Ecological Diversity of Bacteria

Flashcards reviewing the ecological, functional, metabolic, and phylogenetic diversity of bacteria based on Lectures 1 through 5.

How are metabolic, ecological, and phylogenetic diversity defined in microbiology?

Metabolic diversity is defined by cellular processes supporting growth; ecological diversity is defined by microbial interactions between organisms and their environments; phylogenetic diversity is defined by evolutionary relationships between organisms (most commonly based on 16S rRNA phylogeny).

What three evolutionary mechanisms explain why metabolic or ecological traits may be shared by distantly related organisms?

1. Gene loss: A trait present in a common ancestor is lost during divergence over time.
2. Convergent evolution: A trait evolves independently in two or more lineages without homologous genes.
3. Horizontal gene transfer (HGT): Homologous genes coding for a trait are exchanged between distantly related lineages.

In which bacterial phyla do oxygenic and anoxygenic photosynthesis occur?

Oxygenic photosynthesis occurs exclusively in Cyanobacteria. Anoxygenic photosynthesis occurs across six phyla: Proteobacteria (Alpha-, Beta-, and Gammaproteobacteria), Chlorobi, Chloroflexi, Firmicutes, Gemmatimonadetes, and Acidobacteria.

What are the two types of photosynthetic reaction centers found in phototrophic bacteria?

The two types are FeS-type (found in Photosystem I) and Q-type (found in Photosystem II). Both types are found together in Cyanobacteria, whereas anoxygenic phototrophs possess only one type or the other.

What are the five morphological groups used to classify Cyanobacteria?

1. Chroococcales (unicellular, binary fission)
2. Pleurocapsales (unicellular, multiple fission)
3. Oscillatoriales (filamentous, no heterocysts)
4. Nostocales (filamentous, heterocyst-forming)
5. Stigonematales (branching filaments, heterocyst-forming)

How do prochlorophytes such as Prochlorococcus and Prochloron differ pigment-wise from typical Cyanobacteria?

Prochlorophytes contain chlorophyll a and b but lack phycobilins, whereas typical Cyanobacteria contain chlorophyll a and phycobilins (such as phycocyanin).

What are the specific functions of gas vesicles, hormogonia, akinetes, and cyanophycin granules in Cyanobacteria?

Gas vesicles provide buoyancy to keep aquatic cells at optimal light levels; hormogonia are short, motile filaments that break off for dispersal during stress; akinetes are thick-walled resting structures for surviving cold, desiccation, or darkness; cyanophycin granules store nitrogen.

How do heterocysts enable nitrogen fixation in Cyanobacteria despite the oxygen sensitivity of nitrogenase?

Heterocysts are differentiated cells with thick walls that slow oxygen diffusion. They lack Photosystem II, preventing $O_2$ production and $CO_2$ fixation. They import fixed carbon from adjacent vegetative cells to generate electron donors for nitrogenase, and export fixed nitrogen ($NH_3$ / organic carbon) back to vegetative cells.

How do unicellular Cyanobacteria like Cyanothece and Crocosphaera protect nitrogenase from oxygen without heterocysts?

They temporally separate the processes by performing oxygenic photosynthesis during the day and fixing $N_2$ exclusively at night.

What is the global ecological significance of marine unicellular cyanobacteria Synechococcus and Prochlorococcus?

They are the most abundant phototrophs in the ocean, accounting for $80\%$ of marine photosynthesis and $35\%$ of all photosynthesis on Earth.

What electron donor is used by Purple Sulfur Bacteria during autotrophic growth, and what sulfur products are formed?

They use hydrogen sulfide ($H_2S$) as an electron donor, oxidizing it to elemental sulfur ($S^0$) deposited as granules. When $H_2S$ becomes limited, $S^0$ is further oxidized to sulfate ($SO_4^{2-}$).

What structural and physiological differences distinguish the two families of Purple Sulfur Bacteria, Chromatiaceae and Ectothiorhodospiraceae?

Chromatiaceae deposit $S^0$ granules inside cells and have vesicular photosynthetic membranes. Ectothiorhodospiraceae deposit $S^0$ outside cells, have lamellar photosynthetic membranes, and are typically extreme halophiles or alkaliphiles living in saline or soda lakes.

What is the primary metabolic mode of Purple Non-Sulfur Bacteria, and what electron donors do they use when growing autotrophically?

They are typically photoheterotrophs using diverse organic carbon sources. When growing photoautotrophically ($CO_2$ fixation via the Calvin cycle), they use $H_2$, low levels of $H_2S$, or ferrous iron ($Fe^{2+}$) as electron donors.

How do Aerobic Anoxygenic Phototrophs differ from Purple Non-Sulfur Bacteria in terms of carbon fixation and light usage?

Aerobic Anoxygenic Phototrophs are obligate aerobic heterotrophs that cannot fix $CO_2$. They produce bacteriochlorophyll a in the dark and use light via a Q-type photosystem for photophosphorylation strictly when grown on a day/night cycle.

What phylum do Green Sulfur Bacteria belong to, what photosynthetic structures do they possess, and where do they deposit sulfur?

They belong to the phylum Chlorobi. They possess chlorosomes containing bacteriochlorophyll with an FeS-type reaction center, fix $CO_2$ via the reverse citric acid cycle using $H_2S$, and deposit $S^0$ exclusively outside the cell.

What is Chlorochromatium aggregatum and how are its component cells arranged?

It is a symbiotic phototrophic consortium consisting of green sulfur phototrophic epibionts physically attached to and surrounding a central non-phototrophic chemoorganotrophic bacterium.

What phylum and class do Green Non-Sulfur Bacteria belong to, what is their morphology, and which autotrophic pathway do they use?

They belong to Phylum Chloroflexi, Class Chloroflexi. They are filamentous gliding organisms (e.g., Chloroflexus) that fix $CO_2$ via the hydroxypropionate pathway and possess a hybrid photosynthetic system (Q-type reaction center with chlorosomes).

What enzyme catalyzes nitrogen fixation (N2 to NH3), and what factor irreversibly inhibits its activity?

Nitrogen fixation is catalyzed by nitrogenase, which is irreversibly inhibited by molecular oxygen ($O_2$).

How does Azotobacter croococcum perform nitrogen fixation when Molybdenum (Mo) is unavailable?

It produces alternative backup nitrogenases that replace Molybdenum (Mo) with Vanadium (V) or Iron (Fe).

What are nitrifiers, and what two distinct groups of organisms carry out the sequential oxidation of ammonia to nitrate?

Nitrifiers are chemolithotrophs that grow using reduced inorganic nitrogen compounds. Ammonia oxidizers (e.g., Nitrosomonas, Nitrosococcus, Nitrosopumilus) convert $NH_3 \rightarrow NO_2^-$ via ammonium monooxygenase. Nitrite oxidizers (e.g., Nitrobacter, Nitrotoga, Nitrococcus, Nitrospina, Nitrospira) convert $NO_2^- \rightarrow NO_3^-$ via nitrite oxidoreductase.

What is denitrification, and what are its environmental and agricultural impacts?

Denitrification is the anaerobic respiration of inorganic nitrogen ($NO_3^- / NO_2^-$) to gaseous products ($NO$, $N_2O$, $N_2$). In agriculture, it causes the loss of nitrogen fertilizer from soil and releases nitrous oxide ($N_2O$), a potent greenhouse gas that destroys ozone.

What is the biochemical step-by-step pathway for dissimilative sulfate reduction?

1. Sulfate ($SO_4^{2-}$) is activated by ATP sulfurylase using ATP to form adenosine-5'-phosphosulfate (APS).
2. APS reductase reduces APS to sulfite ($SO_3^{2-}$) consuming $2\,e^-$.
3. Sulfite reductase reduces $SO_3^{2-}$ to hydrogen sulfide ($H_2S$) consuming $6\,e^-$.

How do complete oxidizers differ from incomplete oxidizers among dissimilative sulfate-reducing bacteria?

Complete oxidizers (e.g., Desulfobacter, Desulfococcus, Desulfosarcina, Desulfonema) oxidize acetate and other fatty acids completely to $CO_2$. Incomplete oxidizers (e.g., Desulfovibrio, Desulfomonas, Desulfotomaculum, Desulfobulbus) incompletely oxidize organic compounds to acetate.

How do dissimilative sulfur-reducing bacteria differ from dissimilative sulfate-reducing bacteria?

Dissimilative sulfur-reducing bacteria (e.g., Desulfuromonas, Sulfospirillum, Wolinella) conserve energy by reducing elemental sulfur ($S^0$) and sulfite ($SO_3^{2-}$) to $H_2S$, but are unable to reduce sulfate ($SO_4^{2-}$).

How do Thiothrix, Beggiatoa, and Thiomargarita prevent spontaneous chemical oxidation of H2S by O2?

Thiothrix uses a holdfast to attach in high-flow environments where $H_2S$ and $O_2$ mix; Beggiatoa uses gliding motility to move vertically between $O_2$ at night and $H_2S$ during the day; Thiomargarita uses a giant vacuole filled with nitrate to anaerobically oxidize $H_2S \rightarrow S^0$ by reducing $NO_3^- \rightarrow NH_4^+$, storing $S^0$ internally until exposed to $O_2$.

What acid is produced by Thiobacillus species, and what dual oxidation is performed by Acidithiobacillus ferrooxidans?

Thiobacillus generates sulfuric acid ($H_2SO_4$). Acidithiobacillus ferrooxidans oxidizes both sulfur and ferrous iron ($Fe^{2+}$) from iron pyrite ($FeS_2$), which is useful for mineral leaching in mining but causes acid mine drainage.

Which key genera are dissimilative iron reducers, and how do they transport electrons to insoluble ferric iron (Fe3+)?

Key genera include Geobacter and Shewanella. They possess outer membrane cytochromes that facilitate direct electron transfer to insoluble minerals like ferric iron ($Fe^{3+}$) or manganese ($Mn^{6+}$).

What structural adaptation prevents neutrophilic aerobic iron oxidizers like Gallionella and Mariprofundus from entombment in iron oxide crusts?

They excrete a twisted, stalk-like structure containing an organic matrix upon which ferric hydroxide ($Fe(OH)_3$) accumulates away from the cell surface.

What defines methylotrophs versus methanotrophs, and what enzyme is essential for aerobic methane oxidation?

Methylotrophs grow on organic C1 compounds lacking C-C bonds; methanotrophs are a specialized subset that use methane ($CH_4$). Aerobic methanotrophs require methane monooxygenase ($CH_4 + O_2 \rightarrow CH_3OH + H_2O$), located in extensive internal membrane systems.

What are the key physiological, phylogenetic, and structural differences between Type I and Type II methanotrophs?

Type I methanotrophs belong to Gammaproteobacteria, assimilate C1 compounds via the ribulose monophosphate cycle, and possess bundles of disc-shaped membrane vesicles. Type II methanotrophs belong to Alphaproteobacteria, assimilate C1 compounds via the serine pathway, and possess paired peripheral membranes. Both types uniquely contain large amounts of sterols in their membranes.