Detailed Notes on Domain Bacteria and Proteobacterias

Domain Bacteria and the Phylum Proteobacteria

The domain Bacteria is comprised of approximately $42$ phyla, though it is important to note that only about half of these are currently culturable. The remaining phyla are known to science primarily through the mass sequencing of $ARNr$, which serves as a molecular identifier even when phenotypic characteristics remain unknown. Despite this vast potential diversity, $90\%$ of characterized bacterial species belong to just four major phyla: Proteobacterias, Actinobacterias, Firmicutes, and Bacteroidetes. The Proteobacterias represent an exceptionally extensive and complex group, exhibiting highly variable morphology, physiology, and modes of life. They are considered the most diversified group with the greatest variety within the phylogenetic tree and encompass all major nutritional types. These organisms are Gram-negative, and evolutionary theory suggests that mitochondria originated from this group. Proteobacterias are taxonomically divided into six classes: $\alpha$, $\beta$, $\gamma$, $\zeta$, $\delta$, and $\epsilon$-proteobacteria.

Phototrophic Bacteria and Anoxygenic Photosynthesis

Phototrophic bacteria utilize solar light as their primary energy source to carry out anoxygenic photosynthesis. Unlike oxygenic photosynthesis, this process does not release $O_2$ because these organisms do not use $H_2O$ as an electron source. These bacteria contain carotenoids and specific electron sources depending on the group. Electrons are excited in the photosystem and transferred to a pool of quinones, which facilitate the synthesis of $NAD(P)H$. Subsequently, electrons pass through a cytochrome to a second photosystem. It is a critical distinction that performing anoxygenic photosynthesis does not necessarily restrict these organisms to anaerobic environments; they may exist in varied oxygen conditions.

Purple Sulfur Bacteria are classified as anoxygenic phototrophs, specifically photolithotrophs. They utilize $H_2S$, $S^0$, $S_2O_3^{2-}$, and $H_2$ as electron donors, while $CO_2$ serves as their carbon source. Their coloration—appearing as purple, orange, or red—is due to the presence of carotenoids and a specific blue-green chlorophyll. These bacteria can be halophilic or alkaliphilic and typically inhabit anaerobic zones of rivers, lakes, and swamps that are rich in sulfide. This habitat is necessary because $H_2S$ converts into $H_2SO_4$ in the presence of oxygen. Within this group, the Family Chromatiaceae is known for accumulating sulfur granules inside the cell and performing photosynthesis in structures called chromatophores; examples include Chromatium sp. and Thiocapsa sp. In contrast, the Family Ectothiorhodospiraceae accumulates sulfur granules on the cell surface and conducts photosynthesis in lamellae, with examples being Ectothiorhodospira sp. and Halorhodospira sp.

Purple Non-Sulfur Bacteria are mostly anaerobic phototrophic bacteria that utilize organic matter as both an electron donor and a carbon source. They can process various substances including fatty acids, amino acids, sugars, and alcohols. They possess a wide variety of carotenoids and are often found in stagnant waters rich in organic matter, specifically at depths reachable by blue light. Metabolically, they are highly versatile; they are not restricted to anoxic environments and can grow as chemoheterotrophs in the presence of $O_2$ and darkness. Notable examples include Rhodospirillum sp., known as the red spiral, and Rhodobacter sp., known as the red bacillus.

Aerobic Purple Bacteria with Bacteriochlorophylls are obligate aerobes and chemoorganotrophs that also perform anoxygenic photosynthesis. Their photosynthetic apparatus is integrated directly into the membrane. They generate energy through respiration, using $O_2$ as the primary final electron acceptor. Interestingly, they only produce photosynthetic pigments in the presence of $O_2$, though some species can respire in anaerobic conditions using alternative electron acceptors. These organisms were the most recent group to be discovered and can account for up to $5\%$ of the photosynthesis occurring in marine coastal waters. An example of this group is Roseobacter sp., a red bacillus.

Chemolithotrophic Bacteria and the Nitrogen Cycle

Chemolithotrophic bacteria derive their energy from inorganic electron donors, and the majority are autotrophs that fix $CO_2$ as their carbon source. They use inorganic compounds as reducing power, either directly or through reverse electron flow. A vital subgroup is the Nitrifying Bacteria, which are essential for the nitrogen cycle. They convert ammonium ($NH_4^+$) into nitrate ($NO_3^-$), a form that can be assimilated by other organisms. In industrial applications, they are used for treating wastewater through the nitrification and denitrification of sludge to separate nitrogenous compounds. A negative consequence of their activity is the biodeterioration of materials composed of $CaCO_3$.

Nitrous Bacteria use $CO_2$ as a carbon source and $NH_4^+$ as an electron donor, converting it into nitrite ($NO_2^-$). They typically live in environments rich in ammonium, such as the activated sludge of wastewater treatment plants (EDAR). An example is Nitrosomonas sp. (where "monas" denotes a free-living state). Nitric Bacteria utilize $CO_2$ as a carbon source and $NO_2^-$ as an electron donor to produce $NO_3^-$. These bacteria often cohabit with nitrous bacteria, with Nitrobacter sp. being a primary example. Additionally, Comammox organisms are unique for being able to perform the entire conversion process from $NH_4^+$ to $NO_3^-$ within a single organism, such as those in the phylum Nitrospirota.

Sulfur and Iron Chemolithotrophs

Sulfur and Iron-oxidizing chemolithotrophs are metabolically versatile organisms that use $CO_2$ as a carbon source and sulfur or iron as electron donors. Many of these bacteria accumulate $S^0$ as sulfur granules for use as an energy reserve. The oxidation of sulfur releases protons, which acidifies the surrounding environment; consequently, many of these organisms are acidophiles. They produce $H_2SO_4^{2-}$ and sulfates, which can lead to the structural alteration of stone.

Beggiatoa sp. is found in sulfur-rich environments, forming blooms in marine hydrothermal vents, sewage muds, and the rhizosphere of plants. A unique symbiotic-like interaction occurs where Beggiatoa produces hydrogen peroxide that reaches the plant; the plant in turn releases catalase into the environment, protecting Beggiatoa. In water treatment plants, they can cause significant operational issues by forming tangles and dense sediments that block pipes. They are also capable of using organic matter, specifically acetate, as a carbon source.

Thiomargarita sp. is notable for being among the largest microorganisms, reaching sizes up to $2\,cm$. It oxidizes $H_2S$ through either aerobic or anaerobic pathways. It stores nitrates in a vacuole as an electron acceptor, reducing them to $NH_4^+$. It accumulates intracellular sulfur granules and can oxidize $S^0$ in aerobic conditions or $H_2S$ in anaerobic conditions. Starkeya sp. was the first organism described as a facultative chemolithotroph or mixotroph. It is remarkably flexible, capable of utilizing $39$ different carbon sources, including hydrocarbons, and it can produce bacterial cellulose.

Acidithiobacillus ferrooxidans is an acidophile that oxidizes both iron and sulfur, a process that releases a high concentration of protons. This characteristic is harnessed in biomining for the bioleaching of metals from mines. If mines become flooded, the growth of these bacteria is favored, leading to the production of acidic water that must be drained. This phenomenon is known as acid mine drainage, which famously occurs at the Tinto River. These bacteria can also be used to produce copper, iron, and sulfur from minerals like chalcopyrite.

Iron and Hydrogen Chemolithotrophs

Iron Chemolithotrophs use iron as an electron donor and mostly utilize $CO_2$ as a carbon source. They obtain reducing power via reverse electron flow. These organisms generally require an acidic pH to maintain the stability of $Fe^{2+}$ in the presence of $O_2$; however, in the absence of oxygen, the pH becomes less critical. While most are acidophiles, some neutrophilic species exist in rhizospheres and microaerophilic environments. They are closely linked to acid drainage and bioleaching processes. Examples include Leptothrix sp. (meaning "thin hair") and Gallionella sp. Though not in the same taxonomic group, Leptospirillum ferrooxidans shares this metabolism.

Hydrogen Chemolithotrophs use $CO_2$ as a carbon source, and many are carboxydotrophic, meaning they oxidize carbon monoxide ($CO$) into $CO_2$. They possess membrane-bound and/or cytoplasmic hydrogenases. Facultative types will repress the Calvin cycle and their hydrogenases when organic carbon sources are available. Paracoccus denitrificans, which are coccus-shaped bacteria, perform denitrification by using nitrates as electron acceptors. This process produces nitrous oxide ($N_2O$) and nitric oxide ($NO$), which contribute to the destruction of the ozone layer ($O_3$) and enhance the greenhouse effect. Although it was previously theorized that this organism was the ancestor of the mitochondria, this has since been disproven.

Cupriavidus necator is a bacterium that thrives in the presence of copper and acts as a predator to other bacteria. It accumulates carbon in the form of polyhydroxyalkanoate ($PHA$), which is used to create biodegradable plastics. However, these plastics release significant amounts of $CO_2$ when they degrade, which has limited their widespread use. Cupriavidus metallidurans possesses a high tolerance for heavy metals and is utilized in bioremediation and the bioleaching of toxic gold compounds to obtain pure gold.

Methanotrophic and Methylotrophic Bacteria

Methanotrophic bacteria utilize methane ($CH_4$) as both an energy and electron source, while methylotrophs use various other one-carbon compounds. It is a rule that every methanotroph is a methylotroph, but not every methylotroph is a methanotroph. Many of these organisms are capable of fixing atmospheric $N_2$. Their membranes contain high levels of sterols, and it is believed they evolved from nitrous bacteria. The biosynthesis of organic compounds from formaldehyde follows two distinct routes, leading eventually to $CO_2$ to produce reducing power. It is important to distinguish these from methanogens (Archaea in anoxic zones that produce $CH_4$); methanotrophs (Archaea or Bacteria in microaerobic zones) consume $CH_4$.

Type I methanotrophs utilize the ribulose monophosphate cycle. In this pathway, all carbon is derived from formaldehyde. This process does not use $NADH$ and requires $1\,ATP$. It is considered somewhat inefficient and is characterized by a high volume of internal membranes in the cytoplasm. Examples include Methylococcus sp. and Methylobacter sp. Type II methanotrophs utilize the serine cycle, where carbon is sourced from both formaldehyde and $CO_2$. This pathway requires $2\,NADH$ and $2\,ATP$ per molecule of Acetyl-CoA. Although it consumes more resources, it produces molecules that are more readily utilized by other organisms. Examples include Methylosinus sp.

These bacteria typically inhabit microaerobic environments such as lakes, rivers, and swamps, situated between the oxic and anoxic zones where they consume the $CH_4$ produced by methanogens. They serve as primary producers in submarine food chains and can exist as symbionts within the vacuoles of marine mussels and sponges. They play a significant role in bioremediation and are crucial for reducing global $CH_4$ emissions.