Difference between revisions of "Bacillus endoradicis"

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{{Biorealm Genus}}
 
{{Biorealm Genus}}
 
==Classification==
 
==Classification==
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==Description and significance==
 
==Description and significance==
The microbe ''Bacillus endoradicis'' is a strain of ''Bacillus'' bacteria that is gram positive. It was discovered in 2009, and can be found within soybeans, in soil and other vegetation. The microbe is considered a mesophile because it grows ideally at temperatures ranging from 14 and 45°C. The cells are generally motile, with transparent colonies with a slight white pigmentation to them each parent colony has irregular edges. The cells generally occur as a single bacillus, as diplobacilli,and in Streptobacilli form. When analyzed phylogenetically, the 16S rRNA gene showed that the strain of ''Bacillus endoradicis'' showed to be most closely related to a strain of ''Bacillus'' called ''Bacillus muralis'', ''Bacillus simplex'', and ''Bacillus subtilis''. Each of these have a similarity of approximately ~96.4%, which is enough to make ''Bacillus endoradicis'' a separate bacterial species; being lower than the threshold of 97%. The general phenotypic charecterization from the other two ''Bacillus'' strains showed similar charecteristics in a sense that they did not hydrolyse casein or starch, but growth within a MacConkey agar (a selective agar and differential culture medium that is for bacteria, and is designed to isolate Gram-negative and enteric bacilli on whether or not they could ferment lactose) was possible. Because of it similarities to Bacillus simplex, and ''Bacillus endoradicis'' pathogen suppressing ability observed within the soybeans of Shijiazhuang city, Hebei Province, China, the soil bacteria can be associated with the plants roots, and having a positive effect on the plants growth rate. This is generally done through a plant-growth promoting rhizobacteria (PGPR) such as ''Bacillus endoradicis'' or ''Bacillus simplex''. It is the microbes ability to produce dormant, heat and desication-tolerant spores that enable it survive in severe stress in fields. This microbe is found to not be toxic, or harmful to humans, but in turn could be found to prove beneficial by helping increase the protein source found in soybeans by increasing anti oxidation activity and trypsin inhibitors and other antigenic proteins reduced in fermented soybean meal cultures.
+
The microbe ''Bacillus endoradicis'' is a strain of ''Bacillus'' bacteria that is gram positive. It was discovered in 2009, and can be found within soybeans, in soil and other vegetation. The microbe is considered a mesophile because it grows ideally at temperatures ranging from 14 and 45°C. The cells are generally motile, with transparent colonies with a slight white pigmentation to them each parent colony has irregular edges. The cells generally occur as a single bacillus, as diplobacilli,and in Streptobacilli form. When analyzed phylogenetically, the 16S rRNA gene showed that the strain of ''Bacillus endoradicis'' showed to be most closely related to a strain of ''Bacillus'' called ''Bacillus muralis'', ''Bacillus simplex'', and ''Bacillus subtilis''. Each of these have a similarity of approximately ~96.4%, which is enough to make ''Bacillus endoradicis'' a separate bacterial species; being lower than the threshold of 97%. The general phenotypic charecterization from the other two ''Bacillus'' strains showed similar charecteristics in a sense that they did not hydrolyse casein or starch, but growth within a MacConkey agar (a selective agar and differential culture medium that is for bacteria, and is designed to isolate Gram-negative and enteric bacilli on whether or not they could ferment lactose) was possible. Because of it similarities to Bacillus simplex, and ''Bacillus endoradicis'' pathogen suppressing ability observed within the soybeans of Shijiazhuang city, Hebei Province, China, the soil bacteria can be associated with the plants roots, and having a positive effect on the plants growth rate. This is generally done through a plant-growth promoting rhizobacteria (PGPR) such as ''Bacillus endoradicis'' or ''Bacillus simplex''. It is the microbe's ability to produce dormant, heat and dessication-tolerant spores that enable it survive in severe stress in fields. This microbe is found to not be toxic, or harmful to humans, but in turn could be found to prove beneficial by helping increase the protein source found in soybeans by increasing anti-oxidation activity and trypsin inhibitors and other antigenic proteins reduced in fermented soybean meal cultures.
  
 
==Genome structure==
 
==Genome structure==
The genome of B.''endoradicis'' was sequenced in 2009 and was found to have a linear topology, with a single chromosome. The chromosome, because it was partially sequenced has only found to have a sequence length of 1,398 bp, while relating strains of B. ''simplex'' being fairly similar in the ranges of ~96.4%. This makes sense because they are both used as broad antibiotics and plant growth promoting bacteria (PGPB). It is because the sequence of ''Bacillus endoradicis'' is partially sequenced, but found to share the same characteristics of its similar bacillus family and relating to nearly 97% genomicaly, and anecdotal evidence shows that it doesn't vary far from microbes such as B.''subtilis'' and B.''simplex''.
+
The genome of B.''endoradicis'' was sequenced in 2009 and was found to have a linear topology, with a single chromosome. The chromosome, because it was partially sequenced has only found to have a sequence length of 1,398 bp, while relating strains of ''B. simplex'' being fairly similar in the ranges of ~96.4%. This makes sense because they are both used as broad antibiotics and plant growth promoting bacteria (PGPB). It is because the sequence of ''Bacillus endoradicis'' is partially sequenced, but found to share the same characteristics of its similar bacillus family and relating to nearly 97% genomicaly, and anecdotal evidence shows that it doesn't vary far from microbes such as ''B. subtilis'' and ''B. simplex''.
  
 
==Cell and colony structure==
 
==Cell and colony structure==
 
''Bacillus endoradicis'' is a gram-positive and rod-shaped bacillus. It can be bacillus, diplobacilli, or Streptobacilli shaped. The cells are generally 0.7-0.9 μm in diameter and 1.9-2.7 μm in length. Each of these cells are motile and flagellated and have the ability to form spores.  
 
''Bacillus endoradicis'' is a gram-positive and rod-shaped bacillus. It can be bacillus, diplobacilli, or Streptobacilli shaped. The cells are generally 0.7-0.9 μm in diameter and 1.9-2.7 μm in length. Each of these cells are motile and flagellated and have the ability to form spores.  
''Bacillus endoradicis''' optimum growth temperature is determined to be set at 15-45°C.General cell motility and aerotactic ability found by observing the growth and the spread of cells in a test tube containing semi-solid NA medium. This method was conducted so that the researchers can detect the endospore morphology and to determine which strain was grown in the PCA medium (containing 0.5 % peptone, 0.25 % yeast extract, 0.1 % glucose, 1.5 % agar) at 28°C for 36 hours, and was then stained as described by Bartholomew and Mittwer. Cells of this strain were rods ranging from 0.7–0.9 μm wide and 1.9– 2.7 μm long. The strain of B.''endoradicis'' is motile and aerobic. This was determined by observing the growth extending from an inoculating stab line in the semi-solid NA medium and then ended up gathering at the top of the test tubes assuming to absorb maximal amounts of oxygen which was present. Cells produced ellipsoidal spores located centrally or subterminally in swollen sporangia after being cultivated for more than 24 hours. Phenotypic and biochemical properties of B. ''muralis'', B. ''simplex''
+
''Bacillus endoradicis''' optimum growth temperature is determined to be set at 15-45°C.General cell motility and aerotactic ability found by observing the growth and the spread of cells in a test tube containing semi-solid NA medium. This method was conducted so that the researchers can detect the endospore morphology and to determine which strain was grown in the PCA medium (containing 0.5 % peptone, 0.25 % yeast extract, 0.1 % glucose, 1.5 % agar) at 28°C for 36 hours, and was then stained as described by Bartholomew and Mittwer. Cells of this strain were rods ranging from 0.7–0.9 μm wide and 1.9– 2.7 μm long. The strain of B.''endoradicis'' is motile and aerobic. This was determined by observing the growth extending from an inoculating stab line in the semi-solid NA medium and then ended up gathering at the top of the test tubes assuming to absorb maximal amounts of oxygen which was present. Cells produced ellipsoidal spores located centrally or subterminally in swollen sporangia after being cultivated for more than 24 hours. Phenotypic and biochemical properties of ''B. muralis'', ''B. simplex''
and B. ''asahii'' were determined. The temperature range for growth was tested at 4, 10, 15, 20, 28, 37, 45 and 55°C. The pH range for growth in the unique nutrient broth was tested in the pH range of 5.5 to 10.0 with increasing increments of 0.5. Through the anecdotal evidence done, it was seen that as the pH units increased the growth of the microbe decreased and almost became non-existent. Catalase activity was determined by assessing bubble production in 3% H2O2. Growth on MacConkey agar also known as (MAC) containing (20.0 g peptone, 10.0 g lactose, 5.0 g sodium chloride, 16.5 g agar, 0.03 g neutral red, 1.0 mg crystal violet, 1 l water) was also tested.
+
and ''B. asahii'' were determined. The temperature range for growth was tested at 4, 10, 15, 20, 28, 37, 45 and 55°C. The pH range for growth in the unique nutrient broth was tested in the pH range of 5.5 to 10.0 with increasing increments of 0.5. Through the anecdotal evidence done, it was seen that as the pH units increased the growth of the microbe decreased and almost became non-existent. Catalase activity was determined by assessing bubble production in 3% H2O2. Growth on MacConkey agar also known as (MAC) containing (20.0 g peptone, 10.0 g lactose, 5.0 g sodium chloride, 16.5 g agar, 0.03 g neutral red, 1.0 mg crystal violet, 1 l water) was also tested.
  
 
==Metabolism==
 
==Metabolism==
Energy source(s); external electron donor(s) (=reductant source(s)); carbon source(s); oxygen classification; important molecules it produces.
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This microbe, because it is closely related to ''Bacillus endoradicis'' it seems that it has a decreased capacity for the extensive carbohydrate metabolism. It is also believed that ''B. endoradicis'' possesses the genes for the cleavage of extracellular chitin and chitosan, which confirms its close relationship with the insect pathogen ''B. thuringiensis''. Bacilli are rod-shaped, Gram-positive, sporulating, aerobes or facultative anaerobes.
  
 +
==Ecology==
 +
The microbe ''B. endoradicis'' generally resides within the inner tissues of a healthy soybean roots. The microbe can be used to contribute to plant growth by suppressing pathogens from affecting the host plant the microbe resides in. It is also used as a broad antibiotic. This could be the contributing factor as why it is able to suppress certain pathogens. Because it is similar and generally found in the same locations of ''Bacillus sublitis''. It is because ''B. endoradicis'' is relatively new, and has not had many further studies conducted, the assumption of it being located in many diverse environments including the gastrointestinal tracts of animals is assumed. It can also be found and isolated in myriad environments which are terrestrial and aquatic. This makes this microbe seem like it is ubiquitous and broadly adapted to grow in many diverse environments. It is also possible that it has the capacity to create surface-associated multicellular aggregates.
  
==Ecology==
+
==Pathology==
Habitat; symbiosis; contributions to the environment.
+
This microbe does not cause a disease in humans, animals or plant hosts. No known virulence factors that
metagenomic data link
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the microbe ''Bacillus endoradicis.''
  
 +
==References==
 +
Yun Zeng Zhang, Wen Feng Chen, Mao Li, Xin Hua Sui, Hong-Can Liu, Xiao Xia Zhang and Wen Xin Chen. ''Bacillus endoradicis'' sp. nov., an edophytic bacterium isolated from soybean root. International Journal of Systematic and Evolutionary Microbiology (2012), 62, 359-363; published in 2012. [doi:10.1099/ijs.0.028936-0.] http://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.028936-0?crawler=true&mimetype=application/pdf
  
==Pathology==
+
Cruz, J., Liu, Y., Liang, Y., Zhou, Y., & Stothard, P. (2009, August 12). Bacillus subtilis subsp. subtilis str. 168. Retrieved December 6, 2015, from http://bacmap.wishartlab.com/organisms/24
Does this organism cause disease?  Human, animal, plant hosts?  Virulence factors.
 
  
 +
Et al, Z. (2012). ''Bacillus endoradicis'' Zhang et al., 2012. Retrieved December 9, 2015, from http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=959811.
  
==References==
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Bacillus endoradicis strain CCBAU 05776 16S ribosomal RNA gene, partial sequence. (2012). Retrieved December 9, 2015, from http://www.ebi.ac.uk/ena/data/view/GU43467
[Sample reference] [http://ijs.sgmjournals.org/content/62/2/330; Sylvie Cousin, Marie-Laure Gulat-Okalla, Laurence Motreff, Catherine Gouyette, Christiane Bouchier, Dominique Clermont, and Chantal Bizet. Lactobacillus gigeriorum sp. nov., isolated from chicken crop. Int J Syst Evol Microbiol February 2012 62:330-334; published ahead of print March 18, 2011.}
 
[doi:10.1099/ijs.0.028217-0.]
 
  
 +
Isao Yumoto, Kikue Hirota, Shingo Yamaga, Yoshinobu Nodasaka, Tsuneshirou Kawasaki, Hidetoshi MAtsuyama and Kenji Nakajima. ''Bacillus asahii'' sp. nov., a novel bacterium isolated from soil with the ability to deodorize the bad smell generated from short-chain fatty acids. International Journal of Systematic and Evolutionary Microbiology (2004), 54, 1997-2001; published in 2004. [doi:10.1099/ijs.0.03014-0.] http://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.03014-0?crawler=true&mimetype=application/pdf,
  
Edited by PUT YOUR NAME HERE of Dr. Lisa R. Moore, University of Southern Maine, Department of Biological Sciences, http://www.usm.maine.edu/bio
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Zhang, Y.Z (2012). ''Bacillus endoradicis''. Retrieved December 14, 2015, from http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=718002
  
<!--Do not edit or remove this line!-->{{MooreL}}
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Edited by Kevin Li of Dr. Lisa R. Moore, University of Southern Maine, Department of Biological Sciences, http://www.usm.maine.edu/bio

Latest revision as of 15:10, 22 February 2016

This student page has not been curated.

A Microbial Biorealm page on the genus Bacillus endoradicis

Classification

Higher order taxa

Domain:Bacteria; Phylum: Firmicutes; Class:Bacilli; Order: Bacillasles; Family: Bacillaceae; Genus:Bacillus; Species: Bacillus endoradicis [Others may be used. Use NCBI link to find]

Species

Bacillus endoradicis

NCBI: Taxonomy

Description and significance

The microbe Bacillus endoradicis is a strain of Bacillus bacteria that is gram positive. It was discovered in 2009, and can be found within soybeans, in soil and other vegetation. The microbe is considered a mesophile because it grows ideally at temperatures ranging from 14 and 45°C. The cells are generally motile, with transparent colonies with a slight white pigmentation to them each parent colony has irregular edges. The cells generally occur as a single bacillus, as diplobacilli,and in Streptobacilli form. When analyzed phylogenetically, the 16S rRNA gene showed that the strain of Bacillus endoradicis showed to be most closely related to a strain of Bacillus called Bacillus muralis, Bacillus simplex, and Bacillus subtilis. Each of these have a similarity of approximately ~96.4%, which is enough to make Bacillus endoradicis a separate bacterial species; being lower than the threshold of 97%. The general phenotypic charecterization from the other two Bacillus strains showed similar charecteristics in a sense that they did not hydrolyse casein or starch, but growth within a MacConkey agar (a selective agar and differential culture medium that is for bacteria, and is designed to isolate Gram-negative and enteric bacilli on whether or not they could ferment lactose) was possible. Because of it similarities to Bacillus simplex, and Bacillus endoradicis pathogen suppressing ability observed within the soybeans of Shijiazhuang city, Hebei Province, China, the soil bacteria can be associated with the plants roots, and having a positive effect on the plants growth rate. This is generally done through a plant-growth promoting rhizobacteria (PGPR) such as Bacillus endoradicis or Bacillus simplex. It is the microbe's ability to produce dormant, heat and dessication-tolerant spores that enable it survive in severe stress in fields. This microbe is found to not be toxic, or harmful to humans, but in turn could be found to prove beneficial by helping increase the protein source found in soybeans by increasing anti-oxidation activity and trypsin inhibitors and other antigenic proteins reduced in fermented soybean meal cultures.

Genome structure

The genome of B.endoradicis was sequenced in 2009 and was found to have a linear topology, with a single chromosome. The chromosome, because it was partially sequenced has only found to have a sequence length of 1,398 bp, while relating strains of B. simplex being fairly similar in the ranges of ~96.4%. This makes sense because they are both used as broad antibiotics and plant growth promoting bacteria (PGPB). It is because the sequence of Bacillus endoradicis is partially sequenced, but found to share the same characteristics of its similar bacillus family and relating to nearly 97% genomicaly, and anecdotal evidence shows that it doesn't vary far from microbes such as B. subtilis and B. simplex.

Cell and colony structure

Bacillus endoradicis is a gram-positive and rod-shaped bacillus. It can be bacillus, diplobacilli, or Streptobacilli shaped. The cells are generally 0.7-0.9 μm in diameter and 1.9-2.7 μm in length. Each of these cells are motile and flagellated and have the ability to form spores. Bacillus endoradicis' optimum growth temperature is determined to be set at 15-45°C.General cell motility and aerotactic ability found by observing the growth and the spread of cells in a test tube containing semi-solid NA medium. This method was conducted so that the researchers can detect the endospore morphology and to determine which strain was grown in the PCA medium (containing 0.5 % peptone, 0.25 % yeast extract, 0.1 % glucose, 1.5 % agar) at 28°C for 36 hours, and was then stained as described by Bartholomew and Mittwer. Cells of this strain were rods ranging from 0.7–0.9 μm wide and 1.9– 2.7 μm long. The strain of B.endoradicis is motile and aerobic. This was determined by observing the growth extending from an inoculating stab line in the semi-solid NA medium and then ended up gathering at the top of the test tubes assuming to absorb maximal amounts of oxygen which was present. Cells produced ellipsoidal spores located centrally or subterminally in swollen sporangia after being cultivated for more than 24 hours. Phenotypic and biochemical properties of B. muralis, B. simplex and B. asahii were determined. The temperature range for growth was tested at 4, 10, 15, 20, 28, 37, 45 and 55°C. The pH range for growth in the unique nutrient broth was tested in the pH range of 5.5 to 10.0 with increasing increments of 0.5. Through the anecdotal evidence done, it was seen that as the pH units increased the growth of the microbe decreased and almost became non-existent. Catalase activity was determined by assessing bubble production in 3% H2O2. Growth on MacConkey agar also known as (MAC) containing (20.0 g peptone, 10.0 g lactose, 5.0 g sodium chloride, 16.5 g agar, 0.03 g neutral red, 1.0 mg crystal violet, 1 l water) was also tested.

Metabolism

This microbe, because it is closely related to Bacillus endoradicis it seems that it has a decreased capacity for the extensive carbohydrate metabolism. It is also believed that B. endoradicis possesses the genes for the cleavage of extracellular chitin and chitosan, which confirms its close relationship with the insect pathogen B. thuringiensis. Bacilli are rod-shaped, Gram-positive, sporulating, aerobes or facultative anaerobes.

Ecology

The microbe B. endoradicis generally resides within the inner tissues of a healthy soybean roots. The microbe can be used to contribute to plant growth by suppressing pathogens from affecting the host plant the microbe resides in. It is also used as a broad antibiotic. This could be the contributing factor as why it is able to suppress certain pathogens. Because it is similar and generally found in the same locations of Bacillus sublitis. It is because B. endoradicis is relatively new, and has not had many further studies conducted, the assumption of it being located in many diverse environments including the gastrointestinal tracts of animals is assumed. It can also be found and isolated in myriad environments which are terrestrial and aquatic. This makes this microbe seem like it is ubiquitous and broadly adapted to grow in many diverse environments. It is also possible that it has the capacity to create surface-associated multicellular aggregates.

Pathology

This microbe does not cause a disease in humans, animals or plant hosts. No known virulence factors that the microbe Bacillus endoradicis.

References

Yun Zeng Zhang, Wen Feng Chen, Mao Li, Xin Hua Sui, Hong-Can Liu, Xiao Xia Zhang and Wen Xin Chen. Bacillus endoradicis sp. nov., an edophytic bacterium isolated from soybean root. International Journal of Systematic and Evolutionary Microbiology (2012), 62, 359-363; published in 2012. [doi:10.1099/ijs.0.028936-0.] http://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.028936-0?crawler=true&mimetype=application/pdf

Cruz, J., Liu, Y., Liang, Y., Zhou, Y., & Stothard, P. (2009, August 12). Bacillus subtilis subsp. subtilis str. 168. Retrieved December 6, 2015, from http://bacmap.wishartlab.com/organisms/24

Et al, Z. (2012). Bacillus endoradicis Zhang et al., 2012. Retrieved December 9, 2015, from http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=959811.

Bacillus endoradicis strain CCBAU 05776 16S ribosomal RNA gene, partial sequence. (2012). Retrieved December 9, 2015, from http://www.ebi.ac.uk/ena/data/view/GU43467

Isao Yumoto, Kikue Hirota, Shingo Yamaga, Yoshinobu Nodasaka, Tsuneshirou Kawasaki, Hidetoshi MAtsuyama and Kenji Nakajima. Bacillus asahii sp. nov., a novel bacterium isolated from soil with the ability to deodorize the bad smell generated from short-chain fatty acids. International Journal of Systematic and Evolutionary Microbiology (2004), 54, 1997-2001; published in 2004. [doi:10.1099/ijs.0.03014-0.] http://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.03014-0?crawler=true&mimetype=application/pdf,

Zhang, Y.Z (2012). Bacillus endoradicis. Retrieved December 14, 2015, from http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=718002

Edited by Kevin Li of Dr. Lisa R. Moore, University of Southern Maine, Department of Biological Sciences, http://www.usm.maine.edu/bio