Paenibacillus dendritiformis

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1. Classification

a. Higher order taxa

Scientific name: Paenibacillus dendritiformis

Domain: Bacteria

Phylum: Firmicutes

Class: Bacilli

Order: Bacillales

Family: Paenibacillaceae

Genus: Paenibacillus

Species: P.dendritiformis

2. Description and significance

Paenibacillus dendritiformis is a motile, Gram-positive rod that is found in many different environments including the plant rhizosphere, insect larva, and a variety of soils [1] [2]. Originally, this bacteria was a part of the genus Bacillus, but was reclassified in 1993 [3]. This bacteria is biologically significant due to its potential as a bioremediator for environments that have been affected by polycyclic aromatic hydrocarbons (PAH) and motor sludge [4]. It also has the ability to respond to its environment, using tactics such as swarming and killing off its own cells in order to survive. It is, however, unclear why these bacteria swarm the way they do [5].

This bacteria is able to avoid overcrowding by manipulating its phenotype from motile rods to non-motile cocci, and by producing a toxin, sibling lethal factor (Slf), to kill other cells. This genetically encoded process is crucial in the scientific field as this model can be further studied for its ability to naturally reduce overcrowding [6]. In addition, this bacteria is beneficial with respect to agriculture as it has been shown to reduce disease in plants such as potatoes [7].

3. Genome structure

The genome of Paenibacillus dendritiformis was sequenced in April of 2012. In total, its genome is 6,375,964 base pairs long, with a 54% GC (guanine-cytosine) content. P. dendritiformis contains a genome that encodes for molecules that help in resource competition, antibiotics, lytic enzymes, and signaling molecules. It also encodes toxins such as sibling lethal factor (slf) and signals such as rod inducing signals (Ris) that contribute to antibiotic resistance and competition [2].

4. Cell structure

Paenibacillus dendritiformis, a Gram- positive bacteria, is unique due to its ability to change shape between rod and cocci depending on environmental cues [5] [8]. It is also able to form different colonial patterns in order to adapt to different environments. P. dendritiformis can switch back and forth between two different colonial morphologies: the branching and the chiral morphotypes [1] [2]. P. dendritiformis tends to form the branching morphotype, defined by tip splitting, while growing on harder substrates. On softer substrates, it prefers to form a chiral pattern, which is defined by curling branches [9].

5 . Motility

P. dendritiformis uses swarming as its source of movement. How the bacteria swarms depends on its morphology. The branched morphology, referred to as the T morphology, tends to swarm in whirls and jets. The chiral morphology, referred to as the C morphology, swarms in a “densely packed straight but thin long lines” [5]. P. dendritiformis has an internal clock within its cell, and is known to switch directions every 20 seconds on hard surfaces. The motile ability of this bacteria shows advantageous survival skills that they have developed over time. In addition, this bacteria is able to swim in environments by producing lubrication fluids [10].

6 . Metabolic processes

P. dendritiformis is an endospore-forming facultative anaerobe [2]. It is an organotroph that is able to hydrolyse starch and casein, and optimally grows between 30-37 degrees Celsius [11] [12]. It is also catalase and oxidase positive, and unable to reduce nitrate to nitrite. P. dendritiformis is, however, able to decompose urea and egg yolk [11].

7. Ecology

P. dendritiformis can live in various environments. One study discovered in this bacteria in forest soil samples taken in Brazil [13]. Another study discovered this bacteria in marine soil, specifically in the soil located near the Red Sea in Saudi Arabia [14]. In addition, P. dendritiformis can thrive in the rhizosphere and insect larvae [2].

8. Pathology

P. dendritiformis can effectively reduce disease caused by soft rot pectobacteria from the genus Dickeya and Pectobacterium, which causes reduced crop yield and quality. (7) These diseases are mainly spread by contaminated tuber seeds. More analysis on P. dendritiformis’ genome indicates that it encodes for multiple genes that all compete for different resources such as amino acids, sugar transporters and iron. Hence, it has the ability to colonize plant roots and compete against its competitors..This makes it an efficient biocontrol agent against diseases such as potato blackleg and soft rot, caused by Dickeya and Pectobacterium. [7] P. dendritiformis is an effective biocontrol agent that has been shown to significantly reduce the maceration area of tuber slices as well as increase crop yield. [7] No evidence has been found that the bacteria strain causes any harm towards humans.

9. Current Research

One study focuses on the biosurfactant produced by Paenibacillus dendritiformis. This biosurfactant has the effect of degrading Polycyclic Aromatic Hydrocarbons (PAH). PAH are concerning due to their carcinogenicity, mutagenicity, and teratogenicity. Normally, PAH are easy to degrade as long as they have 2-3 benzene rings. However, PAH with 4 benzene rings have low biodegradability, meaning they are harder to degrade. Pyrene, a molecule with 4 rings, was used as the model for this study. It is an important PAH as it is a byproduct of incomplete combustion of organic compounds, and can be detected in the environment. In the experiment, P. dendritiformis was grown on oil and anthracene, where it produced a lipopeptide biosurfactant that enhanced pyrene degradation. Researchers found that at optimal lipopeptide dosage, the pyrene removal rate was 4 times greater than at sub-optimal dosages.This research is important as it shows that the biosurfactant produced by P. dendritiformis can be used in hydrocarbon contaminated environments to clean up 4 ringed polycyclic aromatic hydrocarbons [4] [15].

In another study, researchers analyzed the secretions of Paenibacillus dendritiformis to identify the lethal factors that mutually inhibits the growth of sibling colonies. Researchers grew two sibling colonies of P. dendritiformis on the same agar plate, then analyzed proteins from the plate. They discovered the lethal factor, named “sibling lethal factor”, Slf for short. They also discovered subtilisin, a protease. At a certain concentration, researchers found that subtilisin could regulate colony growth. They also discovered that once subtilisin exceeded a certain threshold, the “sibling lethal factor” was secreted and targeted colonies for destruction. The bacteria’s response to overcrowding may be a common mechanism for population control in nature. This research is important as it shows that P. dendritiformis can conduct self-regulated colony growth. If this self-regulation is occurring in P. dendritiformis, it could be occurring in other microorganism as well. This study can also serve as background research for further studies concerning self-regulated colony growth [6] [16].

Another study, previously discussed in an earlier section, focused on how P. dendritiformis competes against soft rot pectobacteria. Soft rot pectobacteria are pathogens that infects a variety of plants including potatoes. Soft rot pectobacteria are problematic as they contribute to severe crop and major economic loss. The study determined that P. dendritiformis increases crop yield and reduces disease. In addition, this study shows that P. dendritiformis could make an effective biocontrol agent that can lead to an increase in crop yield [7].

10. References

[1] Tcherpakov, M., Ben-Jacob, E., & Gutnick, D. L. (1999). Paenibacillus dendritiformis sp. nov., proposal for a new pattern-forming species and its localization within a phylogenetic cluster. International Journal of Systematic Bacteriology,49(1), 239-246. doi:10.1099/00207713-49-1-239

[2] Sirota-Madi, A., Olender, T., Helman, Y., Brainis, I., Finkelshtein, A., Roth, D., . . . Ben-Jacob, E. (2012). Genome Sequence of the Pattern-Forming Social Bacterium Paenibacillus dendritiformis C454 Chiral Morphotype. Journal of Bacteriology,194(8), 2127-2128. doi:10.1128/jb.00158-12

[3] Grady, E. N., Macdonald, J., Liu, L., Richman, A., & Yuan, Z. (2016). Current knowledge and perspectives of Paenibacillus: A review. Microbial Cell Factories,15(1). doi:10.1186/s12934-016-0603-7

[4] Bezza, F. A., & Chirwa, E. M. (2015). Biosurfactant from Paenibacillus dendritiformis and its application in assisting polycyclic aromatic hydrocarbon (PAH) and motor oil sludge removal from contaminated soil and sand media. Process Safety and Environmental Protection,98, 354-364. doi:10.1016/j.psep.2015.09.004

[5] Be’er, A., Strain, S. K., Hernandez, R. A., Ben-Jacob, E., & Florin, E. L. (2013). Periodic Reversals in Paenibacillus dendritiformis Swarming. Journal of Bacteriology,195(12), 2709-2717. doi:10.1128/jb.00080-13

[6] Beer, A., et al. “Surviving Bacterial Sibling Rivalry: Inducible and Reversible Phenotypic Switching in Paenibacillus Dendritiformis.” MBio, vol. 2, no. 3, 2011, doi:10.1128/mbio.00069-11.

[7] Lapidot, D. , Dror, R. , Vered, E. , Mishli, O. , Levy, D. and Helman, Y. (2015), Disease protection and growth promotion of potatoes (Solanum tuberosum L.) by Paenibacillus dendritiformis. Plant Pathol, 64: 545-551. doi:10.1111/ppa.12285

[8] Beer, A., Smith, R. S., Zhang, H. P., Florin, E., Payne, S. M., & Swinney, H. L. (2009). Paenibacillus dendritiformis Bacterial Colony Growth Depends on Surfactant but Not on Bacterial Motion. Journal of Bacteriology,191(18), 5758-5764. doi:10.1128/jb.00660-09

[9] Ben-Jacob, E., & Levine, H. (2006). Self-engineering capabilities of bacteria. Journal of The Royal Society Interface,3(6), 197-214. doi:10.1098/rsif.2005.0089

[10] Buczek, Monika. “A Bacterial Body Clock: Cryptic Periodic Reversals In Paenibacillus Dendritiformis.” Small Things Considered, 21 Oct. 2013,

[11] Tcherpakov, M., Ben-Jacob, E., & Gutnick, D. L. (1999). Paenibacillus dendritiformis sp. nov., proposal for a new pattern-forming species and its localization within a phylogenetic cluster. International Journal of Systematic Bacteriology,49(1), 239-246. doi:10.1099/00207713-49-1-239

[12] Podstawka, A. (n.d.). Paenibacillus dendritiformis BGSC 30A1, T168 | Type strain | DSM 18844, CIP 105967 | BacDiveID:11606. Retrieved November 21, 2018, from

[13] Mota, F. F., Gomes, E. A., Paiva, E., & Seldin, L. (2005). Assessment of the diversity of Paenibacillus species in environmental samples by a novel rpoB-based PCR-DGGE method. FEMS Microbiology Ecology,53(2), 317-328. doi:10.1016/j.femsec.2005.01.017

[14] Bahamdain L, Fahmy F, Lari S, Aly M. Characterization of Some Bacillus Strains Obtained from Marine Habitats Using Different Taxonomical Methods. Life Sci J 2015;12(4):58-63

[15] Bezza, F. A., & Chirwa, E. M. (2017). Pyrene biodegradation enhancement potential of lipopeptide biosurfactant produced by Paenibacillus dendritiformis CN5 strain. Journal of Hazardous Materials,321, 218-227. doi:10.1016/j.jhazmat.2016.08.035

[16] Lewis, K., & Mulcahy, L. (2011). Faculty of 1000 evaluation for Surviving bacterial sibling rivalry: Inducible and reversible phenotypic switching in Paenibacillus dendritiformis. F1000 - Post-publication Peer Review of the Biomedical Literature. doi:10.3410/f.11590956.12651064

Edited by Nicole McClellan, Yanyun Gao, Heidi Nam, and Allyson Pruski, students of Jennifer Talbot for BI 311 General Microbiology, 2018, Boston University.