Part 1 - microbial biomineralization

Question 1

What is the difference between Induced and controlled Biomineralization?

Answer 1

Induced BM is precipitation caused by the metabolic activity/interactions of cells with their environment

Controlled BM is genetically regulated and the minerals benefit the organism.

Question 2

What are two factors that influence precipitation that are controlled by the organism?

Answer 2

1. Metabolic (abundance of chemical species in the environment)
2. Reactive Surfaces that may increase reaction kinetics.

Question 3

What is SEM and TEM used for, and what are their resolutions?

Answer 3

SEM - surface imaging or chem anal, ~ 10nm
TEM - through ultrathin samples, ~0.07 nm

Question 4

For SEM, Secondary Electrons (SE) and Backscattered Electrons (BSE) show what?

Answer 4

SE - topographic contrast
BSE - (atomic number Z ) Z contrast.

Question 5

What are these images showing and of what microscopy type?

Answer 5

SEM; secondary electrons (top) and backscattered electrons (bottom).

Question 6

What does EDX mapping stand for, what does it do?

Answer 6

Energy Dispersive X-Ray spectroscopy detects and quantifies elements. However difficult for concentrations less than 1% and has an error of - 20 %

Question 7

What are these images showing?

Answer 7

EDX mapping

Question 7

What are stromatolites?

Answer 7

Laminated carbonate sediments formed by microbial communities.

Question 8

What does this fuckn fly show

Answer 8

SEM max field of view and depth

Question 9

What do these fuckn paleozoic microfossils show?

Answer 9

More SEM images - we cant look inside :(

Question 10

What technique is this images showing, and what is it good at showing?

Answer 10

SEM - biominerals. The photo shows scale forming (2), agglutinated (1) Testate, and diatom frustule (3).

Question 11

What is the difference between SEM and TEM?

Answer 11

SEM - 3D image of the surface, detects knocked-off electrons

TEM- 2D projections, transmitted electrons passing through the sample.

Question 12

What are the 2 modes of TEM?

Answer 12

TEM: Electrons arrive parallel, with a big illuminated region. Can see diffraction. “Parallel beam”

STEM: Electrons form on tiny spots, and detect what goes through the sample. Scans pixel by pixel. “Convergent beam”

Question 13

What does TEM require and how is it acquired?

Answer 13

Needs ultrathin samples (50-200nm)

acquired via:

1. Sharp knife
2. Ion gun
3. Focused ion beam.

Question 14

What is this image demonstrating?

Answer 14

FIB section and TEM analysis.

Question 15

What is this image showing

Answer 15

Cellular ultrastructures in TEM. You can see cell structure in TEM

Question 16

What is this image demonstrating?

Answer 16

Left shows defects in crystal structure in TEM, and no defects in STEM.

In a bright-field (BF) particles appear dark because electrons are scattered at high-angles. In an annular dark-field (AF) image, particles appear bright/show reversed contrast because the scattered electrons at high angles are received by the ADF detector.

Brightfield microscopy is best for visualizing absorbing features on samples, whereas darkfield is the best choice for imaging scattering features such as edges and defects.

Question 17

What does ADF and HAADF stand for and what does it show?

Answer 17

Annular Dark Field - Diffraction and Chemical Contrast. Shows lots of chemical diffraction.

High Angle Annular Dark Field - Chemical Contrast. Shows chemical contrast but you don’t see the crystal as much

Question 18

What is this picture demonstrating?

Answer 18

Electron Diffraction in TEM - analysis of crystal orientation.

Question 19

What is this picture showing?

Answer 19

Planes of atoms using High Res (S)TEM

Question 20

What is this picture portraying and what methods were used to achieve these results?

Answer 20

The picture shows microbes unaffected by arsenic in acid mine drainage and instead precipitate it. Both TEM and EDX analyses were used.

Question 21

What is Fluorophore/ fluorochrome and what are some examples of pigments?

Answer 21

Chemical compound that emits fluorescence when excited by light. Contains combined aromatic groups (organic compounds) of plane or cyclic molecules with several double bind.

Question 22

What is this image showing?

Answer 22

False color Confocal Laser Scanning Microscopy fluorescence images, where one color = 1 wavelength range.

Red = cholophyll
Green = carotenoids
Blue = Scytonemin

Question 23

What are DAPI and Fluoresceins (FITC)?

Answer 23

DAPI is a stain - fluorescent dye - that binds to DNA.

FITC binds to protein and is better to use overall.

Stains exist for dead cells, Ca2+ , mg2+ etc.

Question 24

What is FISH, and can you explain this image?

Answer 24

Fluorescence in situ hybridization - probes that bind to specific part of chromosome or RNA sequence. This allows for cell identification at gene level and to see gene expression. generally used for microbes. A- DAPI B - Cells hybridized with bacterial probe C - specific probe hybridization.

Question 25

What does this slide use and what is important?

Answer 25

FISH of biofilms - the importance of biofilm thickness on its composition and function. Greater thickness more detail.

Question 26

What is the difference between widefield and confocal (CLSM) in epifluorescence?

Answer 26

CLSM : higher Z - res and less out of focus. Longer acquisition. 0.5 micro meter res. Wide: fast aquistion, 2 - 3 micrometer res.

Question 27

What is this picture showing?

Answer 27

Green shows a photosynthesis envr with the introduction of O2, Red shows layerd carbonate in lake envr with sulfide oxidation high yield. White shows aerobic respiration Grey shows sulfate reduction completed (molt)

Question 28

What is Mucus in stromatolite and what does it show?

Answer 28

Part of the calcification processes. Substance dependent on ph. It is the function of the cell that traps CA and MG, in which then precipitates occur in dead bacteria. This happens in the mucus around the cell. This happens bc mucus binds switch CA, and the greater the CA trapped, the greater the mucus

Question 29

What is this image showing?

Answer 29

Role of organic matrics of EPS - precipitates on dead cells and on EPS directly, not on the cyanobacteria. Use Ca2+ and Mg2+ at various PH.

Question 30

What is EPS and what are two parts of EPS degradation?

Answer 30

Extracellular polymeric substance that precipitates calcium carbonate produced by cynobacteria. Has a day/ night cycle when photosynthesis ceases, it fementates. 1. EPS biodegradation - feeds bacterial sulfate reduction, frees Ca2+ 2. Saturation of acidic organic functions - complexing Ca2+, Mg 2+ by very high cation concentrations.

Question 31

In terms of carbonate microstructures by organic compounds, what are three things organic compounds can do, and what do you need to keep in mind?

Answer 31

1. Favor formation of nucleation sites 2. limit grain growth via surface poisoning 3. Control mineralogy/ morphology of crystals. There are diff microstructures between abiotic crystals and those of organic matter. THIS IS CONTROLLED BY ORGANIC COMPOUNDS, NOT LIFE.

Question 32

What is this image showing?

Answer 32

Top and bottom left - SEM, right - TEM nanospheres formed in vitro only in the presence of microbes of organic compounds like EPS

Question 33

What is this image showing?

Answer 33

Nano CACO3 formed by controlled biomineralization on corals as seen via SEM

Question 34

What is this image showing?

Answer 34

Left - CLSM Right - Raman Carbonates form depending on microbial population. Aragonite (CaCo3) forms with photosynthetic cyanobacteria (Red) While hydromagnesite (mg- carbonate) forms elsewhere (green)

Question 35

What is this image showing?

Answer 35

Controlled intracellular calcification in SEM, STEM - DF, and STEM EDX. Widespread in cyanobacteria. Some carbonate inside cells in cyanobacteria and some algae.

Question 36

What is this image showcasing?

Answer 36

Some possible oldest traces of life found in Australia. They hold the morphology of carbonate domes similar to modern stromatolites. However, there are most possible abiotic growth of factual structures.

Question 37

What is this image showcasing?

Answer 37

TEM of precambrian stromatolites. nano carbonates preserved in fossil organic matter, however, we do not know what organism did it. nano biological imprint can be preserved.

Question 37

Sulfides...

Answer 37

can be produced by microbial sulfate reduction. microcrystal of uniform size can suggest simultaneous growth. However, some can be abiotic. S - istopes can demonstrate S metabolism.

Question 37

What are banded iron formations?

Answer 37

structures formed before and during Earth's oxygenation by photosynthesis. Iron was soluble as Fe2 in o2 free ocean oxygen was released into sea water through hydrothermal vents.

Question 37

Asides hydrothermal vents, what other ways did BIFs form?

Answer 37

Oxygenetic photosynthesis - directly and indirectly by aerobic fe oxidizing bacteria or by denitrifying bacteria Anoxygenic photosynthesis - without the use of oxygen. BIF may have formed before oxygenic photosynthesis evolved.

Question 38

In terms of Fe- biomineralization, Anoxygenic photosynthesis precipitate... Aerobic Fe - oxidation precipitates... oxidation fe2+ in anaerobic envr.... reduction of FE3 oxides ...

Answer 38

outside cells and on external fibers away from cells on sheaths or stalks nitrate formed with O2 (precipitates external and intracellular) anaerobic or oxic anoxic interface. Fe biominerals can absorb high quantities of toxic metals.

Question 39

What are some species that have controlled biomineralization?

Answer 39

Coccolithophores - precip of carbonates by photosynthesis. stable under supersaturation. use golgi apparatus. diatoms - forams - new chamber shows highest ph gradient. testate - shell fm (intracellular in silica deposition vesicles. magnetotactic bacteria - use of magnetic crystals and precipitate magnetosomes. oldest controlled biomin found in possible in microfossil Testate, or green alage.