the Unusual Resistances Exhibited by Bacillus pumilus SAFR-032 Spores" (PDF). PLOS ONE. 8 (6). doi:10.1371/journal.pone.0066012.
  10. ↑ Aziz, Ramy K; Daniela Bartels; Aaron A Best; Matthew DeJongh; Terrence Disz; Robert A Edwards; Kevin Formsma; Svetlana Gerdes; Elizabeth M Glass; Michael Kubal; Folker Meyer; Gary J Olsen; Robert Olson; Andrei L Osterman; Ross A Overbeek; Leslie K McNeil; Daniel Paarmann; Tobias Paczian; Bruce Parrello; Gordon D Pusch; Claudia Reich; Rick Stevens; Olga Vassieva; Veronika Vonstein; Andreas Wilke; Olga Zagnitko (February 2008). "The RAST Server: Rapid Annotations using Subsystems Technology" (PDF). BioMed Central Genomics. 75 (9). doi:10.1186/1471-2164-9-75. PMC 2265698Freely accessible. PMID 18261238.
  11. ↑ Liu, Yang; Qiliang Lai; Chunming Dong; Liping Wang; Guangyu Li; Zonge Shao (November 2013). "Phylogenetic Diversity of the Bacillus pumilis Group and the Marine Ecotype Revealed by Multilocus Sequence Analysis". PLOS ONE. 8 (11). doi:10.137/journal.poone.0080097.
  12. 1 2 3 4 5 6 7 8 9 Wang, Li-Ting; Fwu-Ling Lee; Chun-Ju Tai; Hiroaki Kasai (2007). "Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA–DNA hybridization in the Bacillus subtilis group" (PDF). International Journal of Systematic and Evolutionary Microbiology. 57 (8). doi:10.1099/ijs.0.64685-0.

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