T. Onstott questions micro Fall 2023

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Brooklyn College, CUNY *

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3004

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Biology

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Jan 9, 2024

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docx

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Micro 3003 Ray Assignment 2 Due Friday, Sept. 22, 2023 (or earlier) Questions refer to : Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth, Chivian et al, Science 2008 (.pdf available on blackboard) 1) What is environmental genomics (metagenomics)? Metagenomics is a process that involves extracting and sequencing DNA from a sample in an environment with the intention to identify members of microbial communities and note the abilities of the dominant members of those communities. 2) Microbial growth, defined as an increase in the number of cells in a population, is related to the time it takes a population to double (generation time). What was the estimated range of doubling times for subsurface microorganisms growing under conditions of severe nutrient limitation? 100s to 1000s of years 3a) What is the genus and species name of the bacterium studied, and what does its Latin name mean? Genus: Candidatus Desulforudis Species: audaxviator – Bold traveler 3b) To which phylum does it belong? Firmicutes 3c) Bacillus and Clostridium spp. both belong to the same phylum that you identified above. What special capability/feature does the bacterium discussed in the article share with them? The special characteristics that the bacterium in the article shares with Bacillus and Clostridium are: movement, spore formation, sulfate reduction, being a chemoautotrophic thermophile, and the ability to fix its own carbon and nitrogen. 4) How many different species were found in the fracture fluid? There was only one species present in the fluid phase of the fracture. 5a) Major environmental factors that influence microbial growth include temperature and pH. What was the ambient temperature and pH in the environment at the depth of the gold mine shaft? The ambient temperature in the environment at the depth of the gold mine shaft was proximately 60 °C and the pH was 9.3. 5b) An organism growing there would be considered a a. psychrophile b. mesophile c. thermophile d. hyperthermophile

6) H ow many liters of fracture water were filtered to collect the sample_______________, and what was the size of the filter pore ?_____________ 1. Approximately 5600 L 2. 2.0 um 7a) What does the microorganism use for energy? a. gold b. sunlight c. radiolytic processes (uranium) provided a source of reductants and oxidants including H 2 d. decomposed organic matter 7b) This would be considered a ___________________ ecosystem a. photoautotrophic b. chemoheterotrophic c. chemoautotrophic d. photoheterolitholytic 8a) Was the bacterium motile? YES 8b) How was this determined? This was determined by the presence of flagellar genes that allowed them to move along chemical gradients. 9a) How many protein-coding genes were found in the genome? 2157 protein coding genes 9b) How many protein-coding genes are typically found in free-living microorganisms? Fewer than 2000 10a) What does the acronym CRISPR stand for? Clustered regularly interspaced short palindromic repeat 10b) What is the proposed function of CRISPR regions that are encoded in the genome? The proposed function of CRISPR regions that are encoded in the genome is viral defense. 11a) What was the most probable electron acceptor used during metabolism? SO4^2- (Sulfate) 11b) What was the most probable electron donor ? Formate and H2 11c) What was the most probable carbon source ?

a) CO b) CO 2 c) formate d) potentially all of the above e) none of the above 11d) At a higher biodensity, and if available, the organism might be able to metabolize carbohydrates , such as glucose, due to the presence of _______in the cell membrane. a) ATP synthase b) nitrogenase c) sugar transporters d) efflux pumps 12) Mention at least one instance of horizontal gene transfer that was discovered in the genome. An instance of horizontal gene transfer discovered in the genome was transformation. More specifically, the antibiotic resistant genes being passed on from one bacteria to another through this process.

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