Assignment Viridibacillus Arvi Biology

4E motility Viridibacillus arvi or Viridibacillus neidei? Coded during experiments as “4E” Use these data if you had the following sample numbers: 3,11,18,27,35,43,51 Oxidase control Catalase 4E control 4E Fluid Thioglycolate Media 4E Agar deep stabs • Is there growth at surface? 4E motility Controls for Mannitol Purple • 4E showed purple solution, only 5 tiny tiny bubbles at top of tube • In control photo • “Man 1A” is yellow solution + large gas bubble • “Man 3B” is only yellow solution, no bubble – + + control control control Phenol Red – Sucrose • Orange color + no bubble control 1 2 3 4 Phenol Red – Lactose • Red at the top, no bubble • Looked similar to #4 in photo control 1 2 3 4 Phenol Red – Dextrose • No color change, no bubble • Looked similar to #3 in photo control 4E Mannitol Salt Agar Eosin Methylene Blue • No Growth = like side A • Side B shows growth, but you should find a better example with growth + heavy fermentation A B 4E Simmons Citrate Media 4E SIM TSI – control A B C A B C 4E TSI • Looked like B • pink slant • red butt A B C D E A B C D BIOL 318 Spring 2020 Adopt a Microbe BioLog GEN III Reference – Metabolic profiles of unknown isolates Layout of Assays in the GEN III MicroPlate How to interpret the plate graphics positive borderlin e negative/borderli ne but based on the ID we’d expect it to be negativ e positive but based on the ID we’d expect it to be negative positive = isolate can use this substrate to grow/grow in the presence of this substrate negative = isolate cannot use this substrate to grow, grow in the presence of this substrate Viridibacillus arvi/neidei Click on the “cited by 39” – this will take you to 39 other papers that referenced this paper! Includes other papers talking about S.s. Some of the papers that you’ll see – these can be helpful for either learning unique properties OR comparing to relatives. Another resource – PubMed Viridibacillus Pigment Test Background: Members of the Viridibacillus genus produce a green color on R2A agar after growing at 25°C for 48-72 hours. Materials: + One R2A agar plate + Slant culture of + Viridibacillus + Another bacterium to serve as your control (whatever you have on hand should be fine–ask Dr. Estes if you’re unsure) + Inoculating loop + Permanent marker Procedure 1. Use a marker to divide the R2A plate into two halves. Label your plate: with your name and lab time and label each section with the name of the appropriate organism. 2.

Using aseptic technique, use a loop to make a single streak of each organism in the appropriate section. 3. Incubate the plate at room temperature for 48-72 hours. Viridibacillus Info Adapted from: https://doi.org/10.1099/ijs.0.65256-0 Description of Viridibacillus gen. nov. Viridibacillus (Vi.ri.di.ba.cil9lus. L. adj. viridis green; L. masc. n. bacillus rod: N.L. masc. n. Viridibacillus the green

bacillus/rod). Gram-positive, spore-forming, motile rods. Endospores are round and are located terminally in a swollen or slightly swollen sporangium. Growth occurs below 10°C and in the presence of 2% NaCl but not at 7% NaCl (w/w). Sporulation and release of endospores (free spores) are abundant on R2A agar after 24 and 48 h, respectively, at 25°C. On R2A, all members of the genus develop a green pigment. The type species is Viridibacillus arvi. Description of Viridibacillus arvi (Heyrman et al. 2005) comb. nov. Viridibacillus arvi (ar9vi. L. gen. n. arvi of a field). Basonym: Bacillus arvi Heyrman et al. 2005. In addition to the characteristics of B. arvi summarized by Heyrman et al. (2005), the species exhibits the traits listed in the genus description. The previous description (Heyrman et al., 2005) is emended with data for strains 433-D9, 121-X1 and 433-E17 and the data generated as a result of this study. All strains, including the type strain, share the following attributes. Cells are straight, roundended and Gram-positive to Gram-variable, occurring singly and in pairs. On PCA, colonies are shiny, opaque, irregular and flat with a lobate edge and range from 365 to 666 mm in size when grown at 25°C for 48 h. On PCA, strains 433-D9, 121-X1 and 433-E17 develop a green pigment in 48–72 h of growth at 25°C, while the type strain does not.

Growth occurs at 5 and 40°C. Gelatin is liquefied, while starch is not hydrolysed. Strains grow at 2% (w/w) NaCl but not at 5%. Catalase-positive and oxidase-negative. Acid is not produced from Dglucose, Dmannitol, D-xylose, D-lactose, glycerol, sucrose, D-ribose, D-mannose, Dgalactose, L-arabinose or D-cellobiose. Acid is produced from fructose. Cell wall peptidoglycan is of the L-Lys–D-Asp type. The type strain, DSM 16317T (5LMG 22165T ), was isolated from soil. Three other strains, 433-D9 (5DSM 16704 5NRRL B-23969), 121-X1 and 433-E17, were isolated from organic-matter-rich samples in Wisconsin, USA. Individual Assignments of Lab Report 1 Section 1 isolation and ecology; references 2 Section 2 Physiology 3 Section 3 Phylogeny and Genomics 4 Rest Due 5/12 5 6 I would highly recommend that you are building your references page as you go along. 7 Title 8 Author 9 ABSTRACT 10 11 12 Instructions – please delete before submission. [Maximum size 250 words] The abstract should briefly state the metabolic features of the microbe, summarize the phylogenetic status of the organism more broadly, and identify interesting features of this microbe. 13 14 15 16 17 Introduction – Instructions – please delete before submission. [Maximum size 300 words] Give a brief overview of the genus of the organism that the BioLog GenIII plates identified your adopted microbe as. Include: 18 o Where is the genus most commonly found 19 20 o What kind of lifestyle (free-living? host-associated? obligate? Facultative? Parasitic? Mutualistic?) are the organisms usually known for? 21 o Specific structural or metabolic characteristics that group is known for 22 o What unusual chacteristics are they know for 23 24 o Any history of the genus (when, where first isolated, type specimen, average genome size) 25 26 27 28 29 30 Isolation and Ecology Instructions – please delete before submission. [Maximum size 300 words] If your isolate was from larvae, please see the “Culturing the microbiome” section of the methods in the following paper for isolation information: Estes, et al. 2013 Brood-ball Mediated Transmission of Microbiome Members in the dung beetle, Onthophagus 31 32 33 34 35 36 37 38 39 40 taurus.

The research students in my lab and I originally isolated the microbes from the gut of a 3rd instar Onthophagus taurus dung beetle larvae. The gut homogenate was serially diluted and plated on LB or 1/10th LB media, incubated at 37oC for 24 hours. Individual colonies were picked and streaked for pure cultures. o The dung beetle, O. taurus, was collected from the dung of an organic dairy cow. State the genus and species (if given) by the BioLog GenIII plate and the Proposed lifestyle of this particular species. (hint – it was found in the gut of a dung beetle. Do you know if it is facultative or obligate with the data you have? Do you know if it is free-living, mutualistic, or pathogenic?) While you will not have definitive results for the lifestyle section, based on the BioLog plate information you might be able to make a hypothesis. 41 42 43 44 45 46 Physiology 47 48 Using the BioLog GenIII phenotypic assay results you were given, identify any other substrates of interest that the bacteria uses. 49 50 Make a Metabolic Table that includes all of the results from the classical microbiology experiments that Dr. Estes gave you on the power point slides. Instructions – please delete before submission. [Maximum size 400 words]. Using classical microbiology techniques you used in class describe the isolate. 1) colony morphology (size, shape, pigmentation, smell?, etc…), 2) cell morphology (using simple stains or negative stain), 3) Gram type (which methods you used), 4) optimal abiotic growth conditions (temperature, salinity, oxygen, UV), 5) carbon sources, 6) other metabolic abilities, 7) motility, 8) antibiotic resistance profile, and 9) other abilities. 51 52 Phylogeny 53 54 55 56 Instructions – please delete before submission. [Maximum size 200 words]. Identify papers in the scientific literature that conduct phylogenetic trees using either 16S rRNA, multiple housekeeping genes, or whole genomes. Write one paragraph on what genes and methods were used for the analysis. Include a figure of the phylogenetic tree with proper citation. 57 58 Genomics 59 60 61 62 63 Instructions – please delete before submission. [Maximum size 200 words]. Identify the closest relatives of your bacterium that have had their genomes sequenced.

Detail the strain sequenced, source of the sequence (environmental isolate, culture collection, etc..), sequencing platform, place sequencing was conducted, %GC, genome size, and any interesting findings. Make a table of the genome sequences using Table 3 in Pitt, et al. 2018 as an example. 64 65 Protologue 66 67 68 69 70 Instructions – please delete before submission. [Maximum size 500 words]. Summarize your findings about the dung beetle isolate compared to what is known about other closely related species or other strains of the same species. Using the growth characteristics, your classical microbiology tests, and the results from the BioLog Gen III plates, discuss the metabolic capabilities of the organism. What kind of ecological role might this organism have in an ecosystem? Given the 71 72 73 phylogenetic and genomic information of related taxa, what predictions could you make about the isolate you studied? Conclude with a few sentences on why this bacterium might be interesting to science or society in general. 74 75 REFERENCES 76 77 78 Instructions – please delete before submission. List your references at the end of the article, 79 Example reference: 80 81 82 Portugal R, Coelho J, Hoper D, Little NS, Smithson C et al. Related strains of African swine fever virus with different virulence: genome comparison and analysis. J Gen Virol 2015;96:408– 419 doi: 10.1099/vir.0.070508-0 83 84 Please include all pertinent information for each reference, e.g. authors, year, article/book title, journal/book name, editors, volume, page/article number, DOI. numbered in the order that they appear in the text. All listed references must be cited in the text, tables, or figure legends. Use the Vancouver style of citation. 85 86 87 FIGURES AND TABLES 88 89 90 91 92 Instructions – please delete before submission. Please list all figures and tables in order of appearance. Figures should not be used to present results that can be described by a brief statement in the text. Labelling criteria e.g. Figures must be referred to in the text as Fig. 1(a) not Fig. 1A or Figure 1(A) or as (Fig. 1a) not (Figure 1A). Multipart figures should be labelled (a), (b), etc., not (A), (B), etc. 93 94 95 Figures should not be used to present results that can be described by a brief statement in the text. The points outlined for tables regarding comprehensibility, relative values and reproducibility also apply to figures and their legends. 96 97 98 99 100 101 Tables should be broadly comprehensible without reference to the text, but it is not necessary to repeat detailed descriptions of methods, etc. The symbols * † ‡ § || ¶ # should be used for footnotes, rather than superscript letters or numbers. When results are expressed as percentages, the absolute value(s) corresponding to 100% must be stated. Statements of reproducibility should be included (see above). Tables should not be used to present results that can be described by a brief statement in the text. 102 103 ***If Figures are used from another manuscript or reference, you MUST properly cite the figure source in the figure legend! 104 105 1 T-Mobile LTE 8:28 AM 93% Х Phylogeny and Genomics; update Re Your Grade 7 / 10 Comments All scientific names need to be italicized. 16S rRNA 23 S rRNA What methods were used to build the phylogenetic tree? Genomics – %GC? YOUR ADDITIONAL CONTENT Phylogeny.docx 1 T-Mobile LTE 8:26 AM 93% Х Assignment Physiology:

Attempt 1 Your Grade 2 / 10 Comments please take a look at the instructions for how to do a this paper and the power point containing the data about your organism. YOUR ADDITIONAL CONTENT Physiology.docx ..11 T-Mobile LTE 8:53 AM 1 @ 87% X Assignment : Isolation and Ecology;… Your Grade 2/5 Comments ð Capitalize “Gram” it is a person’s name. Genus names are capitalized. Species names are not. Both are italicized. Ex: Bacillus cereus. When you first refer to a species in a paragraph or a paper spell out the entire name. The rest of the time you can abbreviate the genus name. B. cereus. ð If you are talking about more than one bacterium whose genus name starts with the same first letter, then abbreviate using the first 2 letters to distinguish between the different genera. E.g. Bacillus cereus and Brevibacterium casei. Ba. cereus and Br. casei are amazing bacteria. ð When you are referring to a group of organisms in the same genus: Bacillus sp. When referring to higher taxonomic groups (Kingdom, Phylum, Class, Order, Family) just capitalize. Bacillaceae In the introduction you can’t simply say “see attached table”, but need to summarize. What is the point of the paragraph starting “Commencement of vegetative growth”? Why did you include it? The language is a bit unusual. Here are the requirements for this section: Introduction ð Less than 300 words ð Brief overview of the genus of the organism that the Biolog Genlll plates identified your adopted microbe as. Where the genus is most commonly found ð The kind of lifestyle of the organism (free-living? host-associated? obligate? Facultative? Parasitic? Mutualistic?) Specific structural or metabolic characteristic bacteria is known for Unusual chacteristics are they know for o History of the genus (when, where first isolated, type specimen, average genome size) Isolation and Ecology ð 1 T-Mobile LTE 8:53 AM 0 87% X Assignment : Isolation and Ecology;… are the requirements for this section: Introduction ð Less than 300 words ð Brief overview of the genus of the organism that the BioLog Genlll plates identified your adopted microbe as. ð Where the genus is most commonly found The kind of lifestyle of the organism (free-living? host-associated? obligate? Facultative? Parasitic? Mutualistic?) ð Specific structural or metabolic characteristic bacteria is known for ð Unusual chacteristics are they know for ð History of the genus (when, where first isolated, type specimen, average genome size) Isolation and Ecology ð Less than 300 words ð Includes isolation information from “Culturing the microbiome” section of the methods in the following paper for isolation information: Estes, et al. 2013 Brood-ball Mediated Transmission of Microbiome Members in the dung beetle, Onthophagus taurus. o The research students in my lab and I originally isolated the microbes from the gut of a 3rd instar a Onthophagus taurus dung beetle larvae. The gut homogenate was serially diluted and plated on LB or 1/10th LB media, incubated at 370C for 24 hours. Individual colonies were picked and streaked for pure cultures. The dung beetle, O. taurus, was collected from the dung of an organic dairy cow. ð Stated the genus and species (if given) by the BioLog Genlll plate. Proposed lifestyle of this particular species (hint – it was found in the gut of a dung beetle. Do you know if it is facultative or obligate with the data you have? Do you know if it is free-living, mutualistic, or pathogenic?) While you will not have definitive results for the lifestyle section, based on the BioLog plate information you might be able to make a hypothesis. 0 IISEM Taxonomic description rubric v2 di

Important information for writing discussion questions and participation

Welcome to class

Hello class and welcome to the class and I will be your instructor for this course. This is a -week course and requires a lot of time commitment, organization, and a high level of dedication. Please use the class syllabus to guide you through all the assignments required for the course. I have also attached the classroom policies to this announcement to know your expectations for this course. Please review this document carefully and ask me any questions if you do. You could email me at any time or send me a message via the “message” icon in halo if you need to contact me. I check my email regularly, so you should get a response within 24 hours. If you have not heard from me within 24 hours and need to contact me urgently, please send a follow up text to

I strongly encourage that you do not wait until the very last minute to complete your assignments. Your assignments in weeks 4 and 5 require early planning as you would need to present a teaching plan and interview a community health provider. I advise you look at the requirements for these assignments at the beginning of the course and plan accordingly. I have posted the YouTube link that explains all the class assignments in detail. It is required that you watch this 32-minute video as the assignments from week 3 through 5 require that you follow the instructions to the letter to succeed. Failure to complete these assignments according to instructions might lead to a zero. After watching the video, please schedule a one-on-one with me to discuss your topic for your project by the second week of class. Use this link to schedule a 15-minute session. Please, call me at the time of your appointment on my number. Please note that I will NOT call you.

Please, be advised I do NOT accept any assignments by email. If you are having technical issues with uploading an assignment, contact the technical department and inform me of the issue. If you have any issues that would prevent you from getting your assignments to me by the deadline, please inform me to request a possible extension. Note that working fulltime or overtime is no excuse for late assignments. There is a 5%-point deduction for every day your assignment is late. This only applies to approved extensions. Late assignments will not be accepted.

If you think you would be needing accommodations due to any reasons, please contact the appropriate department to request accommodations.

Plagiarism is highly prohibited. Please ensure you are citing your sources correctly using APA 7th edition. All assignments including discussion posts should be formatted in APA with the appropriate spacing, font, margin, and indents. Any papers not well formatted would be returned back to you, hence, I advise you review APA formatting style. I have attached a sample paper in APA format and will also post sample discussion responses in subsequent announcements.

Your initial discussion post should be a minimum of 200 words and response posts should be a minimum of 150 words. Be advised that I grade based on quality and not necessarily the number of words you post. A minimum of TWO references should be used for your initial post. For your response post, you do not need references as personal experiences would count as response posts. If you however cite anything from the literature for your response post, it is required that you cite your reference. You should include a minimum of THREE references for papers in this course. Please note that references should be no more than 5 years old except recommended as a resource for the class. Furthermore, for each discussion board question, you need ONE initial substantive response and TWO substantive responses to either your classmates or your instructor for a total of THREE responses. There are TWO discussion questions each week, hence, you need a total minimum of SIX discussion posts for each week. I usually post a discussion question each week. You could also respond to these as it would count towards your required SIX discussion posts for the week.

I understand this is a lot of information to cover in 5 weeks, however, the Bible says in Philippians 4:13 that we can do all things through Christ that strengthens us. Even in times like this, we are encouraged by God’s word that we have that ability in us to succeed with His strength. I pray that each and every one of you receives strength for this course and life generally as we navigate through this pandemic that is shaking our world today. Relax and enjoy the course!

Hi Class,

Please read through the following information on writing a Discussion question response and participation posts.

Contact me if you have any questions.

Important information on Writing a Discussion Question

• Your response needs to be a minimum of 150 words (not including your list of references)
• There needs to be at least TWO references with ONE being a peer reviewed professional journal article.
• Include in-text citations in your response
• Do not include quotes—instead summarize and paraphrase the information
• Follow APA-7th edition
• Points will be deducted if the above is not followed

Participation –replies to your classmates or instructor

• A minimum of 6 responses per week, on at least 3 days of the week.
• Each response needs at least ONE reference with citations—best if it is a peer reviewed journal article
• Each response needs to be at least 75 words in length (does not include your list of references)
• Responses need to be substantive by bringing information to the discussion or further enhance the discussion. Responses of “I agree” or “great post” does not count for the word count.
• Follow APA 7th edition
• Points will be deducted if the above is not followed

• Remember to use and follow APA-7th edition for all weekly assignments, discussion questions, and participation points.
• Here are some helpful links
• The is a great resource