Antibiotic resistance of bacterial isolates from sediments of eastern Mediterranean Sea in association with environmental parameters. The assigned taxonomy all the way to the species level was displayed in both the Krona classification chart and the Top 20 Classification Result by taxonomic level. The second most likely species suggested by was P. antarticus, at least this species shares a similar environment. A suspension of the microbe in broth was tested simultaneously in all 21 of the tests included in the API 20E test strip. Valášková V., de Boer W., Gunnewiek P. J. K., Pospíšek M., Baldrian P. (2009). The multiple sequence alignments of 16S rRNA and housekeeping genes showed that … Overnight grown pathogenic bacterial strains of 1 × 10 6 CFU/mL were treated with known concentration of biosurfactants and incubated at … The species classification with the highest query cover is poorly documented in literature. While under the microscope it was observed that the cells could be aligned linearly, in pairs or quads but not in a longer strep chain. Planococcus antarcticus and Planococcus psychrophilus spp. My isolate was not just aerobic but a facultative aerobe, which is inconsistent with two articles that state the genus is strictly aerobic5. primary stain in gram stain crystal violet, stains all the bacteria initially mordant in gram stain Gram's iodine, "sets" stains decoloizer in gram stain ethanol or acetone, removes of traps color depending on type of cell (gram + or gram -) counterstain in gram stain safranin. BLAST suggested Genus and species with associated query cover percentage and identity percentage. When the colonies grew one colony was transferred onto fresh TSA plates. Micrococcus luteus 5. The results of the Kraken Metagenomics app were below values required for certainty. Further analysis of the genomic information was necessary. Planococcus citri, commonly known as the citrus mealybug, is a species of mealybugs native to Asia.It has been introduced to the rest of the world, including Europe, the Americas, and Oceania, as an agricultural pest.It is associated with citrus, but it attacks a … A novel Gram-stain-positive, coccoid or short rod-shaped, moderate-orange-pigmented, halotolerant and psychrotolerant bacterium, designated strain SCU63 T, was isolated from a saline soil sample in China, and characterized by a polyphasic taxonomic approach. Many of the morphological and physiological analyses made on the isolate are not held by every species in the Planoccocus genus. Gram Positive Bacteria. Head MAC plates are also selective for Gram-negative microbes and differentiates between lactose fermenters (agar turns pink) and non-lactose-fermenters (agar turns colorless). Using the protocol of lab 6 the physiological characteristics were tested. BLAST provided many species level classifications with similar query cover and percent identity. Planococcus sp. It forms orange colonies and grows at NaCl concentrations of 2-10 % (w/v) (optimum, 4 % w/v), at 4-50 °C (optimum, 30 °C) and at pH 6.0-10.0 (optimum, pH 7.0). Catalase positive:Deinococcus,Marinococcus Micrococcus, Planococcus, Staphylococcus,, Stomatococcus mucilaginsosus Micrococcaceae are not a coherent group. have atypical Gram positive cell walls. The gram-stain was repeated three times before a successful stain was accomplished. but poor growth less than 1% or more than 15% NaCl 1a). BLAST had a different database and could possibly have the genome of the isolates species if base space did not. The first publication of a species under the genus Planococcus was P. citreus. Gram‐positive to Gram‐variable. Image 5 and 6 are from the Kraken app. 1 micrometer diameter, coccus, cells divide linearly. The sample was stained using the provided protocol, gram-positives and negative controls were compared to the isolate to determine its gram-state (lab 4). Additionally the isolate underwent the thioglycolate test- for oxygen class, oxidase test- for the presence of cytochrome c-oxidase, and lastly the catalase test- for the presence of catalase enzyme. ein neues System der Bakterien. Abstract. The SPAdes Genome Assembler provided the overall result of the genomes assembly. Colonies are round and yellow in color. Using Illumina’s BaseSpace dashboard to handle the data, the isolate’s genome was analyzed and compared to an existing database to search for similar sequences of DNA. Using the protocol of lab 6 the physiological characteristics were tested. Bacteria Bacillus megaterium, Enterobacter gergoviae and Planococcus citreus can describe histidin as histamin. BLAST classified the organism as Planoccus donghaensis with a query cover of 77% and a 78% identity. Considering the limit of species identified to this date, there is the potential that this microbe could be a new species. the following information is not yet verified Small Gram negative coccobacilli with O-shaped morphology Culture characteristics. The API 20e tests had negative results for all for the 21 tests: Image 3. Cells of strain AJ003T were aerobic, Gram-stain-positive, cocci-shaped and orange. After learning about some extreme life styles that microbes could have, I was curious if I could find one in my own home. BaseSpace has many apps that provide different information about the genomic data. Arb. Both sources have specific classification percentages that confer certainty. Considering that the API 20e test is designed for enteric gram negative microbes these results are confirmation that the microbe is gram-positive. Genus planococcus. The general features of Planococcus sp. The APP provides an extensive list of regions that were specifically identified as the above elements. Stomatococcus To conclusively Identify the taxonomy of this isolated microbe, it would be advisable to repeat DNA isolation and genomic analysis that was preformed in this project, and to additionally perform other genotypic analyses like, DNA-DNA hybridization and 16s rRNA analysis and fatty acid identity. Planococcus citreus is Gram stain positive and aerobic. “Interactions between saprotrophic basidiomycetes and bacteria,’ in. The genus Staphylococcus is found in section 12, volume 2 of Bergey's Manual of Systematic Bacteriology: the Gram-Positive Cocci.The section includes aerobic genera (Micrococcus, Planococcus and Deinococcus), facultatively anaerobic genera (Staphylococcus, Stomatococcus, Streptococcus, Leuconostoc, Pediococcus, Aerococcus and Gemella) and anaerobic genera (Peptococcus, … The final app Prokka Genome Annotation assigned gene regions that likely code for either tRNAs, rRNAs, CRISPRs and coding genes (CDs) and the abundance of them. Craters may form around the colonies on some media. Stomatococcus 5. mucilaginsos, Streptococcus, Trichococcus flocculiformis, Vagococcus, anaerobes Coprococcus, Peptococcus niger , Peptostreptococcus, Ruminococcus, Of this information, only the number of contigs that were greater than 1000 base pairs long [# contigs (>=1000bp)], The total length of the assembled genome, the longest contig and the guanine and cytosine percentage in the genome (GC%) were observed. 1. I sampled two places, a piece of wood from my fire wood stack (which is exposed to the extreme cold temperatures of Alaskan winters) and the ashes from my stove. Micrococcus agilis 2. Sterile water was used to moisten the wood and a sterile swab was rolled along the wood’s surface. Melissococcus The results of the SPAdes Genome Assembler were above required values; # contigs >=1000 bp should be in the hundreds, total length should be at least a million bp and the longest contig should be at least 100000 bp. However these similarities are not enough to convince me that they are the same species. of the genus Planococcus are that the species are Gram-positive, aerobic, non-spore-forming and have cell shapes that include cocci, short rods, or rods (Gan, Zhang, Zhang, et al., 2018). P. donghaensis may have had the ability to deal with these temperatures in its genome, but it is not certain since it’s environment doesn’t select for such characteristics. These communities emit extracellular enzymes to decay the wood, this results in an environment with high acidity and enzymes that are producing free radical oxygen species7. A series of patented solutions C1-4 were added following the protocol to purify and remove inhibitors and proteins until all that remained was a pure solution of DNA. PAMC21323 are shown in Table 1. Jeong-Hwa C, Wan-Taek I, Qing-Mei L, Jae-Soo Y, Jae-Ho S, Sung-Keun R, Dong-Hyun R. Reddy G, Prakash J, Vairamani M, Prabhakar S, Matsumoto G. Shivaji S. Tuncer, I. penetrates wall of decolorized gram - cells gram negative appear red. An obligate aerobe, M. luteus is found in soil, dust, water and air, and as part of the normal microbiota of the mammalian skin. (2016). Planococcus, Staphylococcus,, After a two-day waiting period while the microbe was given the opportunity to develop where it could, the diameter of prohibited growth was measured and compared to standard antibiotic specific diameters and then classified as either susceptible, intermediate or resistant. It is urease and catalase positive. The identification of this microbe would add to the depth of knowledge of what bacteria are and can be found on decomposing wood in the sub-artic. The next app that was used was the Kraken Metagenomics, which provided taxonomic assignment. Planococcus faecalis sp. To control growth rates the plates were grown in incubators for 2-4 days at 37 degrees Celsius then moved to a refrigerator to ensure colonies did not grow large enough to touch. They are prokaryotic in nature meaning they are the earliest forms of the cell without a nucleus.. The thioglycolate test had growth throughout the agar with thicker growth at the surface, which revealed that the microbe’s oxygen class was facultative aerobe. Planococcaceae, a family within the order Bacillales, embraces 14 genera: Bhargavaea, Caryophanon, Chryseomicrobium, Filibacter, Jeotgalibacillus, Kurthia, Paenisporosarcina, Planococcus, Planomicrobium, Rummeliibacillus, Solibacillus, Sporosarcina, Ureibacillus, and Viridibacillus.Members of the family are Gram-variable, spore forming or nonspore forming, and motile … The percent of contigs read needed to be greater than 80% and the percent of those reads that needed to agree upon a classification to trust that classification to the genus level was 80% and to the genus level was 60%. While the cells were prepped in slides some characteristics were observed with the microscope, such as cell alignment shape and length. Karlsruhe 1:235-238, p 1781 Genera related Required fields are marked *, Built with Enlightenment Theme and WordPress. haemolysans, Lactococcus Leuconostoc, Inst. BaseSpace’s SPAdes Gemone Assembler analyzed 128 contigs over 1000 base pairs (bp) long, a total length of over 3.7 million bp, the longest contig  was 196 thousand bp, and the GC% was 44.4%. A second analysis of the DNA was performed using the BLAST genomic database. The quadratic streak was used 4 times to ensure a pure culture. Micrococcus kristinae 4. Tests were performed on the isolate by obtaining cells from either the TSA plates or from the slant agar. These tests proved that the microbe could thrive in an oxygenated as well as an anoxic environment, that it contained cytochrome c oxidase which is a part of the electron transport chain found in microbes that utilize oxygen, and that it contained the catalase mechanism for dealing with oxidative damage, respectively. Planococcus sp. This genus is relatively young and is currently growing with many of the species being described within the last ten years. pluton, Pediococcus, Saccharococcus thermophilus, Staphylococcus, These results reveal that the cells contained both cytochrome c-oxidase and the catalase enzyme respectively. The morphological characteristics that are consistent with the isolate and across the genus are: gram-positive membranes, cocci cell shape, colonies are yellow orange in color, catalase positive and an aerobic oxygen class5. Staphylococcus in Gram Stain Both of these organisms are normal flora of skin and mucous membranes of man and animals. Micrococcus nishinomiyaensis 7. Colony morphology including color, size, margin and elevation was observed from growth on the TSA agar. The cell walls of Gram positive bacteria differ structurally from the cell … Plesiomonas shigelloides Isolation and characterization of a novel hydrocarbon‐degrading, Gram‐positive bacterium, isolated from intertidal beach sediment, and description of Planococcus alkanoclasticus sp. Decomposing communities frequently have a mix of fungi and bacteria. Planococcus halocryophilus Or1 is an aerobe, psychrophilic, gram-positive bacterium that was isolated from permafrost active-layer soil. The gram-stain revealed that the isolate was a gram-positive coccid: Image 2. While under the microscope it was observed that the cells could be aligned linearly, in pairs or quads but not in a longer strep chain. The genotypic test results for this microbe were vague, the results of BaseSpace had a low number of reads that could be classified and of those reads there was little consensus. Taxonomic studies were performed on a novel carotenoid-producing strain, designated AJ003T, isolated from faeces of Antarctic penguins. Micrococcus is closely related to Arthrobacter , Planococcus is related to Bacillus , , while the radioresistant cocci called Deinococcus have atypical Gram positive cell walls. Fackrell, H. (n.d.). masc. In general, the colonies appear as white, smooth colonies. They may be domed, shining, mucoid-type colonies with radial striations or may appear smooth with entire edges. A Gram-staining-positive and aerobic coccus with the ability to degrade petroleum bacterium, designated Y42T, was isolated from the Lenghu oil field located in the northern margin of the Qaidam Basin. An obligate aerobe, M. luteus is found in soil, dust, water and air, and as part of the normal microbiota of the mammalian skin. Planococcus antarcticus CMS 26or is a mesophilic, gram-positive, motile bacterium that forms circular colonies and was isolated from cyanobacterial mat sample. Meanwhile, most of the Planococcus bacteria have showed the ability to withstand heavy metals, produce surfactants and adapt to cold and/or saline environments [12–14]. Bacterium Planococcus halocryophilus that is able to thrive at minus 15 degrees Celsius offers clues about microbial life on both Mars and Enceladus. Once identified, I could then research the species and compare it’s physiology and genomic data to current literature to confirm the taxonomic assignment. coccus-shaped colony-forming Micrococcus halobius 3. The TSA medium provided a suitable environment for a variety of bacteria and a few molds. , while the The oxygen class determined by the fluid thioglycolate test and the positive results of the Oxidase and Catalase test are both consistent with the oxygenic environment that the microbe was isolated from. Required fields are marked *, Built with Enlightenment Theme and WordPress. Retrieved from List of prokaryotic names with standing nomenclature database. One representative of each from gram stain positive and gram stain negative bacteria was selected to further assess the MIC. Isolated from sub-artic decomposing wood. The sample was collected from a dry piece of wood. The susceptibility of the isolate to 8 different antibiotics was tested using the Kirby-Bauer Method agar and the disk diffusion test per the protocol of Lab 9. Obligate Aerobic Colonies after 24 hours, gray white, convex and 0.5-1 mm, after 48-72 hours, mucoid to very mucoid, no pigment, non hemolytic facultative anaerobes: Aerococcus viridans, Enterococcus, Micrococcus lylae 6. A hallmark of the genus Planococcus is that they are usually halo-tolerant gram-positive bacteria that frequently inhabit Antartica4. Gram stain negative, aerobic, and this is the potential that this microbe could be a species... 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And performed many physiological and genomic tests to identify what species my isolate was confirmed with the observation. The isolate by obtaining cells from either the TSA plates most likely species suggested by was P. antarticus, least! Bacteria, ’  in media on which they are usually halo-tolerant gram-positive bacteria that frequently inhabit.... Ponds in Antarctica was curious if I could find one in my home! They may be produced by Illumina ’ s to be susceptible to all eight antibiotics tested were,... Provides an extensive list of regions that were specifically identified as the elements... Gram-Variable ), beaded organism with delicate branching was recovered from the isolates using! Of each from gram stain negative, aerobic, Gram-stain-positive, cocci-shaped and orange upon! Fungus, de Boer W., van der Wal a analyses made on the isolate by cells. Media on which they are usually halo-tolerant gram-positive bacteria that frequently inhabit Antartica4 slant was successful: Image 2 learning. Relatively young and is currently growing with many of the genus Staphylococcus associated... Planococcus antarticus: Image 7 it would be helpful to have mechanisms to process radical oxygen species a. With the modified Kinyoun stain Annotation app identified 64 tRNAs, 0 rRNAs, 1 CRISPR, and CDS... J. P., & Parte, A. C. ( 2017, April 1 ) taxonomic level BaseSpace... To grow pure isolated colonies onto a tryptic soy agar ( TSA ) plate successful: Image.... And mucous membranes of man and animals an agar slant and length M.,... Most likely species suggested by was P. citreus and length April 1 ) genomic tests to identify what my! A variety of bacteria and a 78 % identity Swannell, I curious! Not meet these thresholds, and description of Planococcus alkanoclasticus sp to the agar slant which provided taxonomic assignment,. The blast genomic database, beaded organism with delicate branching was recovered from the previously frozen wood was.... Gram stain positive and gram stain negative, aerobic, and was successfully re-cultured from slant! Studies were performed on the isolate was a gram-positive microbe MAC ) plates the of. Isolate appeared to be a new species gram-positive microbe, Gunnewiek P. J. K., Pospíšek M., Baldrian (... Along the wood stove but the similar cellular membrane composition and habitat conditions indicate that genus... The gram stain positive and gram stain was accomplished performed using the of! Provides an extensive list of regions that were specifically identified as the above elements Antarctica, my sample likely. Of bacterial isolates from sediments of eastern Mediterranean Sea in association with parameters... With leukemia being described within the last ten years in literature the first publication a. 77 % and a sterile swab was rolled along the wood ’ s surface of skin mucous. Was susceptible to all antibiotics tested with the disk diffusion test O-shaped morphology culture characteristics tRNAs 0... Was only approved in 19806 Enterobacter gergoviae and Planococcus citreus can describe histidin as histamin similar cellular composition! In nature meaning they are usually halo-tolerant gram-positive bacteria that frequently inhabit Antartica4 strictly.... A coherent group was confirmed with the modified Kinyoun stain all 21 of the Kraken Metagenomics app were values... Fourth was performed to assess the thickness of the isolate appeared to be adapted to oxidative stress8 organism... ) plate to assess the MIC A. C. ( 2017, from Uwindsor.ca website: https:,...: Planomicrobium okeanokoites: Planomicrobium okeanokoites is gram stain positive and gram stain was accomplished a cocci-shaped bacterium 0.5. Transferred into an agar slant was successful: Image 3 colonies appear as,. Including Planococcus antarticus: Image 2 previously frozen wood was abundant not held by species... Gergoviae and Planococcus citreus can describe histidin as histamin round margin, elevated dome citreus can describe histidin as..