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COJ Reviews & Research

Microbial Mediated Soil Carbon Sequestration and Mitigation of Green House Gases

Pooja Arora* and Smita Chaudhry

Institute of Environmental Studies, India

*Corresponding author:Pooja Arora, Institute of Environmental Studies, Kurukshetra University, Kurukshetra, Haryana, India

Submission: July 06, 2021; Published: August 19, 2021

DOI: 10.31031/COJRR.2021.03.000562

ISSN 2639-0590
Volum3 Issue3


Anthropogenic development activities have resulted in rapid global climate change. The effects of increasing surface temperatures are evident from unprecedented loss in plant and animal species. However, microbial life has not been well discussed in context of climate change. The present review has been done to understand the basic processes that soil microbial communities carry out in context of climate change such as microbial mediated soil carbon sequestration and mitigation of greenhouse gases. Soil microbes play a crucial role in decomposition of organic matter and soil respiration processes that are fundamental in sequestering carbon in the soil and CO2 emissions from the soil. The emissions of other important greenhouse gases such as methane and nitrous oxide are also mitigated by microbial actions. The mitigation of methane is brought about by its oxidation by methanotrophic bacteria while that of nitrous oxide is achieved by manipulating soil microbiome in situ along with manipulation in biotic and abiotic factors in soil. Hence, an understanding of the role of soil microbes as both contributors to and reactive components of climate change is much needed to clarify their roles whether they can be used to mitigate the emissions of GHGs or accelerators of climate disaster at the macroscopic level and even at the global scale.

Keywords: Soil microbes; Carbon sequestration; Climate change; Mitigation; Greenhouse gases; Carbon dioxide; Methane; Nitrous oxide


Earth’s environment has been undergoing changes due to increasing human population and its activities. The most significant change is the increase in concentration of carbon dioxide and other greenhouse gases in the troposphere resulting in increase in average surface temperature of Earth. The change in climate is the result of continuous but nonlinear interaction among components of the climate system at varying time scales (minutes to billions of years). But the “enhanced greenhouse effect” and resulting rapid global climate change is posing great threat to the well-being of humankind and other life forms on the earth as evident from unprecedented loss in plant and animal species. By contrast, microbial life has not been well discussed in context of climate change.
Although invisible to the naked eye, the abundance and diversity of microorganisms is very crucial in determining the resilience of many organisms and ecosystems and thereby their ability to respond to changing climate scenarios. A typical soil sample may contain more than 106 individual species-level Operational Taxonomic Units of Bacteria, Archaea, and Fungi Fierer et al. [1]. Estimation of soil microbial communities and biomass is of fundamental importance to study a wide range of soil processes such as nutrient cycling, organic matter decomposition, soil quality, soil respiration and mineralization. Hence, microbes can be viewed as the engines that drive these processes.
Climate Change mitigation necessitates the management of terrestrial carbon (C) by creating new C sinks and also by preserving and enhancing the existing ones. Carbon capture in living biomass, in soil (roots and microbes) and recalcitrant organic and inorganic carbon all in terms of carbon sequestration is one such option. Even the seasonal variations of soil microbial biomass as a potential stock of carbon reflect the degree of immobilization and mineralization of soil carbon Chaudhry [2]. Microbial diversity in different ecosystem has many contributions in controlling the climate change and combating its negative impacts owing to their amazingly versatile metabolism and ability to flourish in broad environmental conditions.

Microbial Mediated Soil Carbon Sequestration

Soil micro-organisms have a crucial role in cycling of the nutrients, promoting and accelerating the decomposition of the organic matter, the release of nutrients contained therein and précising the processes that control the flow of these nutrients to plants and hydrological & gaseous losses to surrounding environments. The dominating factor in the terrestrial carbon cycle is the balance between two processes of photosynthesis and respiration. Autotrophic organisms, especially photosynthesizing plants, and also photo and chemoautotrophic microorganisms fix atmospheric carbon dioxide (CO2) into organic material (Figure 1); [3] which is then returned back to atmosphere via autotrophic and heterotrophic respiration and decomposition pathways. Decomposition is carried out by ‘organic carbon-consuming’ heterotrophic microorganisms that feed on carbon of either plant, animal or microbial origin as a substrate. Some amount of this carbon is retained in their biomass while the rest is released as metabolites or as CO2 back to the atmosphere. In this way, soil microorganisms directly regulate the amount of organic carbon stored in soil and released back to the atmosphere. They also indirectly influence carbon storage in plants and soils by providing macronutrients (N & P) to regulate productivity Singh et al. [4], Bardgett [5]. Further, in many ecosystems, mycorrhizal fungi are responsible for substantial amounts of nitrogen and phosphorus acquisition by plants Fellbaum et al. [6].

Figure 1: Microbial mediated terrestrial carbon cycle Gouglias C et al. [3].

Therefore, many studies suggest that soil microorganisms have a key role in controlling formation, decomposition and accumulation of Soil Organic Matter Mellado-Vazquez et al. [7]; Liang et al. [8]; Cotrufo et al. [9]; Lange et al. [10]; Balser [11]; Gleixner et al. [12]. In vice versa situation, plant derived C resources largely influence the soil microbial activity apart from other factors such as soil temperature, soil humidity or pH Voroney [13]. Also, the impact of different photosynthetic pathways on the microbial community may be triggered by confounding effects of other environmental parameters Chen et al. [14].

Decomposition of Soil Organic Matter

Soil Organic Matter (SOM) consists of fresh to progressively decomposing plant, microbial and faunal-derived debris and exudates. The microbial biomass, responsible for primary decomposition of these materials also forms a part of Soil Organic Matter. The process of decomposition starts with complex plant detritus and other organic matter producing carbon gases and humus (Figure 2); [15]. The process can efficiently be characterized by the rate of mass loss, and rates of nutrient immobilization and release into the soil. The decomposition process can be distinguished in three phases: early, late and humus-near stage. In the early stage, decomposition of soluble, unshielded cellulose and hemicelluloses takes place. The process is influenced by climate. In the late stage, the influence of climate on decomposition gradually decreases to essentially zero. Also, negative influence of N on lignin degradation may come into effect through a repression of de novo ligninase synthesis. In final, humus-near stage, the decomposition reaches a limit value. From the very onset of decomposition, the concentrations of Nitrogen and lignin increase (Figure 3); [16].
Soil microorganisms act as decomposers and indicators of soil quality by regulating the key process of soil carbon cycling, including lignin and cellulose degradation and soil carbon turnover Lei et al. [17]; Li et al. [18]; Sun et al. [19] and Mele [20]. Complex compounds such as lignin are degraded by enzyme oxidases, which are produced primarily by fungi while cellulose is degraded by hydrolases, produced primarily by bacteria in the soil You et al. [21]. The decomposition of litter and deadwood is a key step in biogeochemical cycling of carbon and nitrogen as it contributes to CO2 release Van Geffen et al. [22]. Litter and wood decomposition is considered to be mainly carried out by fungi and, to a lesser extent, by bacteria Allmer et al. [23]; Baldrian [24]; Bässler et al. [25]; Purahong et al. [26]; Tlaskal et al. [27]. However, bacteria are able to degrade lignin and catabolize side products being derived from incomplete degradation of litter by fungi Bugg et al. [28,29].
Decomposition proceeds through several steps whereby bacterial community shows a succession of colonizers with most abundant taxa of Proteobacteria, Actinobacteria and Bacteroidetes Purahong et al. [26], Tlaskal et al. [27]; Urbanová et al. [30] over the entire stages of litter decomposition. Similarly, fungal communities also undergo a clear succession process of different taxa which are able to decompose the available biopolymers Fukasawa et al. [31]; Purahong et al. [26], Voriskova [32]. Decomposition stage, type of soil organic matter or quality of litter (lignin or cellulose based), substrate size, physico-chemical properties of soil, soil structure and climate parameters control the decomposition process and hence, play a crucial role in determining the structure and composition of microbial community (bacteria and fungi) and most importantly the decay pattern of organic matter.
Global climate change is likely to intensify the decomposition rates when long-term warming occurs in the absence of moisture constraints. To understand the responses of ecosystems to future climate change in terms of shifts in biodiversity and biogeochemical cycling, it is crucial to understand and quantify the underlying controls on organic matter decomposition Salinas et al. [33].

Figure 2: a) Generalized pathways for transformation of litter to humus and inorganic C.

b) Stages in litter decomposition Berg and McClaugherty [15].

The + and - signs indicate positively and negatively related effects, respectively, to increased concentrations of nutrients and lignin.

Figure 3: Direct and Indirect effects of climate changes on soil microbial communities and feedback to global warming through carbon dioxide production (Based on Bardgett et al. [16].

Soil Respiration

Soil respiration is the production of CO2 from the soil when plant roots, microbes, and fauna respire. It is the second largest carbon flux between the land and atmosphere Raich [34]; Zhao et al. [35]. The largest share of these fluxes comes from humid tropical forest. It has been suggested that an increase of 3% in a tropical soil respiration of 1500gCm-2 per year is greater than a 20% increase in a tundra soil-respiration rate of 200gCm-2 per year Raich et al. [36].
Soil respiration is one of the largest elements of carbon cycling in forests Hashimoto et al. [37], main component of ecosystem respiration Granier et al. [38]; Janssens et al. [39], an important aspect of soil quality and an indicator of soil fertility Staben et al. [40]. These facts emphasize the accurate measurement of soil respiration as an essential component for understanding the carbon cycle in any ecosystems since small changes in soil respiration may strongly affect soil carbon sequestration. The rate of soil respiration is affected by many factors such as soil moisture and temperature, physico chemical properties of soil, soil microbial composition, vegetation composition and site productivity. For instance, in case of sufficient water availability, higher temperatures lead to faster decomposition of soil organic matter, less storage of carbon in the slow and passive pools, and greater loss of carbon through respiration Canadell et al. [41]. The type of vegetation alters the rate of soil respiration by influencing the quantity and quality of litter input into the soil that causes variations in soil metabolism.
Climatic factors such as temperature and rainfall also influence the rates of soil respiration. Soil respiration increases quickly following rain events in dry climates; however, temperature sensitivity of soil respiration helps in describing the changes in CO2 flux with respect to change in temperature Arora [42]. Soil respiration is often considered as the measure of total microbial activity in soil. Many studies have reported a significant correlation between soil respiration and soil microbial biomass carbon pool Dube et al. [43]; Iqbal et al. [44]; Wang et al. [45]. It is an important indicator of soil health because it represents the diversity of organisms occupying microhabitats throughout the soil profile, level of microbial activity, SOM content and its decomposition.
These microbial mediated decomposition and respiration pathways act as positive feedback to global warming and may also in turn be accelerated as a response to increase in atmospheric temperature. Since, soil respiration is considered to be the sum of heterotrophic and autotrophic respiration, the combined effect of microclimatic factors and anthropogenic activities can be modeled to advance the understanding of the concept. The merits of these estimations will be helpful in reflecting the important soil-toatmosphere CO2 efflux Chaudhry [42]. Increased flux of carbon to roots and soil due to elevated carbon dioxide can stimulate microbial activity. This stimulation intensifies the degradation of organic matter, thereby leading to carbon loss from soil.

Mitigation of Green House Gases

There are innumerable ways that soil microbes and their metabolic activity can affect climate change through land– atmosphere carbon exchanges. These can broadly be divided into two categories
a) the ways that affect ecosystem carbon dioxide and methane uptake, and
b) the ways that control carbon loss from soil through respiration and production of methane.
Also, changing climate influences soil microbial activity. Climate change has both direct and indirect effects on the activities of soil microbes. Direct effects include the influence on soil microbes, greenhouse gas production under variable conditions of temperature, precipitation and extreme climatic events. Indirect effects are climate-driven changes in plant productivity and diversity which alter soil physicochemical characteristics, carbon supply to soil, structure and activity of microbial communities involved in decomposition processes and carbon release from soil (Figure 3); [16].
The three most important greenhouse gases, CO2, CH4 and N2O occur naturally in the atmosphere and are produced in soils, sediments and waters through various microbiological processes. But due to anthropogenic developmental activities, the concentration of GHGs has increased substantially in the atmosphere resulting in accelerated climate warming. Microbial mediated mitigation of carbon dioxide can well be understood through the processes of organic matter decomposition and soil respiration as discussed earlier.
The major source of Methane is landfills where it is produced through the decomposition of organic wastes. Soil microbial activity acts as a sink for methane gas. The process follows the oxidation of CH4 into other forms of carbon by a class of microorganisms specifically bacteria known as methanotrophs. These methanotrophs utilize CH4 as its sole carbon and energy source in the presence of O2. It has been estimated that methanotrophic bacteria oxidize 10 to 100 % of the CH4 generated in landfills Borjesson et al. [46]; Chanton & Liptay [47]; Chanton et al. [48]; Czepiel et al. [49]; Liptay et al. [50] and Whalen et al. [51] making landfills to act as sink of CH4 rather than as its source Bogner et al. [52,53]. Hence, it can be inferred that stimulating the activity of these bacteria in landfill cover soils could possibly reduce emission of CH4 from landfills.
The stimulation of methane oxidation can be achieved through the application of nitrogen-based fertilizers Bodelier et al. [54]; De Visscher et al. [55], Mohanty et al. [56] as the nitrogenous fertilizers are used as nitrogen sources by the soil microorganisms. However, the drawback of this application is the production of yet another greenhouse gas, N2O. Methane-consuming microorganisms are actually capable of extracting atmospheric methane even at very low concentrations Zimmerman [57]. These microorganisms are found both in soil and also in aquatic habitats and at home. Hence, microbes contribute toward controlling methane emission which in turn regulates climate change.
Bacterial and fungal-mediated nitrification and denitrification are the key processes that account for approximately two-third of total N2O emissions from the soil predominantly due to the application of nitrogenous fertilizers Zhu et al. [58]. The abundance, diversity, community structure and biological pathways of the soil microbial communities (including ammonia oxidizers, bacterial and fungal denitrifiers) are affected by a wide range of biotic, abiotic and emerging global change factors and their interactions. Hence, any strategy that can enhance the plant capacity to readily uptake nitrogen from the soil and making it unavailable to microorganisms can substantially add to the mitigation of soil N2O emissions. The aim can be achieved through the development of three categories of technologies
a. physicochemical technologies (by manipulating soil abiotic factors),
b. plant community-based technologies (by manipulating soil biotic factors) and
c. microbiome-based technologies (by manipulating soil microbiome in situ) for future mitigation of climate change (Figure 4); [59].

Figure 4: The relationships and interactions among N-cycling microorganisms, biotic factors, abiotic factors, global change factors, mitigation strategies and dryland N2O emissions Redrwan from Hu et al. [61].


Climate change and warming have direct and indirect consequences on soil microbial communities Castro et al. [60] through modifications in various factors simultaneously. Such immense alterations can have considerable impacts on the soil microbiome as well as on plants and ultimately soil carbon balance. Soil microorganisms contribute significantly to the production and consumption of greenhouse gases, such as carbon dioxide (CO2), methane (CH4), nitrous oxide (N2O), and nitric oxide (NO). This contribution towards production of GHGs by microbes is further stimulated by anthropogenic activities such as waste disposal and intensive agriculture. The feedback responses of soil microbes to increasing GHGs concentration in atmosphere can accelerate or slow down global warming up to different unknown extent.
Hence, an understanding of the role of soil microbes as both contributors to and reactive components of climate change can help us determine whether they can be used to mitigate the emissions of GHGs or they will accelerate the speed of climate disaster at the macroscopic and even the global scale. Although various ecosystem specifically agriculture sector where productivity is very much dependent on soil microbial activity has been predicted to combat the adverse impacts of climate change till now, but in near future this situation may get reversed. Arora et al. [61]. This necessitates the implementation of appropriate measures to deal with the problems of changing and climate and their aftereffects on soil microbiome.
Microbes are involved in many processes, such as the carbon and nitrogen cycles, and are responsible for both the production and consumption of greenhouse gases such as carbon dioxide and methane. Microbes could have various positive and negative feedback responses to temperature, but the extent of these is not completely understood. The reason is that microbes live in very diverse communities that interact with other organisms and the environment in complex ways, which makes it difficult to make predictions about the effects of microbes on climate change, but scientists are trying to include microbial activity in climate change models. What is certain is that human activities have helped to increase the production of greenhouse gases by microbes.
Microorganisms have been changing the climate, and have been changed by the climate, throughout Earth’s history. As we experience unprecedented environmental impacts from climate change, microorganisms will respond, adapt, and evolve in their surroundings. Because they have generation times as short as a few hours, they will do so at higher rates than most other organisms. This makes microbes ideal sentinels for understanding the effects of climate change on biological systems and the global biogeochemical cycles that microbes mediate. Scientists can study the effects of climate change on microbes to both understand and hopefully predict the future effects of climate change on all forms of life. This colloquium brought together members of the American Society for Microbiology and the American Geophysical Union because understanding climate change impacts requires experts from many scientific disciplines. The collaboration between these two societies intermingled scientists knowledgeable about microbial contributions and responses to climate change across global settings (terrestrial polar regions; soil, agriculture, and freshwater; oceans) and able to think broadly about the functions of microbiomes. Although scientists have been studying microbial ecosystems for many years, we realize we have much more to learn and understand about complex and interconnected microbial functions. The information in this report reflects the current understanding of microbes and our changing climate, as well as gaps and priorities for future study.
More than 30 microbiologists from 9 countries have issued a warning to humanity -- they are calling for the world to stop ignoring an ‘unseen majority’ in Earth’s biodiversity and ecosystem when addressing climate change. ‘Scientist’s warning to humanity: microorganisms and climate change’ was published today in the journal Nature Reviews Microbiology. Professor Rick Cavicchioli, microbiologist at the School of Biotechnology and Biomolecular Sciences at UNSW Sydney, has led the global effort. With their statement, the researchers are hoping to raise awareness both for how microbes can influence climate change and how they will be impacted by it -- calling for including microbes in climate change research, increasing the use of research involving innovative technologies, and improving education in classrooms. “Microorganisms, which include bacteria and viruses, are the lifeforms that you don’t see on the conservation websites,” says Professor Cavicchioli.
“They support the existence of all higher lifeforms and are critically important in regulating climate change.
“However, they are rarely the focus of climate change studies and not considered in policy development.”
Professor Cavicchioli calls microbes the ‘unseen majority’ of lifeforms on earth, playing critical functions in animal and human health, agriculture, the global food web and industry. For example, the Census of Marine Life estimates that 90% of the ocean’s total biomass is microbial. In our oceans, marine lifeforms called phytoplankton take light energy from the sun and remove carbon dioxide from the atmosphere as much as plants. The tiny phytoplankton form the beginning of the ocean food web, feeding krill populations that then feed fish, sea birds and large mammals such as whales.
Sea ice algae thrive in sea ice ‘houses’. If global warming trends continue, the melting sea ice has a downstream effect on the sea ice algae, which means a diminished ocean food web. “Climate change is literally starving ocean life,” says Professor Cavicchioli. Beyond the ocean, microbes are also critical to terrestrial environments, agriculture and disease. “In terrestrial environments, microbes release a range of important greenhouse gases to the atmosphere (carbon dioxide, methane and nitrous oxide), and climate change is causing these emissions to increase,” Professor Cavicchioli says. “Farming ruminant animals releases vast quantities of methane from the microbes living in their rumen -- so decisions about global farming practices need to consider these consequences.
“And lastly, climate change worsens the impact of pathogenic microbes on animals (including humans) and plants -- that’s because climate change is stressing native life, making it easier for pathogens to cause disease. “Climate change also expands the number and geographic range of vectors (such as mosquitos) that carry pathogens. The end result is the increased spread of disease, and serious threats to global food supplies.” Greater commitment to microbe-based research needed. In their statement, the scientists call on researchers, institutions and governments to commit to greater microbial recognition to mitigate climate change. “The statement emphasizes the need to investigate microbial responses to climate change and to include microbe-based research during the development of policy and management decisions,” says Professor Cavicchioli.
Additionally, climate change research that links biological processes to global geophysical and climate processes should have a much bigger focus on microbial processes. “This goes to the heart of climate change, so if micro-organisms aren’t considered effectively, it means models cannot be generated properly and predictions could be inaccurate,” says Professor Cavicchioli. “Decisions that are made now impact on humans and other forms of life, so if you don’t take into account the microbial world, you’re missing a very big component of the equation.” Professor Cavicchioli says that microbiologists are also working on developing resources that will be made available for teachers to educate students on the importance of microbes. “If that literacy is there, that means people will have a much better capacity to engage with things to do with microbiology and understand the ramifications and importance of microbes.”


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