The article is attached on the bottom thank you. 1) Microbial growth, defined as

Question

The article is attached on the bottom thank you.
1) 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? ________________________________ 2a) What is the genus and species name of the bacterium studied, and what does its Latin name mean? _______________________________________________________________________ 2b) To which phylum does it belong? ___________________________________________________ 2c) 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? ____________________________________________________________________________ 3) How many different species were found in the fracture fluid? _______________________ 4a) 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? _______________________________________ 4b) An organism growing there would be considered a a. psychrophile b. mesophile c. thermophile d. hyperthermophile 5) How many liters of fracture water were filtered to collect the sample, and what was the size of the filter pore? _________________________________________________________ 6a) What does the microorganism use for energy? a. gold b. sunlight c. radiolytic processes provided a source of reductants and oxidants (uranium) d. decomposed organic matter NAME_______________________________________ 6b) This would be considered a ___________________ ecosystem a. photoautotrophic b. chemoheterotrophic c. chemoautotrophic d. photoheterolitholytic 7a) Was the bacterium motile?_________________ 7b) How was this determined?________________________________________________ 8a) How many protein-coding genes were found in the genome? _____________________ 8b) How many protein-coding genes are typically found in free-living microorganisms? _______________________________________ 9a) What does the acronym CRISPR stand for? _____________________________________ 9b) What is the proposed function of CRISPR regions that are encoded in the genome? _________________________________________________________________________________________________ 10a) What was the most probable electron acceptor used during metabolism?_________________ 10b) What was the most probable electron donor?______________________ 10c) What was the most probable carbon source? a) CO b) CO2 c) formate d) potentially all of the above e) none of the above 10d) 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 all of the metabolic capabilities necessary for le. This gene complement Reveals a Single-Species Ecosystema i i ous ceorh Deep Within Earth Dylan Chivian,12+ Eoin L. Brodie, Eric J. Alm,24 David E. Culley, Paramvir S. Dehal, 12 Todd Z DeSantis, Thomas M. Gihring, Alla Lapidus, Li-Hung Lin, Stephen R. Lowry, Duane P. Moser, Paul M. Richardson, Gordon Southam,10 Greg Wanger,10 Lisa M. Pratt, Gary L. Andersen,23 Terry C. Hazen, 2312 Fred J. Brockman,13 Adam P. Arkin,1214 Tullis C. Onstott 12,15 analyses at the ambient -60°C temperature and pH of 9.3, which indi- cated radiolytically generated chemical species as providing the energy and nutrients to the system (I), with formate and H2 as possessing the greatest potential among candidate electron donors, and sulfate (SO) reduction as the ting process (Il). DNA was from -5600 liters of fi- tered fracture water by using a protocol that has DNA from low-biodiversity fracture water collected at 2.8-kilometer depth in a South Africanbeen demonstrated to be effective on a broad fluid phase of this particular fracture. Its genome indicates a motile, sporulating, sulfate-reducing. plete, 2.35-megabase pair (Mbp) genome w well suited to long-term isolation from the photosphere deep within Earth's crust and offers anilar to other studies that obtained near-complete gold mine was sequenced and assembled into a single, complete genome. This bacterium, Candidatus Desu or dis oudar ator, composes >99.9% of the microorganisms inhabiting the range of bacterial and archacal species, includ- ng recalcit ant organisms (16) A single com- chemoautotrophic thermophile that can fix its own nitrogen and carbon by using machinery shared with archaea. Candidatus Desulforudis au assembled with a combination of shotgun Sanger r is capable of an independent life-style sequencing and 454 example of a natural ecosystem that appears to have its biological component entirely encodeg consensus genomes from environmental sam- within a single genome. ples (5, 17), heterogeneity in the population of more complete picture of life on, and even in, Earth has recently become because they permit insight into a mode of life showing only 32 positions with a SNP observed the dominant species as measured with si nucleotide Such microorganisms are of particular interest (SNP) was quite low of the DNA from an environmental sample, a process One bacterium belonging to the Firmicutes called environmental genomics or metagenomics phylum (Fig. 1A), which we herein name Can- Phiysical Bicsciences Division (1-8). This approach allows us to identify mem- bers of microbial communities and to character- in small subunit (SSU or 165) ribosomal RNA Earth Sciences Division, Lawrence Laboratory, Berkeley, CA 94720, USA. Virtual Institute prominent Microbial Stress and Survival, Berkeley, CA 94720, USA. ze the abilities of the dominant members even (RNA) gene clone libraries (1-14) from almost oratory, Berkeley, CA 94720, USA. "Departments of Bidlogical when isolation of those organisms has proven all fracture fluids sampled to date from depths and Chil However, with a few exceptions (5, 7, greater than 1.5 km across the Witwatersrand basin Institute of assembling complete or even near-complete ge- (covering 150 km by 300 km near nomes for a substantial portion of the member South Africa). This bacterium was shown in MA 02139, USA. Energy Richland, WA 99352, USA Department of Division, a Oceanography, Florida State University, by the complexity of previous geoc and 16S rRNA gene study 32306, USA Genomic Technology Program, ment of Energy (DOE) Joint Genomics ln (II) to dominate the indigenous microorga nisms found in a fracture zone at 2.8 km below - 94598, In addition to elevated t lack of O2, conditions emperatures and a within Earth's crust at USA Department University, Taipei 106, Tainan. 'Diision of Earth and Sciences, Desert Research Institute, Las Vegas, NV land surface at level 104 of the Mponeng mine

Explanation / Answer

Ans

1) 100 sec to 1000sec.

2a) Genus name is Candidatus Desulforudis and the species name is audaxviator,(Candidatus Desulforudis audaxviator) the Latin means Bold traveler i.e the habitat is subterranean.

2b) Firmicutes

2c) Bacillus and Clostridium spp. both are not found in the sample due to severe nutrients limitation in subsurface conditions and permit only independent life. The 16s rRNA gene study indicates that the studied microbes are motile (flagellated), sporulating, sulfate-reducing, obligate anaerobes, chemo-autotrophic thermophile and capable of fixing nitrogen and carbon.

3) only one species.

4a) 2.8km depth of gold mine shaft have a temp. 60oC and pH of 9.3.

4b) An organism growing there would be considered a

a. psychrophile

b. mesophile

c. thermophile (correct answer) because due to high temperature in the gold mine shaft.

d. hyperthermophile

5) 5000lit and 0.2µm

6a) What does the microorganism use for energy?

a. gold

b. sunlight

c. radiolytic processes provided a source of reductants and oxidants (uranium) (correct answer)

d. decomposed organic matter

Reason: because the sunlight is unavailable in the depth therefore radioactivity generated by the decay of Uranium rocks which split ambient H2O molecule into H+ and OH- which then forms H2O2.

6b) This would be considered a ___________________ ecosystem

a. photoautotrophic

b. chemoheterotrophic

c. chemoautotrophic (corret Answer) Becaause they utilize chemical energy to make their own food.

d. photoheterolitholytic

7a) Was the bacterium motile?

yes

7b) How was this determined?

Because bacteria perform chemotaxis along chemical gradients.

8a) How many protein-coding genes were found in the genome? 2

2157

8b) How many protein-coding genes are typically found in free-living microorganisms?

210

9a) What does the acronym CRISPR stand for?

Clustered Regularly Interspaced Short Palindromic Repeats

9b) What is the proposed function of CRISPR regions that are encoded in the genome?

Bacteria used CRISPR for the viral defense.

10a) What was the most probable electron acceptor used during metabolism?

Sulfate (SO4-2)  because a long-term quiet from oxygen has lead to the complete loss of oxygen tolerance system which makes it an obligate anaerobe therefore bacteria cannot utilize the oxygen as its electron acceptor and use sulfate a favorable alternative of oxygen.

10b) What was the most probable electron donor?

H2S/H2

10c) What was the most probable carbon source?

a) CO

b) CO2

c) formate

d) potentially all of the above (Correct Answer) because the primary source of Carbon is CO2 but in place of it also used formate and CO as an alternate of CO2

e) none of the above

10d) 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 (Correct Answer)

d) efflux pumps

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