TMCB 405: Soil Microbiology (3 Units; L30 P30)

Week 6: Nutrient cycling in nature

• Carbon transformations and soil organic matter formation
• Transformation of nitrogen, sulphur and phosphorus
Carbon transformations
The most important element in the biological realm is carbon because the chemistry of
all life forms is based on carbon. Carbon is the primary building block of life, including
DNA, proteins, sugars and fats. Carbon is found in all living things, soils, the ocean, and
atmosphere. One of the most important carbon compounds in the atmosphere is carbon
dioxide (CO2), while in rocks carbon is major component of limestone, coal, oil and gas.
Carbon cycles through the atmosphere, biosphere, geosphere, and hydrosphere via
processes that include photosynthesis, fire, the burning of fossil fuels, weathering, and
volcanism. Carbon cycling is the continuous transformation of organic and inorganic
carbon compounds by plants and micro- and macro-organisms between the soil, plants
and the atmosphere. A discussion of the transformations of carbon at the soil level is
best introduced from the view of the global carbon cycle. The global carbon cycle
describes the movement of carbon in and out of various reservoirs on Earth, including
the atmosphere, oceans, forests, and soils. Plants capture carbon dioxide from the
atmosphere through photosynthesis, converting it into organic carbon stored in plant
tissues. When plants die, their organic matter is transferred to the soil, where it can be
decomposed by microorganisms. Soil organisms, such as bacteria, fungi, and
earthworms, break down the plant material into smaller molecules, some of which are
rereleased as CO₂ through respiration (Fig. 1). Soil serves as a critical component of this
cycle, acting as both a source and a sink of carbon. On a global scale, soils store more
carbon than the atmosphere and all terrestrial vegetation combined. However, the
balance between carbon inputs (such as plant material) and outputs (such as microbial
respiration and decomposition) can vary based on numerous factors, including climate,
soil type, and land management practices. Soil organic matter is the fraction of the soil
composed of plant and animal residues at various stages of decomposition, along with
microorganisms, roots, and their by-products. It is a critical component of healthy soil,
playing a vital role in maintaining soil structure, fertility, and overall ecosystem health.
The amount of carbon contained in the soil organic matter of terrestrial soils is
approximately three to four times the content of carbon contained in the atmosphere.
The atmospheric concentration of carbon dioxide is traditionally given as 0.03%.
Concern has been expressed because the level of carbon dioxide in the atmosphere is
increasing.
Fig 1: Carbon cycle

Soil organic matter

Soil organic matter (SOM) refers to the collection of decomposed plant and animal
residues, microbial biomass, and humic substances that are found in soil. It plays a
crucial role in maintaining soil fertility, promoting healthy plant growth, and supporting
biodiversity. The primary components of SOM are particulate organic matter (POM),
humic substances (such as humic and fulvic acids), and microbial biomass, which
together contribute to soil structure, nutrient cycling, and water retention. Soil organic
matter is also of significant importance in the global carbon cycle. As plants
photosynthesize, they capture carbon dioxide (CO₂) from the atmosphere and convert it
into organic compounds. These compounds are then transferred to the soil when plant
materials (such as leaves, stems, and roots) decompose. Through this process, soils act
as carbon sinks, storing large amounts of carbon that would otherwise contribute to
atmospheric CO₂ levels, which is a key driver of climate change. Therefore,
understanding the formation and transformation of carbon in soil is essential not only for
soil science but also for environmental science and climate change mitigation.

Soil organic matter formation

The formation of soil organic matter begins with the input of organic material from plants
and animals. Plants contribute to SOM through their roots, which exude organic
compounds, and through the fall of plant litter (leaves, stems, and other plant parts).
Additionally, animal inputs, such as the decomposition of dead animals or their waste
products (e.g., manure), further contribute to SOM. Once organic material enters the
soil, it undergoes a process of decomposition. Decomposition is carried out by a variety
of soil organisms, including bacteria, fungi, and invertebrates such as earthworms.
These organisms break down the complex organic molecules into simpler compounds,
such as sugars, amino acids, and fatty acids. As decomposition progresses, some of the
carbon is released back into the atmosphere as carbon dioxide through microbial
respiration. The remainder of the organic matter is further transformed through a process
called humification. Humification is the transformation of decomposed organic material
into stable, long-lasting compounds known as humic substances. These substances,
which are highly complex and resistant to further decomposition, form the bulk of the
soil’s organic carbon pool, contributing to the long-term stability of SOM. Humus, the
end product of humification, has high nutrient and moisture holding capacities and plays
a critical role in soil structure by enhancing aggregation, improving aeration, and
reducing soil erosion.

Factors Affecting Carbon Transformations in Soil

Several factors influence the rate at which carbon is transformed in soil, including both
abiotic and biotic factors. Soil properties such as texture, structure, and pH play a
significant role in carbon transformations. Soils rich in clay tend to store more carbon
than sandy soils, as clay particles have a higher surface area, allowing for better
retention of organic matter. Soil structure, which refers to the arrangement of soil
particles into aggregates, affects how easily air and water move through the soil, which
in turn affects microbial activity. pH also influences microbial activity and
decomposition rates, with most microbes preferring neutral to slightly acidic conditions.
Climate factors such as temperature and precipitation are also crucial in determining
how carbon is cycled in soil. Higher temperatures generally accelerate microbial activity
and decomposition, leading to faster carbon turnover and potentially greater carbon loss
in the form of CO₂. Precipitation affects moisture availability, which can either enhance
or limit microbial activity. In areas with frequent droughts or waterlogging,
decomposition can be slowed, and the stability of SOM may increase, as microbial
processes are inhibited.
Human land management practices, such as tillage, crop rotation, and the use of
fertilizers, also impact soil carbon dynamics. Tillage, for example, breaks up soil
aggregates and exposes organic matter to oxygen, accelerating decomposition and
carbon loss. Conversely, practices such as no-till farming, crop rotation, and the
addition of organic amendments (e.g., compost, manure) can increase soil carbon
content by enhancing organic matter input and reducing decomposition rates. Soil
erosion, on the other hand, can lead to the loss of SOM, as wind or water removes the
topsoil, which contains the most organic material.
Microbial communities are essential for carbon cycling in soil. Different groups of
microbes have different capabilities in breaking down organic materials and shifts in
microbial communities can alter the rate of carbon decomposition. For instance, fungi
are more efficient at breaking down lignin (a tough structural component of plant cell
walls) than bacteria, while bacteria are generally more effective at breaking down sugars
and proteins. The diversity and activity of soil microbes can therefore have significant
effects on the amount and type of SOM formed in soils.
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Measuring and Monitoring Soil Organic Carbon
Accurately measuring and monitoring soil organic carbon is essential for understanding
how carbon is cycled in soils and for assessing the effectiveness of carbon sequestration
practices. There are several methods for measuring SOM, including laboratory
techniques such as loss on ignition (which measures the amount of carbon in soil by
burning it at high temperatures) and chemical oxidation methods. Spectroscopy
techniques, such as near infrared reflectance spectroscopy (NIRS), are also becoming
increasingly popular for estimating SOM content in a more rapid and non-destructive
manner.
Monitoring changes in soil organic carbon over time is particularly challenging because
SOM can vary greatly across different soil types, climates, and land uses. Soil sampling
must be done carefully to ensure that samples are representative of the entire area of
interest. Advances in remote sensing technologies, such as satellite imagery and
unmanned aerial vehicles (UAVs), are being explored to track soil health and carbon
changes on a broader scale, providing valuable data for largescale land management
strategies.

Carbon Sequestration and Climate Change

Soils play an essential role in mitigating climate change by storing carbon that would
otherwise contribute to rising levels of atmospheric CO₂. Carbon sequestration in soils
refers to the long-term storage of carbon in soil organic matter, preventing it from being
released into the atmosphere. This process is particularly important given that soil
contains more carbon than the atmosphere and vegetation combined. Maintaining and
enhancing soil carbon sequestration is a key strategy for mitigating climate change.
Sustainable land management practices, such as agroforestry, no-till farming, and the
use of cover crops, can increase the amount of carbon stored in soils. For example, trees
in agroforestry systems help sequester carbon not only in their biomass but also in the
soil beneath them, as their root systems contribute organic material to the soil. No-till
farming reduces the disturbance of soil, preserving existing SOM and increasing the
stability of soil carbon.
On the other hand, practices that disturb the soil, such as intensive tillage, deforestation,
and overgrazing, can lead to the release of stored carbon into the atmosphere. When soil
organic matter decomposes more rapidly, it releases CO₂, contributing to the
greenhouse effect and global warming. Therefore, soil management practices that
enhance carbon storage are crucial for climate change mitigation.
Nitrogen Cycle
The nitrogen cycle is a biogeochemical cycle in which nitrogen is transformed into
numerous chemical forms as it moves through the atmospheric, land, and sea
ecosystems. Nitrogen is found in proteins and nucleic acids; therefore it is necessary for
the existence of life on earth. Although nitrogen gas makes up 78 percent of the
atmosphere by volume, it is in an unusable condition for most species. Both biological
and physical methods can be used to convert nitrogen. Fixation, assimilation,
ammonification, nitrification, and denitrification are all important processes in the
nitrogen cycle (Fig. 2).

Fig. 2: Nitrogen cycle

1. Nitrogen Fixation: This process converts nitrogen gas (N₂) from the atmosphere
into ammonia (NH₃) or related compounds, typically through biological fixation by
symbiotic bacteria in the roots of legumes or through industrial processes.
2. Nitrification: Ammonia is converted to nitrite (NO₂⁻) by nitrifying bacteria, and
then to nitrate (NO₃⁻).
3. Assimilation: Plants absorb nitrates and ammonia and incorporate them into
plant proteins and nucleic acids.
4. Ammonification: Decomposing microorganisms convert organic nitrogen from
dead plants and animals back into ammonia.
5. Denitrification: Nitrate is converted back to nitrogen gas (N₂) by denitrifying
bacteria, completing the cycle.
Sulphur Cycle
• The sulphur cycle is a biogeochemical cycle that describes the movement of
sulphur through the Earth's ecosystems, involving various chemical
transformations and biological processes. Sulphur is an essential element for all
living organisms as it is a key component of amino acids, vitamins, and
coenzymes (Fig. 3). Sulphur is released from rocks through weathering, and then
assimilated by microbes and plants. It is then passed up the food chain and
assimilated by plants and animals and released when they decompose. Many
bacteria can reduce sulphur in small amounts, but some specialized bacteria can
perform respiration entirely using sulphur. They use sulphur or sulphate as an
electron receptor in their respiration, and release sulphide as waste. This is a
common form of anaerobic respiration in microbes.

Fig. 3: Sulphur cycle

The cycle ensures the recycling of sulphur, making it available for plants, animals, and
microbes. The following processes are involved:
1. Mineralization: Organic sulphur in dead organisms is mineralized into inorganic
forms like hydrogen sulphide (H₂S).
2. Oxidation: Hydrogen sulphide is oxidized to elemental sulphur (S) and sulphate
(SO₄²⁻) by sulphur-oxidizing bacteria.
3. Assimilation: Plants and microorganisms take up sulphate and incorporate it into
amino acids and proteins.
4. Reduction: Sulphate is reduced back to hydrogen sulphide by sulphate-reducing
bacteria under anaerobic conditions.
Phosphorus Cycle
The phosphorus cycle describes the movement of phosphorus through the biosphere,
hydrosphere, and lithosphere. Phosphorus is a vital nutrient for life on Earth, and is
involved in many processes, including energy transfer within organisms, component of
genetic material, cell membranes, bones, and teeth. Phosphorus is transformed in the
various ways:
1. Weathering: Phosphate ions are released from rocks through weathering.
2. Absorption: Plants absorb phosphate from the soil and use it to form ATP, DNA,
and other important molecules.
3. Decomposition: When plants and animals die, decomposers return phosphates
to the soil.
4. Sedimentation: Some of the phosphorus can be lost to sedimentation in aquatic
environments and incorporated into new rock formations.