Soil Microbial Dynamics in Carbon Farming of Agro-Ecosystems: In the Era of Climate Change


The backbone of life on the Earth, the carbon, cannot be ignored, and every living creature on the planet earth is made up of it (Kane 2015). Starting from the industrial period, the carbon cycle of the earth has been heavily troubled with the inputs of carbon dioxide mainly through fossil fuel combustion and with the conversion of natural ecosystems to agricultural lands (Canadell et al. 2007). The balance of carbon is maintained by the major biogeochemical cycle through the biotic and abiotic parts of an ecosystem. All the earth’s carbon is also prevented from entering the atmosphere and from being stored in the earth’s crust entirely, which make the earth’s temperature more stable. This stable thermostat system works over a few hundred thousand years as part of the slow carbon cycle (Riebeek and Robert 2011). The principal components of the global carbon cycle are the dynamics of soil microflora and its biome. To regulate the flow of materials to and from the atmosphere, hydrosphere, and pedosphere, key interactions between the biotic and abiotic components take place (Sharma et al. 2012). Besides the many-fold necessities of carbon, its balance has been entwined with a major serious problem, and we must be aware of it in terms of climate change. This state of imbalance in the global carbon cycle is largely due to the continuous industrial emissions of carbon dioxide and other greenhouse gases (GHGs), burning of fossil fuels, deforestation, and the land use system like the conversion of grassland and forestland to agricultural land, which have resulted in the historic losses of soil carbon (Kane 2015) to the atmosphere (FAO 2019). Therefore, the removal of carbon dioxide from the atmosphere or diversion from the emission source and its storage in terrestrial ecosystems and in oceans and other geological formation are necessary for the carbon sequestration process (Kambale and Tripathi 2010). The storage is a long-term technique in the reservoir pool, and soil, which is the largest terrestrial sink and also a larger potential sink, can store atmospheric carbon dioxide (Zomer et al. 2017). The carbon sequestration takes place in several ways such as reduction of global energy use, development of low or no carbon fuel, and sequestration from point sources or atmosphere by natural or engineering techniques (Schrag 2007). However, restoration of the lost soil carbon will not only benefit the environment, but also be given due importance to the producer’s bottom line. Moreover, carbon accumulation in the soil will promote soil particles’ aggregation, water retention, microbial activity, biogeochemical cycle, and other various processes of importance, thereby increasing the fertility and productivity (McDowell 2019). However, in the context of climate change, there is less attention given to the concept of carbon sequestration in agricultural ecosystems, which is supposed to be the alternative means in offsetting future emissions effect on the GHG concentrations in the atmosphere. In this chapter, the possible ways and the factors that impact the increased rate of removal of carbon dioxide from the atmosphere to accelerate the gigantic tasks, storing carbon through ecosystems like in plant material, decomposing detritus, and organic soil are overviewed. In this way, the soil of the agricultural lands which are highly productive ecosystems can become biological scrubbers through C02 sequestration from the atmosphere (Kaur et al. 2016). Furthermore, if we go down deep inside the soil ingredients, we found that all such chore duty of biological scrubbing for carbon farming mainly depends on microbial communities that fix the atmospheric carbon, promote the growth of plants, and enhance organic material transformation or degradation in the environment (Weiman 2015).


In the terrestrial biosphere, soil microbes are some of the smallest organisms in soil that have key roles in moving and transforming huge amounts of carbon compounds in their ecosystems. The organic carbons are found to lock in permafrost, which is in high latitude, grassland soil, tropical forests, and the agricultural ecosystems. On the other hand, the microbes play a great role in the determination of longevity and stability of carbon and in determining whether or not the carbon is released in the atmosphere as GHGs, which implies the importance of the processes involved in the carbon cycle (Weiman 2015). They also influence the fertility of the soil and the exchange of CO, and other gases within the atmosphere. Hence, they are the primary players within the soil food web and excellent indicators of soil health and functioning (Van Den Hoogen et al. 2019). In these integral components of the complex ecosystem-soil microbial communities, they are the hosting ground of fungal and bacterial dominances, protists, and animals (Bonkowski et al. 2009; Muller et al. 2016), and also mycorrhizal associations and microalgae. The aforementioned microbial organisms have been considered as the contributors of soil carbon sequestration. In the process of carbon sequestration, the soil microbes play an important role in the transformation of plant residues into smaller carbon molecules, and they are more likely to be protected and get sequestered in the soil (Six et al. 2006). Different types of carbon that are of different size and have complex chemical nature are produced at every point of the decomposition pathway. The carbons get associated with silt and clay particles and get incorporated into soil aggregates (Rao and Chhonkar 1998). The nutrient cycling is done in order to sustain the agricultural soil productivity as it is the source and sink for the mineral nutrition and biochemical transformations are being carried out (Jenkinson and Ladd 1981). The decomposition of organic matter produces nutrients that are assimilated by microorganisms and get incorporated into biomass. Also, microbes are immobilized in the soil biomass form or are mineralized (Wani and Lee 1995). Microbes are essential for breaking down and transforming the dead organic material into the forms that other organisms can use. This is the reason why the microbial enzyme systems that involved are known as the key ‘engines’ which drive the biogeochemical cycles of the earth

(Falkowski et al. 2008). Therefore, sequestering a vast amount of carbon which can improve the soil quality and help in benefitting the environment can happen when the microbial communities and environmental conditions that control the transformation of the organic carbon in the soil are understood.

Mechanism of Carbon Sequestration by Soil Microbes

The amount of carbon present in the Earth’s soil is more than the amount present in the atmosphere. It is the largest and most stable carbon reservoir in terrestrial ecosystems. Soil carbon sequestration is the process of removing CO, from the atmosphere and storing it in the soil carbon pool (Ontl and Schulte 2012). The carbon is transfer from the atmosphere to the soil by carbon fixing autotrophic organisms, which convert carbon dioxide into organic matter. These are driven mainly by the photosyn- thesizing plants and photo and chemoautotrophic microbes (Lu and Conrad 2005). Then, the fixed carbon is returned to the atmosphere through different pathways which account for respiration for both the autotrophic and heterotrophic organisms (Trumbore 2006).

The main factors that determine the amount of carbon sequestered in the soil are (i) input of organic matter rate, (ii) the decomposability of organic matter inputs, (iii) the depth at which the organic carbon is placed in the soil, and (iv) intra-aggregate or organo-mineral complexes during physical protection. The biotic activities of plants (which are the main source of carbon through litter and root systems), microorganisms (fungi and bacteria), and ‘ecosystem engineers’ (termites, ants, earthworms) alter the soil organic carbon (SOC) stocks. In the past, decomposition biotic processes were investigated at the levels such as molecular, organismal, and community (Sinsabaugh et al. 2002a, 2002b; Tate 2002). In the meantime, modification of these stocks is done by abiotic processes that are related to the physical structure, porosity, and mineral fraction of the soil (Marie-France et al. 2017). It is estimated that at least three times the carbon which is stored in the atmosphere is equivalent to the global organic carbon stocks in soil (Gougoulias et al. 2014). Annually, the terrestrial ecosystems and the atmosphere exchange about 8% of the total atmospheric carbon pool through a net primary production and respiration of terrestrial heterotrophic organisms (predominantly microbial) (Gougoulias et al. 2014). In other words, at current rates to exhaust atmospheric carbon stocks for primary production, it would take about 12years if soil microbial respiration stopped [(if all other components of the carbon cycle are ignored, e.g. oceanic CO, exchange) (Sylvia et al. 2005)].

More than 100 years ago, the emphasis of several co-workers was on microbes that are important for soil organic matter (SOM) synthesis (Waksman 1936). The SOM consists of the continuum from fresh to progressively decomposing plant, debris which are of microbes and fauna and exudates, including the microbial biomass, which is responsible for exudate primary decomposition and detrital inputs (Dungait et al. 2012). The role of microbes was thought to be restricted only to the decomposition of the plant and animal matter, but later, the role of microbes in the resynthesis of SOM was recognized (Waksman 1936). The quality and the quantity of organic matter are influenced by the soil microorganisms and again by the soil ecology and properties (Hashem et al. 2019). Increasing the SOC has two benefits: mitigating climate change and improving soil health and fertility. According to the soil, climate, landscape, and change in the same paddock over time depending on the climate and the farming methods, the amount of SOC present in the soil varies (Dignac et al. 2017). The multistep conversion of the dead plant tissues is mediated by the microbes and exudate organic compounds from plant roots into carbon dioxide or SOM. Reduction of carbon present in the atmosphere takes place if more amount is stored in the soil as SOC. This will also reduce global warming (Dignac et al. 2017).

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