Phototrophy

Question 1

Define phototrophy.

Answer 1

The conservation of energy from light, catabolic process. This process involves light-driven proton translocation. ETC, but there are exceptions, such as light-driven proton pumps. In all cases, phototrophy results in a proton-motive force (PMF).

Question 2

Define photophosphorylation.

Answer 2

Use of light energy to make ATP. 2 steps: phototrophy and phoshorylation of ADP.

Question 3

Define autotrophy.

Answer 3

Carbon fixation. Photoautotrophy = photosynthesis.

Question 4

Describe Proteobacteria.

Answer 4

Purple bacteria. Invaginated membranes, photocomplexes, anoxygenic, H2O not a donor. The membrane area and the pigment content of phototrophs are typically adjusted in response to light intensity, with both being increased at low light intensity. By contrast, protective pigments may be increased at high light intensity.

Question 5

What methods do purple bacteria use for anabolism?

Answer 5

Autotrophy, Calvin cycle (C), nitrogen fixation (N).

Question 6

Describe purple sulfur bacteria.

Answer 6

Members of Gammaproteobacteria, specialists in photoautotrophy, many are obligate anaerobes and phototrophs, sulfur (sulfide) as main e- source, elemental sulfur accumulates as granules in the cells for storage, H2 other donor.

Question 7

What are the habitats of PSB?

Answer 7

Ponds, lakes, sulfur springs, stratified lakes. Within these habitats, PSB require zones with the necessary light, sulfide and anoxia.

Question 8

How do PSB control their position?

Answer 8

Many use flagella and/or gas vesicles to control their position in a water column. One ideal habitat is a meromictic lake, a permanently stratified lake with a lower layer of saline water separated by a chemocline from overlying fresh water.

Question 9

Describe purple nonsulfur bacteria.

Answer 9

Members of the Alpha- and Betaproteobacteria, generalists, versatile, anoxygenic. Members are variously capable of aerobic respiration, fermentation, photoautotrophy and photoheterotrophy.

Question 10

Why do organisms who can use both use heterotrophy over autotrophy when they can?

Answer 10

Heterotrophy requires less energy and reductant.

Question 11

What e- donor do PNSB use?

Answer 11

Most PNSB can use sulfide as an electron donor, but cannot tolerate high concentrations and do not accumulate sulfur granules like the PSB. Most PNSB also use other electron donors, including H2, Fe2+, and organic compounds.

Question 12

What respiration do PNSB use?

Answer 12

Facultative aerobes, prefer aerobic respiration over phototrophy. Synthesis of phototrophic membranes is suppressed by oxygen.

Question 13

What anabolism do PNSB use?

Answer 13

Many PNSB simultaneously use a combination of autotrophy & heterotrophy, often referred to as mixotrophy. Membrane invaginations available when needed.
Diazotrophy. Most PNSB also fix nitrogen, a common capability among anaerobes. The enzyme that fixes N, nitrogenase, is inactivated by oxygen, so it is only expressed under anoxic conditions.

Question 14

What habitats do PNSB live in?

Answer 14

Wide range of aquatic environments. They tend to live at lower sulfide concentrations than PSB. PNSB also probably take advantage of their versatility to live in dynamic environments, where nutrient availability changes quickly.

Question 15

Describe Aerobic anoxygenic phototrophs (AAP).

Answer 15

Members of the Alphaproteobacteria, ex. Roseobacter, obligate aerobes. Discovery overturned the previous dogma that anoxygenic phototrophs grow phototrophically under only anaerobic conditions. Common in large regions of the oceans where they can comprise > 10% of the bacterial community. Can fix CO2, facultative phototrophs, induce phototrophy when nutrient availability is low. An adaptation to the oligotrophic conditions in the open oceans. AAP probably grow mixotrophically, using phototrophy and chemoorganotrophy simultaneously. AAP are similar to the PNSB, except that O2 does not repress phototrophy in the AAP.

Question 16

Describe cartenoids in AAP.

Answer 16

Even when not growing phototrophically the AAP retain their bright pigmentation, which is largely due to carotenoids. In addition to their role in light harvesting, carotenoids serve a protective function under high light intensity.

Question 17

Describe amplicon sequencing.

Answer 17

PCR amplify a part of the SSU rRNA gene. This is done with primers that target broad groups, such as Bacteria, Archaea or Eukarya. The resulting PCR amplicons are then sequenced. The sequences are used to taxonomically identify community members. Similar sequences (eg, 97% identical) are typically combined into operational taxonomic units (OTUs), which are proxies for species. The proportions of sequence reads representing the different OTUs are assumed to represent the relative abundances of the corresponding populations.

Question 18

What are advantages of amplicon sequencing?

Answer 18

Organisms can be taxonomically identified. And, high-throughput methods can be employed.

Question 19

What are disadvantages to amplicon sequencing?

Answer 19

These group-specific primers are not perfect, so some taxa within the target group may be missed. This approach cannot determine the density of populations, because it only provides relative abundances.

Question 20

What are the components of the purple bacteria photocomplex?

Answer 20

Light-harvesting (LH) complexes, reaction centre (RC), ETC.

Question 21

Describe the role of LH complexes of the purple bacteria photocomplex.

Answer 21

Serve as antennae, broadening the spectrum of light that can be used. They transfer resonance energy (not electrons) to the reaction centre (RC). LH complexes are more abundant than RCs, with each RC surrounded by several LH complexes.

Question 22

Describe the role of the RC of the purple bacteria photocomplex.

Answer 22

The RC is a protein complex containing several bacteriochlorophylls. In the RC, light energy excites electrons to a low reduction potential, at which point they can enter the electron transport chain (ETC). The excited electrons leaving the RC are replaced by others from the ETC that have a high reduction potential.

Question 23

Describe the role of the ETC of the purple bacteria photocomplex.

Answer 23

Proton translocation, creating a PMF. The resulting PMF is used to drive ATP synthesis as well as other types of cellular work. In this ETC, the only site of proton translocation is the quinone pool.

Question 24

Describe the cyclic e- transport of the purple bacteria.

Answer 24

e- returning to the RC to repeat the process. However, the process is not 100% cyclic, as some electrons are diverted from the ETC to reduce NAD(P) to NAD(P)H, which is mainly needed for anabolism. The diverted electrons must be replaced and are obtained from various electron donors, including sulfide. These electrons enter the ETC via cytochrome c2. This explains the need of phototrophs for electron donors.

Question 25

Describe the reverse e- flow of the purple bacteria.

Answer 25

No free electron carrier (outside of the RC) with a sufficiently low reduction potential to reduce NAD(P)H in an exergonic reaction. Use a reduced quinone to reduce NAD(P)H in an endergonic reaction, which is driven by the PMF. Done by a membrane-associated, proton-driven oxidoreductase that transfers protons and electrons from quinone to NAD(P)+. The free Q pool in the membrane donates electrons to the oxidoreductase.

Question 26

Describe the green sulfur bacteria (GSB).

Answer 26

The GSB comprise the Chlorobiaceae, which is one of two families in the phylum Chlorobi. GSB appear to be specialists that are obligately anaerobic photoautotrophs, anoxygenic. They mainly use sulfide as an electron donor and are very tolerant of sulfide. Small genomes and lack genes encoding two-component systems. Most GSB appear to be non-motile, but many do have gas vesicles to control buoyancy. Many GSB are adapted to low-light environments.

Question 27

Describe the autotrophy of GSB.

Answer 27

CO2 fixation. They use the “reverse TCA cycle” to fix CO2. They use ATP and reductant to drive the TCA cycle in the reductive direction, which leads to incorporation of CO2. Some of the enzymes require modifications to permit reversal of the cycle.

Question 28

What habitats can GSB be found in?

Answer 28

Eutrophic habitats, anoxic ponds, the hypolimnion of stratified lakes, sulfur springs, relatively deep, anoxic zones in marine systems.

Question 29

Describe the GSB photocomplex.

Answer 29

Similar to purple bacteria, but the RC of GSB has unique bacteriochlorophylls and other characteristics that allow it to excite electrons to a lower reduction potential than the RC of purple bacteria, has electron carrier with a low enough reduction potential to reduce NAD(P) in an exergonic reaction, reverse electron flow is not necessary in GSB. An iron-sulfur protein (FeS) in the ETC reduces ferredoxin (Fd), which can serve as the reductant for NAD(P) reduction as well as for other metabolic processes. Electrons thus diverted from the ETC must be replaced by others obtained from electron donors, mainly sulfide.

Question 30

Define chlorosomes.

Answer 30

Powerful antenna complex, very efficient at harvesting light energy. The chlorosome is critical to the ecophysiology of GSB, permitting them to inhabit environments with very low light intensity. The chlorosome is a membrane-bound organelle located on the inner face of the cytoplasmic membrane. Like LH complexes in purple bacteria, the chlorosome transfers resonance energy, not electrons, to the RC.

Question 31

Describe planktonic consortia with GSB.

Answer 31

Some GSB have been found as epibionts on chemoorganotrophic bacteria, planktonic. This appears to be an obligate, mutualistic symbiosis. The chemoorganotroph may provide motility and/or certain nutrients. The GSB probably provides organic nutrients (photosynthate) to the chemoorganotroph. Synchronous cell division, co-regulatory process and must be a result of co-evolution.

Question 32

Describe cyanobacteria.

Answer 32

Distinct bacterial phylum, aka blue-green algae due to pigments, phycocyanins and chlorophyll a. Oxygenic phototrophs, with most being obligate phototrophs. Autotrophy: Most Cyanobacteria are autotrophic and use the Calvin cycle to fix CO2. Diazotrophy: Many Cyanobacteria can also fix nitrogen.

Question 33

What are some adaptive features of cyanobacteria?

Answer 33

Gas vesicles (buoyancy), gliding motility, desiccation resistance, spores (dormancy), toxins, heterocysts (specialized cells for N fixation, protecting nitrogenase from oxygen, non-phototrophic, non-oxygenic), mutualism (lichen).

Question 34

List the environmental significances of cyanobacteria.

Answer 34

Oxygen in the atmosphere, primary production, nitrogen fixation, evolution of eukaryotic phototrophs (photocomplex of cyanobacteria led to chloroplasts through endosymbiosis), blooms (eutrophication, oxygen depletion, toxins).

Question 35

Describe the photocomplex of cyanobacteria.

Answer 35

Use water as e- donor, makes oxygen. Water is a weak electron donor, its this oxidation is thermodynamically possible because of the very positive reduction potential of the chlorophyll, P680, in the RC of Photosystem II. Non-cyclic, but a cyclic part comes from Fd of PS I giving e- to quinone pool of PS II.

Question 36

How do the PS of cyanobacteria compare to PB and GSB?

Answer 36

PS I similar to GSB, PS II similar to phototrophic Proteobacteria. A critical difference is the very positive reduction potential of P680 in PS II versus that of P870 in the proteobacterial RC.

Question 37

Describe the paradigm shift of picoplankton.

Answer 37

Epifluorescence microscopy led to a paradigm shift when it revealed a vast community of marine picoplankton, which comprise the majority of marine biomass. Low cell density because environment is oligotrophic. However, given the tremendous area of the oceans and the depth to which these prokaryotes extend, their total biomass is enormous.

Question 38

Describe the Prochlorococcus and Synechococcus.

Answer 38

Cyanobacteria, tropical and subtropical waters, responsible for up to 30% of photosynthesis. Prochlorococcus smaller than Synechococcus, most abundant. Synechococcus also very abundant in places with more nutrients, temperate zones. Both are among cyanobacteria most related to chloroplasts.

Question 39

What are the features that allow Prochlorococcus and Synechococcus to survive in oligotrophic areas?

Answer 39

Small size, high surface area to volume ratio, small genomes (streamlining, minimizes energy cost), very particular niche.

Question 40

How do Procholorococcus ecotypes differ?

Answer 40

Ex. High light adapted ecotypes are particularly adapted for efficiency, further reduced genome compared to low light ecotypes. The high light ecotypes have lost various capabilities during their evolution, such as responsiveness to their environment, nutritional versatility, and morphological variation. This streamlining has allowed them to specialize in highly efficient growth under very particular conditions, including low nutrient availability.

Question 41

Describe the paradigm shift of the microbial loop.

Answer 41

The discovery of a large population of chemoorganotrophic (heterotrophic) prokaryotes in the open ocean. These chemoorganotrophs live on dissolved organic matter (DOM), reducing the amount of C passing to higher trophic levels (grazers, animals). DOM accounts for > 50% of marine organic C flux, so the microbial loop diverts a large fraction of total C from the classical food chain.

Question 42

Describe the paradigm shift of viruses.

Answer 42

Abundant viral populations in the ocean. Kill half of all prokaryotes in the system daily, via lytic infection, prokaryotes must double to survive, and it favours rapid growth. Viruses drive rapid turnover of marine biomass impact food web, killing of prokaryotes short-circuits the food chain (microbial loop), provides nutrients. Viruses are also hypothesized to select for diversity. The rate of viral infection is proportional to the likelihood of a virus encountering its host. “Kill the winner”. Prochlorococcus and Synechococcus have evolved mechanisms to succeed in spite of viruses. One proposed mechanism is mutation of the cell surface features recognized by viruses, leading to new strains resistant to existing viruses. However, the viruses mutate rapidly to recognize the new strains.

Question 43

Describe the microbial “carbon pump.”

Answer 43

Carbon sequestration, ocean carbon sink, offset greenhouse effect of CO2. Previously, carbon sequestration in the marine environment was thought to occur mainly via marine snow, organic aggregates that form in the water column and then sink, without complete degradation of the organic material and associated respiration. A recent observation is the additional sequestration of carbon in the marine environment by microorganisms. Carbon pump: microbes form recalcitrant dissolved organic carbon via anabolism and remains in the water column for a long time (low turnover rate). Carbon can be released via cell lysis.

Question 44

Define rhodopsins.

Answer 44

Rhodopsins are membrane proteins that use light energy to perform various types of biological work.

Question 45

Describe light-driven proton pumps.

Answer 45

An unusual case of phototrophy, which does not involve electron transport. This process does not appear to be the main catabolic process in organisms. Rather, chemoorganotrophy is the main catabolic process, while additional energy is conserved via phototrophy.

Question 46

What are the bacteriorhodopsin found in Halobacterium?

Answer 46

Halobacterium is an archeon. In Halobacteria, the primary mode of catabolism is chemoorganotrophy with aerobic respiration. These organisms induce bacteriorhodopsin (light-driven proton pump) production when nutrients or oxygen become limiting. Salt limits oxygen solubility.

Question 47

Discuss the discovery of proteorhodopsin.

Answer 47

The discovery of proteorhodopsin was one of the first major advances in metagenomic research. Genes encoding rhodopsins were identified because of their similarity to ones encoding bacteriorhodopsins. Present in approx 13% of planktonic bacteria. Does not prove that the genes are expressed, but it shows that they’re important. To prove the function of proteorhodopsin, one of the proteorhodopsin genes was cloned from a metagenome and heterologously expressed in E. coli. The recombinant E. coli strain expressed the proteorhodopsin, which was inserted into the cytoplasmic membrane. The expressed proteorhodopsin produced a PMF when the cells were exposed to light.

Question 48

Where did proteorhodopsins get their name?

Answer 48

Marine metagenomic assemblies further revealed that the new rhodopsin genes were associated with (linked to) genes from Proteobacteria, so it was recognized that these rhodopsins were not in Archaea, and they were named proteorhodopsins.

Question 49

Describe shotgun metagenomes.

Answer 49

Shotgun metagenomes are random surveys of total community DNA, more data and more complex than amplicon sequencing. Typically, the total DNA from a community is extracted, as for amplicon sequencing. If necessary, the DNA is sheared into fragments that are small enough to sequence. This approach of sequencing all DNA from a community avoids biases in amplicon sequencing due to the PCR. Shotgun sequencing normally yields short sequence reads that are often assembled into contigs and/or scafflolds, which correspond to fragments of individual genomes. Bioinformatic analysis can determine what proteins are encoded by many of the genes or gene fragments in the metagenome and can also identify the taxonomy of the organisms from which many of the genes originated.

Question 50

A disadvantage of both shotgun metagenomes and amplicon sequencing.

Answer 50

An important limitation of both amplicon sequencing and shotgun metagenome analysis is the databases available for data analysis. Many, sometimes most, of the genes in shotgun metagenomes cannot be identified, highlighting how much we have left to discover in microbial communities.

Question 51

Describe the Pelagibacter.

Answer 51

Not long after the discovery of proteorhodopsin, an organism with this pigment was cultured and isolated from the marine environment. The name of the organism, Pelagibacter ubique, reflects its ubiquitous distribution in the pelagic zone of the oceans. P. ubique is a representative of a broader group of Alphaproteobacteria, the SAR11 group. This is the most abundant group of planktonic organisms in the world’s oceans, and account for approximately 25% of the total planktonic bacteria. The extreme success of the SAR11 group is based on their ability to grow efficiently in an oligotrophic marine environment, they are aerobic chemoorganotrophs that augment their catabolism with proteorhodopsin-based phototrophy. They play a very important role in the marine carbon cycle, are specialists with ecological similarities to Prochlorococcus and Synechococcus, have very small cells, maximizing their surface to volume ratio, minimal genomes. At 1.3 megabases, the genome of P. ubique is the smallest know of any free-living organism.