Shewanella oneidensis

Shewanella oneidensis
Scientific classification
Kingdom: Bacteria
Phylum: Proteobacteria
Class: Gamma Proteobacteria
Order: Alteromonadales
Family: Shewanellaceae
Genus: Shewanella
Binomial name
Shewanella oneidensis

Shewanella oneidensis is a bacterium which can reduce poisonous heavy metal ions and can live in both environments with or without oxygen. This proteobacterium was first isolated from Lake Oneida, NY in 1988, which is where the name is derived from.[1] This species is referred to as Shewanella oneidensis MR-1, indicating "manganese reducing", a special feature of this particular organism. It is a very common misconception to think that MR-1 refers to "metal-reducing" instead of the original intended "manganese-reducing" named by Professor Kenneth H. Nealson, who first isolated Shewanella oneidensis MR-1. Shewanella oneidensis is a facultative bacterium, capable of surviving and proliferating in both aerobic and anaerobic conditions. The special interest in S. oneidensis MR-1 revolves around its behavior in an anaerobic environment contaminated by heavy metals such as iron, lead and uranium. Some experiments suggest it may reduce ionic mercury to elemental mercury,[2] and ionic silver to elemental silver.[3] Cellular respiration for these bacteria is not restricted to heavy metals though; the bacteria can also target sulfates, nitrates and chromates when grown anaerobically.

Applications

Applications in Metal Reduction

S. oneidensis MR-1 belongs to a class of bacteria known as "Dissimilatory metal-reducing bacteria (DMRB)" because of their ability to couple metal reduction with their metabolism. The means of reducing the metals is of particular controversy, as current research using Scanning Electron Microscopy and Transmission Electron Microscopy has revealed abnormal structural protrusions resembling bacterial filaments that are thought to be involved in the metal reduction. This process of producing an external filament is completely absent from conventional bacterial respiration and is the center of many current studies.

The mechanics of this bacterium's resistance and using of heavy metal ions is deeply related to its metabolism pathway web. Putative multidrug efflux transporters, detoxification proteins, extracytoplasmic sigma factors and PAS domain regulators are shown to have higher expression activity in presence of heavy metal. Cytochrome c class protein SO3300 also have an elevated transcription.[4] For example, when reducing U(VI), special cytochromes such as MtrC and OmcA are used to forming UO2 nanoparticles and associate it with biopolymers.[5]

Applications in Nanotechnology

Shewanella oneidensis MR-1 can change the oxidation state of metals. These microbial processes have opened up new opportunities for us to explore novel applications, for example, the biosynthesis of metal nanomaterials.[6] In contrast to chemical and physical methods, microbial processes for synthesizing nanomaterials can be achieved in aqueous phase under gentle and environmentally benign conditions. This approach has become an attractive focus in current green nanotechnology research towards sustainable development. Many organisms can be utilized to synthesize metal nanomaterials. Among them, the bacterium Shewanella oneidensis is able to reduce a diverse range of metal ions extracellularly and this extracellular production greatly facilitates the extraction of nanomaterials. The extracellular electron transport chains responsible for transferring electrons across cell membranes are relatively well-characterized, in particular outer membrane c-type cytochromes MtrC and OmcA.[7] A recent study suggest that it is possible to alter particle size and activity of extracellular biogenic nanoparticles via controlled expression of the genes encoding surface proteins. An important example is the synthesis of silver nanoparticle by Shewanella oneidensis, where its antibacterial activity can be influenced by the expression of outer membrane c-type cytochromes. Silver nanoparticles are considered a new generation of antimicrobial as they exhibit biocidal activity towards a broad range of bacteria, and is gaining importance with the increasing resistance in antibiotics by pathogenic bacteria.[8] Shewanella has been seen in laboratory settings, to bioreduce a substantial amount of palladium and dechlorinate near 70% of polychlorinated biphenyls [9] The production of nanoparticles by Shewanella oneidensis MR-1 are closely associated to the MTR pathway[10] (e.g. silver nanoparticles), or the hydrogenase pathway[11] (e.g. palladium nanoparticles).

Pellicle formation

Pellicle is a variety of biofilm which is formed between the air and the liquid in which bacteria grow.[12] In a biofilm, bacterial cells interact with each other to protect their community and co-operate metabolically (Microbial communities).[13] In Shewanella oneidensis, pellicle formation is typical and also related to the process of reducing heavy metal; so pellicle formation is extensively researched in this species. Pellicle is usually formed in three steps: cells attaching to the triple surface of culture device, air and liquid, then developing a one-layered biofilm from the initial cells, and subsequently maturing to a complicated three-dimensional structure.[14] In a developed pellicle, there are a number of substances between the cells (extracellular polymeric substances) which help maintain the pellicle matrix. The process of pellicle formation involves a number of significant microbial activities and related substances. For the extracellular polymeric substances, many proteins and other bio-macromolecules are required.

Interestingly, many metal cations are also required in the process. EDTA control and extensive cation presence/absence tests show that Ca(II), Mn(II), Cu(II) and Zn(II) are all essential in this process, probably functioning as a part of a coenzyme or prosthetic group. Mg(II) have partial effect, while Fe(II) and Fe(III) are not only un-needed but even inhibitory to some point. As for the cellular structures, flagella are considered to be contributing to the formation of pellicle. This is easy to understand since the biofilm needs bacterial cells to move in a certain manner, while flagella is the organelle which have locomotive function.[15] However, mutant strains lacking flagella can still form pellicle, only with a much slower progress speed.

Genome

Table showing S. oneidensis MR-1 gene annotations.

As a facultative anaerobe with branching electron transport pathway, Shewanella oneidensis is considered a model organism in microbiology. In 2002, the complete genome sequence was published, it has a 4.9Mb circular chromosome that is predicted to encode 4,758 protein open reading frames. It also has a 161kb plasmid with 173 open reading frames.[16] A re-annotation was made in 2003.[17] The genome is accessible on the Internet, such as on NCBI (refer to external links).[18][19]

References

  1. ↑ http://ijs.sgmjournals.org/cgi/content/abstract/49/2/705 Kasthuri Venkateswaran, Duane P. Moser, Michael E. Dollhopf, Douglas P. Lies, Daad A. Saffarini, Barbara J. MacGregor, David B. Ringelberg, David C. White, Miyuki Nishijima, Hiroshi Sano, Jutta Burghardt, Erko Stackebrandt, Kenneth H. Nealson Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.// Int J Syst Bacteriol, 1999, № 49
  2. ↑ Wiatrowski HA; Ward PM; Barkay T. (2006). "Novel reduction of mercury (II) by mercury-sensitive dissimilatory metal reducing bacteria". Environmental Science and Technology. 40 (21): 6690–6. doi:10.1021/es061046g. PMID 17144297.
  3. ↑ Ng, CK; Sivakumar K; Liu X; Madhaiyan M; Ji L; Yang L; Tang C; Song H; Kjelleberg S; Cao B (4 Feb 2013). "Influence of outer membrane c-type cytochromes on particle size and activity of extracellular nanoparticles produced by Shewanella oneidensis.". Biotechnology and Bioengineering. 110 (7): 1831–7. doi:10.1002/bit.24856. PMID 23381725.
  4. ↑ http://jb.asm.org/cgi/content/abstract/187/20/7138 Journal of Bacteriology, October 2005, p. 7138-7145, Vol. 187, No. 20
  5. ↑ http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0040268 Marshall MJ, Beliaev AS, Dohnalkova AC, Kennedy DW, Shi L, et al. (2006) c-Type Cytochrome-Dependent Formation of U(IV) Nanoparticles by Shewanella oneidensis. PLoS Biol 4(8): e268. doi:10.1371/journal.pbio.0040268
  6. ↑ Ng, CK; Sivakumar K; Liu X; Madhaiyan M; Ji L; Yang L; Tang C; Song H; Kjelleberg S; Cao B (4 Feb 2013). "Influence of outer membrane c-type cytochromes on particle size and activity of extracellular nanoparticles produced by Shewanella oneidensis.". Biotechnology and Bioengineering. 110 (7): 1831–7. doi:10.1002/bit.24856. PMID 23381725.
  7. ↑ Shi, L; Richardson, David J. Wang, Zheming Kerisit, Sebastien N. Rosso, Kevin M. Zachara, John M. Fredrickson, James K. (August 2009). "The roles of outer membrane cytochromes of Shewanella and Geobacter in extracellular electron transfer.". Environmental Microbiology Reports. 1 (4): 220–227. doi:10.1111/j.1758-2229.2009.00035.x. Cite uses deprecated parameter |coauthors= (help)
  8. ↑ Ng, CK; Sivakumar K; Liu X; Madhaiyan M; Ji L; Yang L; Tang C; Song H; Kjelleberg S; Cao B (4 Feb 2013). "Influence of outer membrane c-type cytochromes on particle size and activity of extracellular nanoparticles produced by Shewanella oneidensis.". Biotechnology and Bioengineering. 110 (7): 1831–7. doi:10.1002/bit.24856. PMID 23381725.
  9. ↑ De Windt W; Aelterman P; Verstraete W. (2005). "Bioreductive deposition of palladium (0) nanoparticles on Shewanella oneidensis with catalytic activity towards reductive dechlorination of polychlorinated biphenyls.". Environmental Microbiology. 7 (3): 314–25. doi:10.1111/j.1462-2920.2005.00696.x. PMID 15683392.
  10. ↑ Ng, CK; Sivakumar K; Liu X; Madhaiyan M; Ji L; Yang L; Tang C; Song H; Kjelleberg S; Cao B (4 Feb 2013). "Influence of outer membrane c-type cytochromes on particle size and activity of extracellular nanoparticles produced by Shewanella oneidensis.". Biotechnology and Bioengineering. 110 (7): 1831–7. doi:10.1002/bit.24856. PMID 23381725.
  11. ↑ Ng, Chun Kiat; Cai Tan, Tian Kou; Song, Hao; Cao, Bin (2013). "Reductive formation of palladium nanoparticles by Shewanella oneidensis: role of outer membrane cytochromes and hydrogenases". RSC Advances. 3 (44): 22498. doi:10.1039/C3RA44143A. Cite uses deprecated parameter |coauthors= (help)
  12. ↑ http://www.biomedcentral.com/1471-2180/10/291 Yili Liang, Haichun Gao, Jingrong Chen, Yangyang Dong, Lin Wu, Zhili He, Xueduan Liu, Guanzhou Qiu, Jizhong Zhou, BMC Microbiology 2010, 10:291
  13. ↑ http://www.nature.com/nature/journal/v441/n7091/full/441300a.html Kolter R, Greenberg EP: Microbial sciences-The superficial life of microbes. Nature 2006, 441:300-302.
  14. ↑ Lemon KP, Earl AM, Vlamakis HC, Aguilar C, Kolter R: Biofilm development with an emphasis on Bacillus subtilis. In Bacterial Biofilms 2008, 1-16.
  15. ↑ http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.1998.01061.x/full Pratt LA, Kolter R: Genetic analysis of Escherichia coli biofilm formation: roles of flagella, motility, chemotaxis and type I pili. Mol Microbiol 1998, 30:285-293.
  16. ↑ http://www.nature.com/nbt/journal/v20/n11/abs/nbt749.html Nature Biotechnology 20, 1118 - 1123 (2002) Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis John F. Heidelberg et al.
  17. ↑ http://www.liebertonline.com/doi/abs/10.1089%2F153623103322246566 Reannotation of Shewanella oneidensis Genome N. Daraselia, D. Dernovoy, Y. Tian, M. Borodovsky, R. Tatusov, T. Tatusova. OMICS: A Journal of Integrative Biology. July 2003, 7(2): 171-175. doi:10.1089/153623103322246566.
  18. ↑ Shewanella oneidensis MR-1 Genome Page
  19. ↑ Whole genome of Shewanella oneidensis
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