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. The SPAdes Genome Assembler provided the overall result of the genomes assembly. Gram Positive Bacteria. The sample was collected from a dry piece of wood. 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. Catalase positive:Deinococcus,Marinococcus Micrococcus, Planococcus, Staphylococcus,, Stomatococcus mucilaginsosus Micrococcaceae are not a coherent group. pluton, Pediococcus, Saccharococcus thermophilus, Staphylococcus, ValÃ¡Å¡kovÃ¡ V., de Boer W., Gunnewiek P. J. K., PospÃÅ¡ek M., Baldrian P. (2009). Micrococcus is closely related to Arthrobacter , Planococcus is related to Bacillus , , while the radioresistant cocci called Deinococcus have atypical Gram positive cell walls. The purity of the isolate was confirmed with the microscopic observation of a mono-culture. Bakt. 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. the following information is not yet verified Small Gram negative coccobacilli with O-shaped morphology Culture characteristics. See-Too, W. S., Ee, R., Lim, Y.-L., Convey, P., Pearce, D. A., Yin, W.-F., & Chan, K.-G. (2017). The contig.fasta file from the SPAdes Genome Assembly produced by Illumina’s BaseSpace was analyzed by BLAST. Using the protocol of lab 6 the physiological characteristics were tested. Halotolerant will grow in nutrient agar The API 20e tests had negative results for all for the 21 tests: Image 3. Gram‐positive to Gram‐variable. 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. Image 5 and 6 are from the Kraken app. Micrococcus sedentarius 9. Colony morphology including color, size, margin and elevation was observed from growth on the TSA agar. A hallmark of the genus Planococcus is that they are usually halo-tolerant gram-positive bacteria that frequently inhabit Antartica4. 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%. 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. The cells were measured to be 1 micrometer in diameter. Planococcus. The Prokka Genome Annotation app identified 64 tRNAs, 0 rRNAs, 1 CRISPR, and 3739 CDS. The quadratic streak was used 4 times to ensure a pure culture. The bacterium was found to be aerobic and Gram-stain positive. Micrococcus kristinae 4. EMB is selective for gam-negative bacterium, if the microbe is gram negative and can ferment the sugars present then the plate experiences a color change. Colony morphology on the TSA agar revealed a yellow colony that’s size increased with time, a smooth round margin and the colony was an elevated domed. Planococcus, Staphylococcus,, 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]. Head 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. P. antarticus thrived in an Antarctica, my sample would likely have similar mechanisms for surviving temperatures around -45 degrees Celsius in Faribanks winters. 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, … An orange pigmented bacterium, S1, was isolated from a cyanobacterial mat sample collected in the vicinity of Schirmacher Oasis, Maitri, the Indian station, inAntarctica. They are prokaryotic in nature meaning they are the earliest forms of the cell without a nucleus.. radioresistant cocci called Deinococcus Planococcus halocryophilus Or1 is an aerobe, psychrophilic, gram-positive bacterium that was isolated from permafrost active-layer soil. Planococcus sp. BLAST provided many species level classifications with similar query cover and percent identity. Tests were performed on the isolate by obtaining cells from either the TSA plates or from the slant agar. to the Genus. 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). Bacterium Planococcus halocryophilus that is able to thrive at minus 15 degrees Celsius offers clues about microbial life on both Mars and Enceladus. Antibiotic resistance of bacterial isolates from sediments of eastern Mediterranean Sea in association with environmental parameters. Microscopically, it is a cocci-shaped bacterium measuring 0.5 to 0.7 μmin diameter (Fig. The negative results and lack of growth in the API 20e, MAC, and EMB are all consistent with the microbe’s gram-positive cell wall. The catalase test produced bubbles and the oxidase test produced a blue color change on the strip indicating that the microbe was positive in both tests. These results reveal that the cells contained both cytochrome c-oxidase and the catalase enzyme respectively. Phylogenetic and signature nucleotides analyses revealed that strain Y42T belongs to the genus Planococcus. Melissococcus It is urease and catalase positive. The specimen produced orange, glabrous, waxy colonies on Middlebrook's agar that showed partial acid-fast staining with the modified Kinyoun stain. Planococcus faecalis sp. The antibiotics tested were Amikacin, Cefazolin, Cefoperazone, Gentamicin, Piperacillin, Tobramycin, Trimethoprim and Vancomycin. coccus-shaped colony-forming Using the protocol of lab 6 the physiological characteristics were tested. Inst. 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. While the cells were prepped in slides some characteristics were observed with the microscope, such as cell alignment shape and length. 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. The Isolate appeared to be a pure culture by the third quadratic streak; a fourth was performed for certainty. 16S rRNA gene sequence similarity of strain SCU63 T to species in the genera Planococcus and Planomicrobium ranged from 96.5 to 98.6 %. Micrococcus luteus 5. Kraken Metagenomics app was only able to classify 2.67% of reads, and of those reads only 17% of those reads identified the microbe as Lysinibacillus sphaericus. Micrococcus nishinomiyaensis 7. (2008). Micrococcaceae are not a coherent group. In general, the colonies appear as white, smooth colonies. Gram stain. Sarcina, Catalase positive:Deinococcus,Marinococcus 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. Pigments may be produced by some species; ranging from cream, pale yellow to light pink. haemolysans, Lactococcus Leuconostoc, (2016). Planococcus citreus is Gram stain positive and aerobic. My isolate was not just aerobic but a facultative aerobe, which is inconsistent with two articles that state the genus is strictly aerobic5. have atypical Gram positive cell walls. Of the few documents that relate to Planococcus donhaensis, there is one that notes the origin of the sample, the South Korean Sea. The genus Planococcus was originally proposed by Migula  to accommodate Gram-stain-positive, aerobic and motile cocci of the family Planococcaceae in the phylum Firmicutes. 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. Planococcus sp. The analysis of the DNA with BaseSpace revealed unreliable data. Considering the environment in which it was found, there were a few expected results: such as the microbe’s oxygen class and catalase test results. The gram-stain was repeated three times before a successful stain was accomplished. 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. Sterile water was used to moisten the wood and a sterile swab was rolled along the wood’s surface. Firmicutes / “Bacilli” / Bacillales / Planococcaceae / Planococcus Cells coccoid , 1.0–1.2 µm in diameter, occurring singly, in pairs, in groups of three, or as tetrads or clumps of cells. Image 5: Krona Classification Chart from BaseSpace displays the large portion of unclassified reads. “Interactions between saprotrophic basidiomycetes and bacteria,’ in. I was unable to grow any microbes from the wood stove but the growth from the previously frozen wood was abundant. Abstract. Further analysis of the genomic information was necessary. nov. M. Engelhardt , K. Daly , R. Swannell , I. Overnight grown pathogenic bacterial strains of 1 × 10 6 CFU/mL were treated with known concentration of biosurfactants and incubated at … 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 … Throughout the course of this study I isolated one colony and performed many physiological and genomic tests to identify what species my isolate was. 1 micrometer diameter, coccus, cells divide linearly. The multiple sequence alignments of 16S rRNA and housekeeping genes showed that … The Microbes transfer to the agar slant was successful: Image 1, and was successfully re-cultured from the slant when necessary. A suspension of the microbe in broth was tested simultaneously in all 21 of the tests included in the API 20E test strip. The second most likely species suggested by was P. antarticus, at least this species shares a similar environment. 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. 1. Micrococcus lylae 6. The DNA was then sent to the UAF’s DNA Core Lab sequenced using the Illumina MiSeq DNA sequencer which utilized the next-generation sequencing methodology. The results did not meet these thresholds, and this is the reason that the BaseSpace indentified taxanomy of Lysinibacillus sphaericus was rejected. The APP provides an extensive list of regions that were specifically identified as the above elements. These tests reveal nothing more than a conformation that it is indeed a gram-positive microbe. BLAST had a different database and could possibly have the genome of the isolates species if base space did not. To thrive in this community it would be helpful to have mechanisms to process radical oxygen species. The gram stain was performed to assess the thickness of the peptidoglycan wall. At the genus level, morphology can vary greatly. 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. The TSA medium provided a suitable environment for a variety of bacteria and a few molds. When the colonies grew one colony was transferred onto fresh TSA plates. Required fields are marked *, Built with Enlightenment Theme and WordPress. but poor growth less than 1% or more than 15% NaCl The Inhibition Zones exceed the antibiotic specific threshold diameter for susceptibility see table 2 for details. This genus is relatively young and is currently growing with many of the species being described within the last ten years. coccus-shaped gram-positive Isolation and characterization of a novel hydrocarbon‐degrading, Gram‐positive bacterium, isolated from intertidal beach sediment, and description of Planococcus alkanoclasticus sp. By Ethan Hanson Classification: Kingdom: Bacteria Phylum: Firmicutes Class: Bacilli Order: Bacillaes Family:Planococcaceae Genus: Planococcus Species: Planococcus halocryophilus Planococcus halocryophilus is an aerobic, gram-positive bacterium that is found in arctic permafrost. Stomatococcus Cell lysis was accomplished through adding sodium dodecyl sulfate (SDS), which is a surfactant that chemically weakened the cell walls, and the use of PowerBeads and the centrifuge to mechanically break the cell walls. 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. This app provided sample information such as the total number of reads that were used for classification and the percent of reads that were classified. 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 The bacterium is Gram-positive and possesses all the characteristics of the genus Planococcus. If any microbes grew from the firewood it would mean that they were able to withstand temperatures below -50 degrees Celsius and be psycrophiles, if any microbes grew in my wood stove they would have had to be thermophiles. The gram-stain revealed that the isolate was a gram-positive coccid: Image 2. 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. masc. nov., a carotenoid-producing species isolated from stools of Antarctic penguins. , while the Micrococcus is closely related to Arthrobacter , Planococcus is related to Bacillus, 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%. Micrococcus luteus is a Gram-positive, to Gram-variable, nonmotile, coccus, tetrad-arranging, pigmented, saprotrophic bacterium that belongs to the family Micrococcaceae. This is consistent with a study that found, to the level of the genus, that Planococcus’ were susceptible to all antibiotics tested3. Cells of strain AJ003T were aerobic, Gram-stain-positive, cocci-shaped and orange. 5. Craters may form around the colonies on some media. Gemella The species classification with the highest query cover is poorly documented in literature. MAC plates are also selective for Gram-negative microbes and differentiates between lactose fermenters (agar turns pink) and non-lactose-fermenters (agar turns colorless). Fackrell, H. (n.d.). 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. Phylogenetic composition and properties of bacteria coexisting with the fungus, de Boer W., van der Wal A. The general features of Planococcus sp. mucilaginsos, Streptococcus, Trichococcus flocculiformis, Vagococcus, anaerobes Coprococcus, Peptococcus niger , Peptostreptococcus, Ruminococcus, Colony morphology for these organisms vary depending upon the type of media on which they are cultivated. Based on multiple ein neues System der Bakterien. They may be domed, shining, mucoid-type colonies with radial striations or may appear smooth with entire edges. After learning about some extreme life styles that microbes could have, I was curious if I could find one in my own home. The gram stain was performed to assess the thickness of the peptidoglycan wall. Stomatococcus nov. isolated from cyanobacterial mat samples collected from ponds in Antarctica. Image 6 To 20 Classification Results by Taxonomic Level from BaseSpace. PAMC21323 is a gram (+), motile, psy-chrotrophic bacteria, which can grow over a broad temperature range (5–40 °C). 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. Micrococcus varians 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). Many of the morphological and physiological analyses made on the isolate are not held by every species in the Planoccocus genus. The isolate failed to grow on EMB or MAC plates, considering that both plates are selective for gram negative, these results confirm the results of the gram positive test: Image 4. BLAST suggested Genus and species with associated query cover percentage and identity percentage. Genus planococcus. 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 … Colonies are round and yellow in color. Micrococcus, A second analysis of the DNA was performed using the BLAST genomic database. Member of the genus Staphylococcus are associated with clinical infections whereas that of Micrococcus are rarely involved in infection. Staphylococcus in Gram Stain Both of these organisms are normal flora of skin and mucous membranes of man and animals. Several other species had similar query cover, including Planococcus antarticus: Image 7. The gram-stain was repeated three times before a successful stain was accomplished. Once identified, I could then research the species and compare it’s physiology and genomic data to current literature to confirm the taxonomic assignment. 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. There are some qualities that are consistent between my sample and P. donghaensis, they are both, gram-positive, aerobic, coccus and oxidase positive 1. compare with Marinococcus, Migula W. (1894) Uber At this time the culture was transferred into an agar slant. 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 sample was stained using the provided protocol, gram-positives and negative controls were compared to the isolate to determine its gram-state (lab 4). It was identified in 1894, and was only approved in 19806. The sample was streaked using the quadratic method to grow pure isolated colonies onto a tryptic soy agar (TSA) plate. An obligate aerobe, M. luteus is found in soil, dust, water and air, and as part of the normal microbiota of the mammalian skin. Both sources have specific classification percentages that confer certainty.
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