A review on biological carbon sequestration: A sustainable solution for a cleaner air environment, less pollution and lower health risks

6.2.1 Bacteria

Bacteria are unicellular, a microscopic organism with 19 groups. Most of them fall under the following groups: Actinomycetes, Mycoplasma, Rickettsia’s, Archaebacteria, Cyanobacteria and Eubacteria etc. Among these six groups, the Archaebacteria, Cyanobacteria, and Eubacteria are autotrophic, which fixes CO₂ for organic carbon production.

1. Clostridium

Anaerobic gram-negative bacteria were playing a substantial role in degrading organic carbon materials, acid synthesis and carbon cycle (Migliardini et al., 2014). Various species are chiefly involved in the bio-fixation of CO₂ such as Clostridium autoethanogenum, Clostridium pasteurianum, C. formicoaceticum, Acetobacterium woodi, Clostridium thermoaceticum incorporates atmospheric carbon dioxide into acetyl-CoA through Wood–Ljungdahl pathway/Reductive acetyl CoA pathway which is the direct and most effective thermodynamic pathways (Tracy et al., 2012). The energy required for the fixation of CO₂ is obtained from the hydrogen molecules. Carbon monoxide dehydrogenase and acetyl CoA synthetase are the two enzymes that play a chief role in acetyl-CoA synthesis by converting carbon monoxide into carbon dioxide (Liew et al., 2016; Fast and Papoutsakis, 2012; Ezeji et al., 2007; Ni and Sun, 2009). This bacterial sp. cannot survive atmospheric O_2, a major disadvantage (Qureshi et al., 2007). Clostridium thermoaceticum was the first model used to study this pathway.

1. Proterobacterium

Proteobacteria are large phyla which are capable of incorporating atmospheric carbon dioxide via various biological mechanism such as the calvin cycle/reductive pentose phosphate cycle, TCA cycle/Krebs cycle and also directly in the cytoplasm (Paoli and Tabita, 1998; Ding and Yokota, 2004; Hügler et al., 2003). Calvin cycle is used by the following species Oligotropha carboxidovorans, Rhodobacter sphaeroides, Xanthobacter flavus, Rhodobacter capsulatus, Beta proteobacter, Ralstonia eutropha, Herbaspirillum autotrophicum, and Gama proteobacter, Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans, Hydrogenovibrio marinus etc. (Yoshizawa et al., 2004; Wang et al., 2008; Brigham et al., 2011; Albuquerque et al., 2011). Some of the bacterial spp. are used to synthesize commercial products such as biopolymers and medicine (Hügler et al., 2005; Willey et al., 2008). In the cytoplasm of R. eutropha, polyhydroxy alkanes are produced by utilizing CO₂. Sulphur reducing bacteria such as Desulfobacter hydrogenophilus (delta-proteobacteria) and Thiomicrospira denitrificans (epsilon-proteobacteria) utilizes CO₂ and H₂O to produce organic materials through the TCA cycle in which the ATP-citrate lyase splits acetyl-coA and oxaloacetate.

6.2.2 Archaea

Archaea is a unicellular, prokaryotic microbe termed as extremophiles and surviving under intense ecological extremities such as high fluctuating temperature, pH, and absence of O₂. Archaea has three different groups, halophiles (ability to withstand higher salt), thermoacidophiles and methanogens. The methanogens produce biofuel-methane under an anaerobic environment by utilizing CO₂ as raw material and energy obtained from hydrogen for the bioconversion process (Rittmann et al., 2015; Demirel and Scherer, 2008). Two types of methanogens are commercially used to produce methane; they are the acetoclastic and hydrogenotrophic methanogens. These methanogens potentially bioremediate wastewater and capture CO₂; hence they can be used to generate methane from the sludge through the utilization of CO₂ as well as to bioremediate wastewater for recycling and it includes Methanobacteriaceae, Methanospirrillaceae, and Methanosarcinaceae spp (Mohd Yasin et al., 2013, 2015). The 3-hydroxypropionate-4-hydroxybutyrate cycle pathway is used to fix atmospheric CO₂ by Cenarchaeum, Archaeoglobus, and Metallosphaera and Sulfolobus, sp (Berg et al., 2007). Two acetyl-CoA and one bicarbonate molecule are used to produce succinyl-CoA, which undergoes 4-hydroxybutyrate pathway to generate two molecules of acetyl-CoA. In this pathway, Acetyl-CoA/Propionyl-CoA carboxylase is the enzyme that actively fixes atmospheric CO₂ into biomolecules. Thermophilic methanogens produce carbonic anhydrase enzyme to produce methane, which can be used in large scale industries (Smith and Ferry, 2000; Henstra et al., 2007).

6.2.3 Cyanobacteria

Cyanobacteria are prokaryotic, blue-green bacteria or algae serving as a connecting link between bacteria and green plants. They are photoautotrophic gram negative bacteria present in both microscopic and macroscopic forms. They possess carboxysomes in their cytoplasm for carbon fixation. Some of the microorganisms, such as photoautotrophs and chemoautotrophs, have carboxysomes e.g., Bacteria and all cyanobacteria, resulting from an adaptation called the Carbon dioxide Concentration Mechanism (CCM). It is involved in Calvin -Benson cycle. The two enzymes RuBisCO and carbonic anhydrase are enclosed in bacterial microcompartments called carboxysomes located in the cytosol. There are two types of carboxysomes, the alpha carboxysomes with RuBisCO form IA and beta carboxysomes with RuBisCO IB. The alpha carboxysomes exist in all alpha-cyanobacteria, most of the chemoautotrophs and in some purple bacteria, but the beta carboxysomes are only seen in beta-cyanobacteria.

6.2.4 Algae

Algae is the most efficient photosynthetic biofactories that incorporate CO₂ into biomass and energy. They range from macro to micro size. Macroalgae produce high lipid content; hence they are directly used to extract for biodiesel production. Micro-sized algae include cyanobacteria, diatoms, euglenoids, green, blue, red, brown, golden, yellow coloured algal species and they have huge potential to fix CO₂ enzymatically by using RuBisCO in the Calvin–Benson cycle.eg. About 1 kg of micro-sized algae fixes 1.84 kg of atmospheric carbon dioxide. The carbon dioxide fixed by anabaena is 1.46 g/L/d and 6.24 g/L/d by Chlorella vulgaris. They utilize CO₂ to produce biomass and bioenergy (Chen et al., 2009). Cultivating these algae very close to the emitting sources can chiefly reduce elevated CO₂ levels and produce huge quantities of biomass and bioenergy (Cheah et al., 2015). Selection of algal species, optimal growth parameters and proper feedstock are the factors that should be taken into considerations before cultivation practices to obtain the maximum yield (Ghorbani et al., 2014). Perfect algal species should possess the following characters to achieve maximum CO₂ bio fixation and yield. The ability to capture carbon and rate of incorporation should be extreme. It should tolerate maximum CO₂ stress, proper utilization of limited nutrients, and tolerance to fluctuation in thermal and H+, OH− parameters (Rahaman et al., 2011). Algae, which are ideal for maximum carbon capture and fuel production like Botryococcus braunii, Scenedesmus obliquus, Nannochloropsis oculate, Chlorella vulgaris (Pires et al., 2012; Brilman et al., 2013; Singh and Ahluwalia, 2013). The algae Scenedesmus dimorphus was found to be tolerating up to 20% (v/v) of CO₂ stress even though its optimal level to biofix CO₂ was only 2%(v/v). This indicates that the amount of CO₂ to which the algae were exposed would significantly reflect the bioconversion rate and yield. This clearly showed that the tolerance to high CO₂ content by the Chlorella sp is remarkably extreme (Jiang et al., 2013). They show extreme tolerance to CO₂ content, which is up to 40–41% under the temperature and pH of 30 °C and 5–6, respectively (Chen et al., 2014). Nannochloropsis spp. were found to be grown at a rate of 58% with a CO₂ stress of 15% (v/v) (Jiang et al., 2011). It has been reported that a high concentration of carbon dioxide can significantly endorse the rate of photosynthetic CO₂ bio fixation in a short duration and more than 5% (v/v) becomes toxic. Also, the Continuous injection of an elevated level of CO₂ in the culture media inhibits the algal growth (Lee et al., 2000). Calvin Benson pathways are used for carbon fixation in algae. Production of 3-phosphoglycerate takes places through the carboxylation of ribulose 1,5-biphosphate by the catalytic activity of RuBisCO enzyme there by two molecules from which one enters the central metabolism and the other is exploited to continue the cycle.

Microalgae have an adaptation to increase the CO₂ concentration in the surrounding of the enzyme RuBisCO to fix more inorganic carbon and such adaption involves the Carbon Concentration Mechanism CCM (Atomi, 2002). This mechanism is majorly based on a key reaction in which carbon dioxide and bicarbonates' transportation takes place actively there by separating the RuBisCO through single to the multi-layered membrane. This adaptation is seen in all algae and cyanobacteria (Parry et al., 2003). In Cyanobacteria, it involves the transportation of carbon dioxide or bicarbonate inside the functional units of a chloroplast or cell membrane (Kaplan and Reinhold, 1999). Bicarbonate molecules are transported into the cytoplasm cytosol through various carrier molecules, taking place irrespectively to the periplasmic exclusion of dissolved inorganic carbon (DIC). This is reaction is followed by the diffusion of bicarbonates into carboxysomes where the carbonic anhydrase CA enzyme actively takes place in the cytosol (Raven and Beardall, 2003). This mechanism facilitates increased carboxylation activity of rubisco over the oxygenation reaction resulting in photorespiration (Lane and Morel, 2000). In this mechanism, four subsequent reactions are involved and they are the transportation and utilization of carbon dioxide and bicarbonates, separation and concentration of RuBisCO in specific micro-chamber and confined CA activity (Price et al., 2002; Wigmosta et al., 2011; Venteris et al., 2013, 2014). Algal bio-refineries should be located on wastewater bodies as recycling and restoration (Gong and You, 2014).

The following species are the most promising algae used for lipid-based biofuel production (Chisti, 2008; Damiani et al., 2010; Mandal and Mallick, 2009) including Botryococcus, Neochloris oleoabundans, Dunaliella, Chlorella, Scenedesmus spp, Haematococcus pluvialis, Scenedesmus obliquus, Chlorella sorokiniana, Chlamydomonas reinhardtii, Botryococcus braunii and diatoms such as Phaeodactylum tricornutum, Navicula pellicusa, Chaetoceros eg. Chaetoceros muelleri, Chaetoceros gracilis, Cyclotella cryptica, Navicula saprophila were noted for their high lipid content (Dayananda et al., 2006; Hu et al., 2008; Pratiwi et al., 2009; Mata et al., 2010).

Macroalgae or seaweed also utilizes a high amount of atmospheric CO₂ to produce biomass and energy. They produce high amounts of carbohydrates with low lipid content; hence they are used as feedstock for biofuel based on fermentation process such as bioethanol, methanol, and isobutanol etc. Laminaria sp were found to produce carbohydrates over 65%, including Laminaria hyperborea, Sacchorhiza polyschides, Laminaria digitata, Alaria esculenta and Saccharina latissimi. Among different macroalgal species, the Ulva and Laminaria were found to be the most potent bioenergy producers Ulva lactuca, Enteromorpha intestinalis, and Catenella repens, Sargassam wightii, Kappaphycus alverezzi, Ulva lactuca, Gracilariopsis longissima, Chaetomorpha linum contains a high amount of lipids (Bastianoni et al., 2008; Muralidhar et al., 2010). As a result of CO₂ utilization, algae ranks first compared to any other microorganism in carbon sequestration (Fig. 1).

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Fig. 1

Microalgal carbon sequestration and its byproducts.

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6.2.5 Fungi

Fungi are the eukaryotic, multicellular organism with a rigid cell wall. They are heterotrophic and serve as primary decomposers and chief organisms to capture carbon in the terrestrial ecosystem. Based on decomposing organic matter, they are categorized into two groups, saprophytic and mycorrhizal fungi. Saprophytic fungi produce enzymes to decompose substances such as cellulose, hemicellulose, pectin and lignin, etc which are responsible for mineralization and carbon cycle and the decomposition by mycorrhizal fungi is low due to the lack of enzyme (Ahmed et al., 2019). Mycorrhizal fungi form a symbiotic association with plants and exist in three forms, including ectomycorrhizal, arbuscular mycorrhizal form and ericoid mycorrhizas only found in plants belonging to the order Ericales.

6.2.5.1

6.2.5.1 Mechanism

Fungi facilitate carbon sequestration in soil by forming organic humus and maintain the carbon balance, thereby contributing CCS largely in the terrestrial ecosystem when compared to bacteria (Fig. 2); three methods involved in soil carbon storage, including recalcitrant biomass and their secondary products, producing soil aggregate and incorporation of atmospheric CO₂ into fungal biomass. The mycelium acts as a storage site for the carbon. Thus a large amount of biomass is produced by efficiently incorporating CO₂ at a higher percentage.

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Fig. 2

Carbon Sequestration of fungi in soil.

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6.2.6 Yeast

Yeast is a unicellular microorganism widely used for fermentation in the large-scale industries to obtain various commercial products. Saccharomyces cerevisiae is the yeast strain widely used for the fermentation process. During fermentation, carbon dioxide is liberated as exhaust gas due to microbial respiration and a large amount of O₂ is utilized. The mechanism observed in yeast was Glyoxylate and Krebs cycle. Yeast absorb carbon from a variety of carbon-based components such as sucrose, maltose, galactose, lactate, glycerol, ethanol, acetate, and oleate etc, e.g., carbon from glycerol is utilized with cytoplasmic kinase to form glycerol-3-phosphate before reaching the mitochondria. It is further converted into dihydroacetone phosphate in the mitochondria by FAD-dependent glycerol-3-phosphate dehydrogenase enzyme, which enters the glycolytic pathway.

6.3.1 Yeast

Few strains of yeast other than Saccharomyces cerevisiae were found to be the understudy for genetic and metabolic modifications to improve CO₂ bio fixation. Methylotrophic yeast Pichia pastoris is a widely used yeast strain for protein and nucleic acid production; it utilizes methanol as a substrate and the mechanism involved is xylulose-5-phosphate pathway. This pathway occurs in peroxisome and very analogous to the Calvin Benson cycle. The xylulose-5-phosphate pathway has been genetically modified to improvise the production of biomass through CO₂ fixation by recombing it to the CO₂ fixation pathway. The modification includes the deletion of three genes responsible for methanol utilization and the integration of eight new genes to produce enzymes such as RuBisCO and PRK (phosphoribulokinase) involved in CBB pathway. Two genes, the DAS1 and DAS2 were removed to block the methanol utilization metabolism. As a result, the methanol would serve as an electron donor during the oxidation of formaldehyde. The yeast plasmid was genetically modified and the resulting strain showed expected results positively through efficient CO₂ fixation. As a result, the nutrition of Pichia pastoris was modified into chemoorganoautrophic from its original chemoheterotrophic mode.

6.3.2 Bacteria

Gong and You (2014) experimented with quantifying the amount of CO₂ bio fixated by the bacteria E. coli. For effective CO₂ fixation, the bacteria E. coli was genetically modified. Heterotrophic nutrition is modified by integrating genes, resulting in a CO2 fixing bypass pathway in the carbon central metabolic pathway, after incorporating genes responsible for producing the enzymes RuBisCO and PRK involved in Calvin Benson cycle. After incorporation of the metabolic flux, recombinant plasmid into E. coli strain, the CO₂ fixation was reported to be improved at a rate of 13% compared to the central metabolism. After integrating recombinant plasmid with carbonic anhydrase enzyme of CCM mechanism, the resultant E. coli strain showed improved CO₂ fixation at a rate of 17%. The resultant amount of CO₂ fixed by this E. coli was reported to be 19.6 mg CO₂ L⁻¹h^−1, which is equal to CO₂ fixated naturally by autotrophic algae and cyanobacteria.

6.3.3 Algae

Some of the autotrophic algae are recently understudies for genetic modification to improve biomass production via improved CO₂ bio fixation. The following algal species genome has been sequenced and some of them are under the process of recombinant studies to improve biomass production. It includes Chlamydomonas reinhardtii, Phaeodactylum tricornutum, Thalassiosira pseudonana, Cyanidioschyzon merolae, Ostreococcus lucimarinus, Ostreococcus tauri, Micromonas pusilla. Fragilariopsis cylindrus, Pseudo nitzschia, Thalassiosira rotula, Botryococcus braunii, Chlorella vulgaris, Dunaliella salina, Micromonas pusilla, Galdieria sulphuraria, Porphyra purpurea, Volvox carteri, and Aureococcus anophageferrens are still under research.