Phototrophy & Phototrophic Microorganisms

 Microorganisms derive energy not only from the oxidation of inorganic and organic compounds, but also from light energy, which they capture and use to synthesize ATP and reduce power (e.g., NADPH).

The process by which light energy is trapped and converted to chemical energy is called photosynthesis. Usually a phototrophic organism reduces and incorporates CO₂. Photosynthesis is one of the most significant metabolic processes on Earth because almost all our energy is ultimately derived from solar energy. It provides photosynthetic organisms with the ATP and reducing power necessary to synthesize the organic material required for growth. In turn these organisms serve as the base of most food chains in the biosphere.  One type of photosynthesis is also responsible for replenishing our supply of O₂, a remarkable process carried out by a variety of organisms, both eucaryotic and bacterial.

 

Although most people associate photosynthesis with the larger, more obvious plants, over half the photosynthesis on Earth is carried out by microorganisms.

 Photosynthesis as a whole is divided into two parts. In the light reactions light energy is trapped and converted to chemical energy. This energy is then used to reduce or fix CO₂ and synthesize cell constituents in the dark reactions.

 Phototrophic Microorganisms 

Phototrophic organisms are a diverse group of organisms which  carry out photosynthesis. They synthesize their own food and provide energy and nutrients to other organisms. They are important in a variety of ecological and biogeochemical processes and play a vital role in our ecosystem.

 Phototrophic microorganisms are broadly classified as either oxygenic or anoxygenic, based on their ability to produce oxygen during photosynthesis. Major groups include Cyanobacteria (oxygenic) and various anoxygenic bacteria, such as purple bacteria (Rhodospirillineae), green bacteria (Chlorobiineae), and aerobic anoxygenic phototrophs (AAPs). 

 

Beyond their photosynthetic pathway, microorganisms are grouped by how they obtain carbon: 

·        Photoautotrophs: 

Use sunlight to convert carbon dioxide into organic compounds, making their own food. This includes most oxygenic phototrophs and many anoxygenic ones.

·        Photoheterotrophs: 

Convert light into energy but require organic compounds from their environment to make their own food.

  

Oxygenic Phototrophs

These organisms produce oxygen as a byproduct of photosynthesis. Eg, Cyanobacteria, eukaryotic microalgae

 

1. Cyanobacteria: Often referred to as blue-green algae, these prokaryotes were crucial in forming Earth's oxygen-rich atmosphere. 

·        Cyanobacteria can perform oxygenic photosynthesis – producing oxygen from CO₂ and water. Due to their chlorophyll pigments, they are typically greenish blue in color and therefore also known as blue-green algae. They are found in a variety of aquatic and terrestrial habitats, including even extreme locations like hot springs and deserts.

·        Cyanobacteria play a crucial role in the global carbon cycle and have had a significant impact on the evolution of our planet's atmosphere. As one of the oldest organisms on Earth, they were responsible for releasing oxygen into the atmosphere, which initiated the transformation of the atmosphere and created the environment in which we live today.

·        Cyanobacteria are commonly used in research, both as model organisms for studying photosynthesis and as potential sources of biofuels and other useful compounds.

 2. Eukaryotic Microalgae: These are microscopic, single-celled eukaryotic organisms that perform oxygenic photosynthesis. 

 

Anoxygenic Phototrophs

These organisms perform photosynthesis without producing oxygen, as water is not their electron donor. eg, purple bacteria, green bacteria

 

1. Purple Bacteria:  Also known as Rhodospirillineae, purple bacteria uses bacteriochlorophyll and can be further divided into purple sulfur and nonsulfur bacteria. 

Purple bacteria, are a diverse group of phototrophic bacteria that perform anoxygenic photosynthesis, which means they do not produce oxygen. They are called purple bacteria because their main pigments (bacteriochlorophyll pigment a or b located on chromatophores and plasma membranes) give them a purple or red color. They are further divided into: the purple sulfur bacteria and the purple non-sulfur bacteria.

·       The main difference between sulfur and non-sulfur purple bacteria is the electron donor they use during photosynthesis. Sulfur purple bacteria use reduced sulfur compounds, such as hydrogen sulfide or thiosulfate, as electron donors for photosynthesis. In contrast, non-sulfur purple bacteria use organic compounds, such as lactate or succinate, as electron donors.

·       They use sulfide or thiosulfate as their electron donor during photosynthetic pathways. They oxidize sulfide to elemental sulfur, which accumulates as internal globules or granules within the cell. The sulfur deposition occurs inside the bacterial cell.

·       The purple sulfur bacteria can be used to reduce the concentration of harmful compounds like methane and hydrogen sulfide.

·       Sulfur purple bacteria are usually found in environments where sulfur compounds are abundant, such as hot sulfur springs, swamps, and sediments, while non-sulfur purple bacteria are found in a wider range of environments, including freshwater ponds and lakes, soils, and microbial mats.

Eg., Allochromatium and Thiocapsa

 

2.     Green Bacteria: This group, including the Chlorobiineae, uses bacteriochlorophyll but has different pigments than purple bacteria.

·       Green sulfur bacteria are anoxygenic photosynthetic bacteria with a unique photosynthetic apparatus adapted to low light and anaerobic conditions. Their name derives from their characteristic green color, which is due to the presence of chlorosomes – organelles that contain bacteriochlorophyll pigments.

·        Most of them are nonmotile and obligate anaerobes. They have bacteriochlorophyll pigments c, d, a or e.

·       They use sulphide as their ultimate electron donor for photosynthesis. Thus, they can thrive well in sulfur-rich environments with low light intensities.

·       Most of these bacteria can reduce nitrogen to ammonia. This ammonia is later used to synthesise amino acids.

·       They are found in a variety of environments and can use different electron donors for photosynthesis, including hydrogen sulfide and elemental sulfur. 

·       These bacteria can synthesize large amounts of sulfur granules, which protect them from oxidative stress and give them a distinctive appearance, visible under a microscope. The sulfur granules are stored outside the cell  as a byproduct of their anaerobic photosynthesis, distinguishing them from purple sulfur bacteria that store them intracellularly. This extracellular storage of sulfur allows green sulfur bacteria to utilize sulfide as an electron donor for photosynthesis in their aquatic environments. 

·       They are also known for forming complex microbial communities in sulfide-rich environments, called mats or biofilms, playing crucial roles in biogeochemical cycling and ecosystem function.

Eg., Chlorobium tepidum and Chlorobium vibrioforme

 

3.     Aerobic Anoxygenic Phototrophic Bacteria (AAPs): 

        These bacteria require oxygen to synthesize their photosynthetic apparatus and are mostly marine or freshwater genera. AAPB contain bacteriochlorophyll a as its main light harvesting pigment, but are not anaerobic like other bacteria that perform anoxygenic photosynthesis. Aerobic anoxygenic phototrophic bacteria are photoheterotrophic, meaning they obtain their carbon from organic compounds. They exist in a variety of aquatic environments and may constitute over 10% of the open ocean microbial community. Predation, as well as the availability of phosphorus and light, have been shown to be important factors that influence AAPB growth in their natural environments. AAPB are thought to play an important role in carbon cycling by relying on organic matter and acting as sinks for dissolved organic carbon.

 

1.     Acidobacteria and Heliobacteria are two distinct bacterial phyla with unique characteristics, metabolisms, and ecological roles. Heliobacteria perform anoxygenic photosynthesis and form endospore abilities, while Acidobacteria is a vast phylum with diverse metabolic capabilities, primarily found in soil.  Acidobacteria are primarily chemoheterotrophs, though some such as Chloracidobacterium thermophilum are capable of photosynthesis. They are ubiquitous and abundant, especially in soil ecosystems, peatlands and mineral-rich environments. They are motile eg., Acidobacterium capsulatum and non-spore formers

 

Heliobacteria use a unique form of chlorophyll, chlorophyll g as a light-harvesting pigment unlike other photosynthetic bacteria that use bacteriochlorophyll, They are obligate anaerobes and are typically found in anoxic environments such as freshwater sediments or soil. Heliobacteria are important members of the microbial community in these environments, where they play important roles in the cycling of nutrients and carbon. They are obligate aerobes that are able to capture energy from light by photophosphorylation to produce ATP. Water is not used as an electron donor and, therefore, the production of oxygen is non-existent.

 Both phyla are important to soil ecology despite their distinct differences: 

·        Both are significant components of soil microbial communities. Acidobacteria are one of the most abundant phyla in soil, and heliobacteria are widespread in anaerobic soils.

·        Members of both groups are involved in biogeochemical cycles, including carbon and nitrogen cycling. Heliobacteria are known for their nitrogen-fixing capabilities.

·        The two phyla, in their own ways, showcase the vast metabolic diversity found within bacteria. Acidobacteria possess a wide array of genes for degrading complex compounds, while heliobacteria use a unique photosynthetic process. 

 

Ecological Importance of Phototrophic Organisms 

Phototrophic organisms are essential for maintaining the balance of ecosystems and play a crucial role in the global carbon cycle. By converting light energy into chemical energy, phototrophic organisms produce organic matter that is then consumed by other organisms. This process forms the base of most food chains and supports the growth of all other living things in the ecosystem. 

Photosynthetic organisms are also responsible for producing the oxygen that we breathe. Oxygenic photosynthesis has played a critical role in the evolution of life on Earth, as oxygen is required by many organisms for respiration and other metabolic processes.

 In addition to producing oxygen and organic matter, phototrophic organisms also play a significant role in regulating the Earth's climate. By removing carbon dioxide from the atmosphere through photosynthesis, these organisms help to mitigate the effects of climate change.

 Phototrophic organisms have significant economic importance and are used in a wide range of applications in industry, agriculture, and medicine.

·       Plants, algae, and other phototrophs are the primary source of food for humans and many other animals. In addition, photosynthetic bacteria are used in the production of certain types of food, such as fermented dairy products and pickled vegetables. 

·       Photosynthetic organisms are also used in the production of biofuels. Biofuels, such as ethanol and biodiesel, are produced from organic matter, such as crops and algae, that have been grown using photosynthesis. These biofuels are considered to be more sustainable than traditional fossil fuels, as they produce fewer greenhouse gas emissions and are renewable.

·       In medicine, photosynthetic organisms are used in a variety of applications, such as the production of antibiotics and other pharmaceuticals. The ability of photosynthetic organisms to carry out complex biochemical reactions makes them valuable tools in biotechnology and bioengineering. They are an important area of research for the development of new and innovative applications.

 

Modern photobioreactors will help to conduct meaningful research with these interesting organisms. Photobioreactors are closed systems designed to grow photosynthetic microorganisms, such as algae and cyanobacteria, under controlled conditions of light, temperature, and nutrient supply.  These systems are used for a variety of purposes, such as the production of biomass for food, feed, or biofuels, the removal of pollutants from wastewater, and the cultivation of microorganisms for research or biotechnology applications.

 

Hydrogen oxidation and Methanogenesis (definition and reaction).

 

Hydrogen-oxidizing bacteria are a group of  autotrophs that can oxidise H, and reduce O₂ via “knallgas” reaction, which is the reduction of O₂ with H₂. They use hydrogen as an electron donor and O₂ as electron acceptor.  This reaction yields energy for CO₂ fixation. Hydrogen oxidizing bacteria are also called Knallgas-bacteria. These include Hydrogenobacter thermophilus, Hydrogenovibrio marinus, and Helicobacter pylori.

There are both Gram positive and Gram negative knallgas bacteria. They can be aerobes and anaerobes. Aerobic bacteria use hydrogen as an electron donor and oxygen as an acceptor while anaerobes use hydrogen as an electron donor and sulphate or nitrogen dioxide as electron acceptors.

Hydrogen is oxidized by a membrane-bound hydrogenase causing proton pumping along with electron transfer to various quinones and cytochromes. In many organisms, a second cytoplasmic hydrogenase is used to generate reducing power in the form of NADH, which is subsequently used to fix carbon dioxide via the Calvin cycle.

Many organisms are capable of using hydrogen (H₂) as a source of energy. Hydrogenase enzyme helps in hydrogen oxidation, however, hydrogenase enzyme is inhibited by the presence of oxygen. Oxygen is still needed as a terminal electron acceptor. Typically, oxygen levels of about 5-10% support best growth of these bacteria. Most hydrogen-oxidizing bacteria thus grow best under microaerophilic conditions.

The use of hydrogen as an electron donor and the ability to synthesize organic matter characterize the hydrogen-oxidizing bacteria.

Importance of Hydrogenase enzymes 

Hydrogenase enzyme is crucial for energy generation in hydrogen-oxidizing chemolithotrophs. These enzymes catalyze the oxidation of H₂:

H₂→2H⁺+2e⁻

The released electrons (e⁻) are then passed into the electron transport chain (ETC). As electrons flow through the ETC:

• A proton motive force (PMF) is generated across the membrane.
• This PMF drives ATP synthesis via ATP synthase (oxidative phosphorylation).

In addition, hydrogenase enzymes also contribute to the generation of reducing power (e.g., NADH or NADPH), which is essential for:

• Carbon fixation (e.g., via the Calvin cycle in autotrophs)
• Other biosynthetic reactions

Hydrogen oxidizing bacteria are both gram-positive and gram-negative. The best studied genera of this group of bacteria are Ralstonia, Pseudomonas, Paracoccus, and Alkaligenes; others are Acidovorax, Aquaspirillum, Hydrogenophaga, Hydrogenobacter, Bacillus, Aquifex, and Mycobacterium.  

Almost all hydrogen-oxidising bacteria are facultative chemoautotrophs, i.e, they can also grow chemoheterotrophically (chemoorganotrophically) with organic compounds as energy source.

This means that the hydrogen-oxidising bacteria can switch between chemoautotrophic and chemoheterotrophic (chemoorganotrophic) modes of metabolism and generally do so whenever required. This is a major distinction between hydrogen oxidising bacteria and many sulphur-oxidising bacteria or nitrifying bacteria; most of the isolates from latter two groups are obligate chemoautotrophs.

 Hydrogen-oxidizing bacteria have been isolated from a variety of environments, including fresh waters, sediments, soils, activated sludge, hot springs, hydrothermal vents and percolating water. Hydrogen-oxidizing organisms, such as Cupriavidus necator (formerly Ralstonia eutropha), often inhabit oxic-anoxic interfaces in nature to use hydrogen produced by anaerobic fermentative organisms while still maintaining a supply of oxygen.

Helicobacter pylori 

 H. pylori, is a Gram-negative, microaerophilic bacterium found in the stomach, identified in 1982 by Barry Marshall and Robin Warren. It was present in patients with chronic gastritis and gastric ulcers, conditions that were not previously believed to have a microbial cause.

More than 50% of the world’s population harbor H. pylori in their upper gastrointestinal tract. Over 80 percent of individuals infected with the bacterium are asymptomatic.  It can lead to the development of duodenal ulcers and stomach cancer.

Helicobacter pylori is a hydrogen oxidizing (H₂-oxidizing) bacterium, also known as a Knall-gas bacterium. It utilizes hydrogenase to oxidize molecular hydrogen, produced by other intestinal bacteria, as an energy source for its respiration and survival. This allows H. pylori to colonize the stomach and contributes to its ability to cause chronic inflammation and gastritis and stomach cancer. 

Source of Hydrogen: H. pylori obtain hydrogen from the fermentative metabolism of other intestinal bacteria. 

Hydrogenase Enzyme: The bacterium contains a specific enzyme called hydrogenase, which is responsible for oxidizing the molecular hydrogen. 

Energy Production: This oxidation process generates energy for the bacterium, allowing it to meet its metabolic needs. 

Role in Virulence: The hydrogen oxidation pathway, provides H. pylori with a high-energy non-carbon substrate. While most H₂-oxidizing bacteria can use carbon dioxide to fix carbon, H. pylori does not use the Calvin cycle. Instead, it uses organic carbon from its environment, making it a mixotroph. 

 

Hydrothermal vents

H₂ is an important electron donor in hydrothermal vents. In this environment hydrogen oxidation represents a significant origin of energy, sufficient to conduct ATP synthesis and autotrophic CO₂ fixation, so hydrogen-oxidizing bacteria form an important part of the ecosystem in deep sea habitats. The oxidation of sulphide and hydrogen is important among the main chemosynthetic reactions that take place in hydrothermal vents.

Uses

Given enough nutrients, H₂, O₂ and CO₂, many Knallgas bacteria can be grown quickly in vats using only a small amount of land area. For example, the polyhydroxybutyrate producing  Knallgas bacteria can be used to produce biodegradable plastics. Solar Foods is a startup that uses knallgas bacteria to grow a neutral-tasting, protein-rich food source such as artificial meat. Research studies have suggested that knallgas cultivation is more environmentally friendly than traditional agriculture.

 

 Methanogenesis 

Methanogenesis, or biomethanation, is an anaerobic respiration resulting in the production of methane by the reduction of CO₂ to CH₄ and uses carbon as the terminal electron acceptor, H₂ is commonly used as electron donor however, formate, CO₂ and even certain organic compounds such as alcohol may also be used as electron donors.

Methanogenesis (methane production) is characteristic to a group of obligate anaerobic archaea (archaebacteria) called the methanogens (e.g., Methanobacterium, Methanobrevibacter, Methanococcus, Methanogenium, Methanospirillum, Methanomicrobium, etc.).

Methanogenesis thus involves the anaerobic conversion of carbon compounds to methane and typically follows four steps: hydrolysis, acidogenesis, acetogenesis, and methanogenesis. During hydrolysis, complex organic matter is broken down, followed by acidogenesis to produce volatile fatty acids. Acetogenesis converts these fatty acids into acetate. Finally, methanogens (archaea) utilize acetate, CO₂, and hydrogen gas to produce methane. 

The reduction of CO₂ to methane can be summarised in the following way

1. Hydrolysis:

Complex organic matter (proteins, carbohydrates, lipids) are broken down into simpler, smaller molecules, such as sugars, fatty acids and amino acids, by hydrolytic bacteria e.g., Clostridium spp.

2. Acidogenesis:

Acidogenic bacteria further break down the simpler organic compounds into volatile fatty acids (VFAs), alcohols, H₂, and CO₂. e.g., Bacteroides, Lactobacillus. 

3. Acetogenesis:

Acetogenic bacteria convert the volatile fatty acids, alcohols and other products from the previous steps into acetate, carbon dioxide, and hydrogen gas. Acetogenic bacteria include Syntrophomonas, Syntrophobacter etc.

    Acetogenic bacteria occur in syntrophy with methanogens - hydrogen must be kept at low levels for the reaction to proceed efficiently. The ratio of acetogenic bacteria and methanogens are critical to have a good yield of methane.

4. Methanogenesis:

This is the final step, carried out by methanogenic archaea. They consume the acetate, CO₂, and H₂ produced in the earlier stages to generate methane. 

There are three primary types of methanogenesis, depending on the substrates used by methanogens:

• Hydrogenotrophic methanogenesis: Methanogens reduce CO₂ with hydrogen gas (H₂) to produce methane. eg., Methanobacterium 

CO₂ + H₂ → CH₄ + H₂O (Hydrogenotrophic pathway)

• Aceticlastic methanogenesis: Methanogens cleave acetate into methane and CO₂. eg., Methanosarcina and Methanotricha

CH₃COOH → CH₄ + CO₂ (Acetoclastic pathway)

 

• Methylotrophic methanogenesis: Methanogens convert methylated compounds, such as methanol or methylamines, into methane. eg., Methanomethylovorans 

Methyl compounds → CH₄ (Methylotrophic pathway)

 

Ecological Role of Methanogens:

• Key players in anaerobic ecosystems – they remove end products like H₂ and acetate, allowing upstream fermentative and syntrophic processes to continue.
• Major contributors to global methane emissions, influencing climate change.
• Used in biogas production for renewable energy (methane as fuel).

The process of methanogenesis is crucial for the degradation of organic matter in anaerobic environments, such as wetlands, animal digestive tracts, landfills and anaerobic digesters used in waste treatment. The production of methane is the final step in the decomposition of biomass in most environments. Without methanogenesis, a great deal of carbon (in the form of fermentation products) would accumulate in anaerobic environments.

Biogenic methane can be collected and used as a sustainable alternative to fossil fuels.

Methanogenesis also occurs in the guts of humans and other animals, especially ruminants. In the rumen, anaerobic organisms, including methanogens, digest cellulose into forms usable by the animal. Without these microorganisms, animals such as cattle would not be able to consume grass. The useful products of methanogenesis are absorbed by the gut. Methane is released from the animal mainly by belching. The average cow emits around 250 liters of methane per day. 

Methane is one of the earth’s most important greenhouse gases, with a global warming potential 25 times greater than carbon dioxide. Therefore, the methane produced by methanogenesis in livestock contributes to global warming.