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Microbial Ecology and Systematic (Muhamad Haziq bin Shahrom Ravin Daram/ Raja Muhammad Izzat bin Raja Shamsuddin

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Microbial Ecology and Systematic (Muhamad Haziq bin Shahrom Ravin Daram/ Raja Muhammad Izzat bin Raja Shamsuddin

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Hi guys, today I would like to share about you guys some information about the ecological and systematic about the microbe Ideonella sakaiensis. This microbe is actually still new to the world. So scientists still doing research upon this microbe. But these are some information that scientist have been discovered. Hope this was helpful :)

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Biochemical test for Ideonella sakaiensis

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Biochemical test for Ideonella sakaiensis

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A Gram-stain-negative, aerobic, non-spore-forming, rod-shaped bacterium, designed strain 201-F6T, was isolated from a microbial consortium that degrades poly(ethylene terephthalate) (PET) collected in Sakai city, Japan, and was characterized on the basis of a polyphasic taxonomic study. The cells were motile with a polar flagellum. The strain contained cytochrome oxidase and catalase. It grew within the pH range 5.5–9.0 (optimally at pH 7–7.5) and at 15–42 ºC (optimally at 30–37 ºC). The major isoprenoid quinone was ubiquinone with eight isoprene units (Q-8). C16 : 0, C₁ 7 : 0 cyclo, C18 :1ω7c and C12 : 0 2-OH were the predominant cellular fatty acids. The major polar lipids were phosphatidylethanolamine, lyso-phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The G+C content of genomic DNA was 70.4 mol%. Phylogenetic analysis using the 16S rRNA gene sequences showed that strain 201-F6T was affiliated to the genus Ideonella , and was closely related to Ideonella dechloratans LMG 28178T (97.7 %) and Ideonella azotifigens JCM 15503T (96.6 %). Strain 201-F6T could be clearly distinguished from the related species of the genus Ideonella by its physiological and biochemical characteristics as well as by its phylogenetic position and DNA–DNA relatedness. Therefore, the strain represents a novel species of the genus Ideonella , for which the name Ideonella sakaiensis sp. nov. (type strain 201-F6T=NBRC 110686T=TISTR 2288T) is proposed.

Abbreviation:
PET | poly(ethylene terephthalate)

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My part covers on the taxonomy of ideonella sakaiensis.
A bacteria that basically digest plastics.
Idenoella sakaiensis is Gram-negative, aerobic, and rod-shaped. It does not form spores. The individual cells of the organism are motile and have a single flagellum. I. sakaiensis tests positive for oxidase and catalase. The bacterium grows at a PH range of 5.5 to 9.0 (optimally 7 to 7.5) and a temperature of 15-42 °C (optimally at 30-37 °C). Through phylogenetic analysis, the species was shown to be affiliated to the genus Ideonella, and also related to Ideonella dechloratans and Ideonella azotifigens.

The site below is methods on how a newly found microorganism is classified according to their domain, phylum, class, family, genus and species.

hope you guys can take a look and learn something from it.
Thank you.

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US8036997B2 - Methods for data classification - Google Patents

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The present invention provides methods for classifying data and uncovering and correcting annotation errors. In particular, the present invention provides a self-organizing, self-correcting algorithm for use in classifying data. Additionally, the present invention provides a method for classifying biological taxa.

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Current research on Ideonella sakaiensis

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Current research on Ideonella sakaiensis

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There are only one research so far which is carry out by a Japanese team, led by Dr. Kohei Oda from the Kyoto Institute of Technology and Dr. Kenji Miyamoto from Keio University.
Before this , scientist only found very few species of fungi but no bacteria function in breaking down poly[ethylene terephthalate], or PET.

Although ideonella sakaiensis have ability to break down PET , the process takes a long time about 6 weeks at 30°C to fully degrade a thumb-nail-sized piece of PET. so, in order to break down world’s plastic pollutants, ideonella sakaiensis have to be improve to become more powerful.

These three link is summary of the research on Ideonella sakaiensis which easily to let you understand the concept of the research.
1) http://www.sci-news.com/biology/ideonella-sakaiensis-bacterium-can-break-down-metabolize-plastic-03693.html

2 ) https://www.aaas.org/news/science-newly-identified-bacteria-break-down-tough-plastic

3) https://www.newscientist.com/article/2080279-bacteria-found-to-eat-pet-plastics-could-help-do-the-recycling/

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Before this, I found that the scientists cultivated the environmental samples then isolated the bacteria that response distinctly to PET which now called Ideonella sakaiensis. 

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Before this, I found that the scientists cultivated the environmental samples then isolated the bacteria that response distinctly to PET which now called Ideonella sakaiensis. 

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For addition information, I just found out something about why Ideonells Sakaiensis was placed under the Genera Ideonella. Ideonella is recognised to be related genotypically , for example, as determined by 16S rRNA gene sequence analysis to genera Aquabacterium, Lepothrix and Roseateles within the Betaproteobacteria. This determine the characterictics of bacteris Ideonella Sakaiensis as well as  Ideonella dechloratans and Ideonella azotifigens in the same genera. Below attachement is about Ideonella dechloratans and lets explore the beauty of genera Ideonella.

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My part is to write something about microbial nutrition of Ideonella sakaiensis. Ideonella sakaiensis is proven as a microbe that can survive with only PET (polyethylene terephthalate) as its only food source. The following link is an article about the reason Ideonella sakaiensis becoming a PET-eating bacteria.

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My part is to write something about microbial nutrition of Ideonella sakaiensis. Ideonella sakaiensis is proven as a microbe that can survive with only PET (polyethylene terephthalate) as its only food source. The following link is an article about the reason Ideonella sakaiensis becoming a PET-eating bacteria.

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http://acsh.org/news/2016/07/13/some-hope-for-plastics-in-the-environment

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Hey, these are some information that I found to get to know Ideonella sakaiensis. They talk about the researches done by the researchers team from Japan.

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Ideonella sakaiensis was identified in 2016 by a team of researchers from Kyoto Institute of Technology and Keio University after collecting samples of PET debris in a search for bacteria which relied on the plastic for carbon growth. The bacterium was observed to utilize two distinct enzymes that reacted with water to break down PET plastics into terephthalic acid and ethylene glycol, substances which on their own pose no threat to the environment.

Further investigation identified an enzyme, ISF6_4831, which works with water to break down PET into an intermediate substance, which is then further broken down by a second enzyme, ISF6_0224. The scientist explained that by screening natural microbial communities exposed to PET in the environment, we isolated a novel bacterium, Ideonella sakaiensis 201-F6, that is able to use PET as its major energy and carbon source. When grown on PET, this strain produces two enzymes capable of hydrolyzing PET and the reaction intermediate, mono(2-hydroxyethyl) terephthalic acid.Both enzymes are required to enzymatically convert PET efficiently into its two environmentally benign monomers, terephthalic acid and ethylene glycol

Link that explain more about how they identify Idenonella sakaiensis: http://www.bio.keio.ac.jp/labs/kmiyamoto/Yoshida%20et%20al.%20Science%20(2016)%20Accepted%20Version.pdf

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hey guys, this is how the padlet should look like. place each of your findings here. the rest please do comment on what you think about the material.
this is my journal. this journal tells how they inoculate the Ideonella Sakaiensis.

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Yoshida et al. Science (2016) Accepted Version

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My name is Nur Aina Ardani binti Mohd Arif, a first year Biochemistry's student from UPM. I learnt a lot about our team's chosen bacteria; Ideonella Sakaiensis that has intriguing ability of eating plastic, which is considered as non-biodegradable material.  It is able to utilize Poly(ethylene terephthalate)  a.k.a PET as its major energy and carbon source. The journal enclosed here further explains about PET assimilation.