Bacteria in agriculture: soil health
and beyond review
Hannen Ahmed, Mannar Ismail, Mariam El-khouly, Mennaa Tariq,
Mennaa Abo-el ela, Nada Hamed, Sajedah Al-wabari
Department of Botany and Microbiology, Kafrelsheikh University
N102: Plant Taxonomy and Physiology
Dr. Ethar Lastname
March, 15, 2025
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N/Abstract
Nada’s
Introduction: Exploring the Definition and Importance of Bacteria in Ecological Context
As living organisms, bacteria have a natural history that includes interactions with other
living beings, plants, and animals, growth processes, reproductive strategies, aging and death,
dormancy, habitats, and the environmental impacts of bacterial activity. Compared to higher
organisms, it is uncommon to gain a deep understanding of these phenomena. Natural history
research focuses on phenomena that exhibit hierarchical organizational sequences and are
conducted at the highest level of organism complexity. A fundamental biological question that
innovative thinkers should explore is the relationship between the intrinsic benefits of bacteria
and their unique characteristics. Due to their intrinsic value, bacteria should be studied rather
than being considered "model cells," "bags of enzymes," "suitable genetic material," or
"chemicals for commercial exploitation."
Bacteria are unicellular organisms that do not belong to the plant or animal . They live in
colonies of millions and are typically a few micrometres long. Approximately 40 million bacterial
cells can be found in one gram of soil. Approximately one million bacteria can often be found in
one millilitre of fresh water. At least 5 nonillion bacteria are predicted to exist on Earth, and
bacteria are thought to make up a large portion of the planet's biomass
Prokaryotic organisms without a nucleus, bacteria are made up of filaments, pili, ribosomes,
DNA, cytoplasm, cell wall, and plasma membrane. They get their nourishment from
heterotrophic bacteria, which take up organic carbon, whereas autotrophic bacteria use
photosynthesis or chemosynthesis to make their own food
Bacteria are found in various places, including soil, water, plants, animals, radioactive waste,
and deep within the Earth's crust. They thrive at moderate temperatures, around 37 degrees
Celsius, while refractories can withstand high temperatures up to 113 degrees Celsius.
Mesophilic bacteria, responsible for most human infections, thrive at moderate temperatures,
while refractories can withstand temperatures up to 113 degrees Celsius. In the ocean, bacteria
live in darkness near hydrothermal vents, oxidizing sulfur to produce food.
Bacteria use binary fission, an asexual reproductive process, to divide into two daughter cells.
The process is initiated by DNA replication in the parent cell, influenced by temperature and
nutrient availability.
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Bacteria, despite being asexual, can occasionally engage in sexual reproduction through
conjugation, transformation, or transduction, potentially leading to antibiotic resistance due to
varying genetic material.
Classification Of soil bacteria
Bacterial Classification
Historically, bacteria were considered a part of the Plantae, the plant kingdom, and were called
"Schizomycetes" (fission-fungi). For this reason, collective bacteria and other microorganisms in
a host are often called "flora". The term bacteria_ was traditionally applied to all microscopic,
single-cell prokaryotes. However, molecular systematics showed prokaryotic life to consist of
two separate domains, originally called Eubacteria and Archaebacteria, but now called Bacteria
and Archaea that evolved independently from an ancient common ancestor. The archaea and
eukaryotes are more closely related to each other than either is to the bacteria. These two
domains, along with Eukarya, are the basis of the three-domain system, which is currently the
most widely used classification system in microbiology. However, due to the relatively recent
introduction of molecular systematics and a rapid increase in the number of genome sequences
that are available, bacterial classification remains a changing and expanding field. For example,
Cavalier-Smith argued that the Archaea and Eukaryotes evolved from Gram-positive bacteria.
Types of bacteria in soil:
Due to the great variation between soil types in their microbial content, it is not possible to
generalize all genera and species to all soil types, but it can only provide sufficient information
about the types of bacteria that are spread in the soil in general. It was possible to examine
various soil samples and the following types were identified:
1.​ Arthrobacter _this genus represents 5% - 65% of bacterial groups. This genus is
present in a high proportion due to its resistance to harsh conditions for a long period
and has an important role in analyzing organic waste. It was recently discovered that this
genus has the ability to reduce the toxicity of the element chromium Cr, which causes
many diseases in humans such as lung cancer and kidney diseases, in addition to
analyzing chemical pesticides in the soil.
2.​ Bacillus_It represents 7- 67% of bacterial groups, and Bacillus bacteria are among the
genera present in large numbers in the soil and are easy to distinguish as they are
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rod-shaped, spore-forming, necessarily or spore-forming, necessarily or facultatively
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aerobic, and their numbers in the soil range between 10 − 10 per gram of soil and
may exceed that.
Bacillus can be found in soils poor in organic matter in the form of spores that remain
dormant for several years. If suitable nutrients are available, they germinate and begin to
be active as vegetable cells again. It is easy to isolate species belonging to the genus
Bacillus by heating a soil suspension at a temperature of 80 °C for 10-20 minutes to kill
the vegetable cells while keeping the internal spores alive. Through aerial development,
other common spore-forming species belonging to the genus Clostridium can be
excluded.
3.​ Clostridium _It is found in most fertile soils despite the abundance of 02 and although it
is an anaerobic bacteria, when the soil is under natural conditions, the conditions are not
completely aerobic. Bacteria of the genus Clostridium are found in numbers ranging from
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10 − 10 per gram in different soils, by estimation using the plate method, and to obtain
pure cultures, these two physiological characteristics can be exploited for this purpose,
by heating the soil suspension to 80 m for 10 the soil suspension to 80 m for 10 minutes,
then growing the remaining bacteria in the suspension, then growing and multiplying
them under anaerobic conditions
4.​ Pseudomonas_ represents 2% – 12% of the bacterial groups, most of them are aerobic
and their function is to oxidize and analyze organic compounds, some of them are
obligate aerobic such as P. Denitrificans_ which reduces nitrates to nitrogen gas. They
secrete large amounts of enzymes as they have the
ability to analyze sugars, organic acids, amino acids and alcohols, as well as the ability
to analyze compounds with high molecular weights such as humic acid and pesticides.
They are considered important bacteria that dissolve rocks and phosphate and
potassium minerals, which makes the elements phosphorus and potassium available to
plants. Their types are widespread in nature and can be isolated from soil and water,
and there are important types in the soil as well as for humans.
5.​ Nitrogen fixation bacteria_ Nitrogen fixation bacteria for nitrogen fixing bacteria- 5 The
process of nitrogen fixation is the reduction of atmospheric nitrogen 𝑁 to nitrate 𝑁𝑂 or
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ammonium 𝑁𝐻
+
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. This process is called Fixation-N. 80% of the atmosphere is nitrogen
and both plants and animals cannot use it in this gaseous form but must convert it to
ammonium through the fixation process and only prokaryotes can use it in the form of
gas through the fixation process.
Bacteria role in soil and plants
Reproduction and Growth in Bacteria
Primarily, bacteria reproduce through a process known as binary fission, in which a single cell
divides into two genetically identical daughter cells (figure.1). This process can occur rapidly
under optimal conditions. While they mainly reproduce asexually, they on the odd occasion,
engage in sexual reproduction with several methods for the horizontal exchange of
chromosomal DNA: conjugation, transduction, and transformation. These processes are
properly described as parasexual processes, as none involve a wholesale transfer of
chromosomal genetic material (Spratt & Maiden, 1999). Instead, these mechanisms allow for
the transfer of fragments of chromosomal DNA, resulting in bacterial genomes being punctuated
by small chromosomal replacements from other lineages. Additionally, plasmids, prophages,
transposons, and insertion sequences can also be transferred horizontally, facilitating the
movement of DNA among distantly related bacterial species (Spratt & Maiden, 1999).
Other Forms of Reproduction in Bacteria: Research indicates an evolution in the
reproductive strategies of bacteria, beyond binary fission. Diverse bacterial lineages exhibit
fascinating alternative reproductive approaches such as multiple offspring formation and
budding. These adaptations, including endospore formation and multiple fission, highlight the
remarkable versatility and resilience of bacteria in their environments (Angert, 2005).
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Figure 1. Bacterial binary fission in Escherichia coli. a) prior to cell division, the
bacterial DNA molecule replicates. The replication of the double-stranded circular
DNA molecule that constitutes the genome of a bacterium begins at a specific
site, called the origin of replication. b) the replication enzymes move out in both
directions from that site and make copies of each strand in the DNA duplex. The
enzymes continue until they meet at another specific site, the terminus of the
replicator. c) As the DNA is replicated, the cell elongates, and the DNA is
partitioned in the cell such that the origins area, at the ¼ and ¾ position in the
cell and the termini are oriented toward the middle of the cell. d) Septation then
begins, in which new membrane and cell wall material begin to grow and form a
septum at approximately the midpoint of the cell. A protein molecule called FtsZ
(orange dots) facilitates this process. e) when the septum is complete, the cell
pinches in two daughter cells are formed, each containing a bacterial DNA
molecule.
Bacteria in Agriculture
Plant-bacteria Interaction: bacteria are the most abundant microorganisms in soil. Their
populations can rapidly increase in response to environmental changes , as in soil moisture,
temperature, or carbon availability. In semi-arid ecosystems, rhizosphere bacterial abundance
increases during the wet season, while the dry season sees a rise in desiccation-resistant
bacteria. Soil moisture significantly affects fungal communities as well. Flooding adversely
affects rhizosphere microbes, resulting in reduced populations and altered microbial movement.
Additionally, it can damage plant tissues, creating openings for microbial entry (Compant &
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Sessitsch, 2010). Nevertheless, the symbiotic relationship between bacteria and plants, as well
as their varied distribution and metabolic capabilities, assist in the decomposition of organic
matter, facilitate the fixation of atmospheric nitrogen, and enhance soil fertility (Khan & Rao,
2019).
Colonization of the Rhizosphere and Rhizoplane: a process in which microorganisms, such
as bacteria and fungi, establish themselves in the soil region surrounding plant roots (the
rhizosphere) and in the root surface itself (the rhizoplane). This intricate relationship is crucial for
plant health and growth, as these microorganisms play significant roles in nutrient cycling, soil
structure improvement, and disease suppression (Mitter et al., 2013).
The rhizosphere is characterized by a rich organic environment created by root exudates, which
include sugars, amino acids, and other organic compounds released by plants. These
substances attract various microbes, encouraging a complex community that can enhance plant
nutrient uptake, particularly phosphorus and nitrogen (Compant et al., 2009). Similarly, the
rhizoplane, being the direct interface between the root surface and the soil, provides a unique
habitat where beneficial microorganisms can attach and form biofilms, further aiding in the
protection and nourishment of the plant.
Rhizobacteria: Plant growth-promoting bacteria (PGPB): free-living bacteria present in the
soil, as well as rhizobacteria that colonize the root rhizosphere (Gouda et al., 2016). The
application of naturally occurring PGPB in the context of sustainable agriculture has gained
considerable importance in recent years, owing to their beneficial effects on soil health. (Mitter
et al., 2013). PGPB's application in agriculture enhances plant resistance, protection against
pathogens, nutrient acquisition, and beneficial bacteria-plant interactions, thereby increasing
agricultural productivity and crop yields. Besides fostering plant growth, PGPB also aids plants
in managing biotic (living) and abiotic ( non-living) stresses.
Endophytes: bacteria or fungi that live inside plants, either fully or partially colonizing plant
tissues. They can be harmful, causing diseases, or beneficial, forming symbiotic relationships
(Gouda et al., 2016). Their effect depends on factors like the environment, plant genotype, and
surrounding microbiota. Most endophytes are harmless to some plant species but can be
pathogenic to others. Environmental conditions often influence their pathogenicity. They improve
nutrient absorption, and help plants tolerate environmental stresses and pests. Furthermore,
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they produce valuable phytohormones and bioactive compounds with potential applications in
biotechnology (Santos et al., 2022).
Actinomycetes, a significant group of bacteria, develops hyphae similar to fungi and functions
in a comparable manner. Actinomycetes are smaller than fungi and are susceptible to
antibacterial agents. The earthy- scent that emanates when farmers plow or till the soil is
attributed to geosmins produced by streptomycetes. Actinomycetes are known to produce
several antibiotics, including Streptomycin. They decompose various substances, exhibiting
greater activity at high pH levels. Actinomycetes play a crucial role in breaking down recalcitrant
compounds such as chitin, lignin, keratin, and cellulose, as well as animal polymers (Hoorman,
2011.
Environmental Determinants on Bacterial Growth:
Soil pH, nitrogen levels, soil type, and moisture content are key determinants of soil-borne
bacterial growth, affecting nutrient availability, amino acid synthesis, and the physical and
chemical properties of the habitat (Vos et al., 2013). Additionally, moisture content is critical for
microbial metabolism and reproduction, as most bacteria require specific moisture levels to
thrive (Hoorman, 2011) .
The composition of plant communities also affects microbial diversity, as different plants can
alter soil chemistry and provide unique root exudates that serve as substrates for microbes
(Hoorman, (2011). Furthermore, practices such as crop rotation can enhance microbial diversity
by varying root structures and nutrient inputs, thereby promoting a more resilient ecosystem
(Khan & Rao, 2019). Lastly, human activities, including land use changes and pollution, can
disrupt these natural dynamics and significantly alter microbial populations.
Environmental Limits on Microbial Growth:
●​ Changes in temperature: temperature plays a critical role, as each bacterial species
has an optimal range in which it reproduces most efficiently. Most bacteria thrive
between 20°C and 37°C (68°F to 98.6°F) and can be inhibited or killed by extreme
temperatures.
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●​ Changes in pH: bacteria generally prefer neutral to slightly alkaline conditions (pH
6.5-7.5). Extreme pH levels can disrupt their metabolism.
●​ Osmolarity and changes in water activity: the availability of moisture enforces an
environment conducive to bacterial proliferation. In drier conditions, their growth is often
stunted or hindered.
●​ Nutrient Deprivation, Starvation: bacteria require various nutrients, such as carbon,
nitrogen, and essential minerals, to grow and reproduce. The presence or absence of
these nutrients can drastically influence their growth rates.
In general context, bacterias demonstrate remarkable resilience by surviving harsh conditions
and can rapidly multiply when optimal conditions for water, nutrients, and the environment are
present. Some bacterial species are highly sensitive to their environment and can be easily
killed by even slight changes in soil conditions, such as alterations in moisture levels, pH, or
temperature (Hoorman, 2016). Conversely, other species exhibit remarkable resilience,
demonstrating the ability to survive extreme heat, freezing temperatures, or prolonged drying
(Burges & Raw,1967). Certain bacteria can remain dormant in a spore state for decades,
patiently awaiting the right conditions—such as optimal moisture or nutrient availability—to
reactivate and thrive.This adaptive strategy not only allows certain bacterial species to flourish
but also helps suppress harmful, disease-causing microorganisms that could threaten plant
health (Hoorman, 2011).In this way, maintaining soil and ecosystem health depends heavily on
the intricate balance of microbial interactions.
The Impact of Bacteria on Agriculture
Definition of Biofertilizers
Biofertilizers are products containing living microorganisms, such as bacteria and fungi, that are
added to the soil or plants to enhance fertility and promote growth. These fertilizers help supply
essential nutrients to plants and improve the environmental balance of the soil.
Benefits of Bacteria in Agriculture and Soil
1.​ Improving Soil Fertility _certain types of bacteria, such as Azotobacter and Rhizobium,
fix atmospheric nitrogen, converting it into a form that plants can use. This fixation
increases nitrogen content in the soil, thereby enhancing its fertility.
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2.​ Dissolving Phosphorus_ Some bacteria, like Bacillus and Pseudomonas, contribute to
dissolving phosphorus present in the soil and converting it into a soluble form. This
increases phosphorus availability for plants, aiding in root growth and enhancing
productivity.
3.​ Decomposing Organic Matter _bacteria play a crucial role in decomposing plant
residues and organic matter, which helps increase the availability of essential nutrients
for plants. With the assistance of bacteria, biomass is converted into beneficial nutrients,
improving soil health.
4.​ Promoting Root Growth_ some bacteria produce natural growth hormones such as
auxins and gibberellins, which promote root development and enhance plants' ability to
absorb nutrients.
5.​ Disease Resistance_ certain beneficial bacteria help combat diseases. Some species
can produce compounds that inhibit the growth of harmful fungi and microbes,
contributing to plant health and reducing the need for chemical pesticides.
6.​ Improving Soil Structure_ bacteria aids in the formation of soil aggregates, enhancing
soil structure and improving its ability to retain moisture. This helps reduce water loss
and increases nutrient retention.
Biofertilizers and Their Types
Biofertilizers consist of a variety of bacteria that promote plant growth. Some well-known types
include:
Nitrogen-fixing Bacteria Biofertilizers: Such as Rhizobium, which live in the roots of legumes.
Phosphorus-Dissolving Bacteria Biofertilizers: Bacillus and Pseudomonas, which help
convert insoluble phosphorus into a usable form.
Organic Fertilizers Containing Beneficial Bacteria: These improve organic content and
increase microbial activity in the soil.
Agricultural Applications _Biofertilizers can be utilized in various areas, such as:
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Cereal Crop and Legume Cultivation: Exploiting nitrogen-fixing bacteria to enhance
nitrogen content in soil.
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Organic Farming: Utilizing biofertilizers to reduce dependence on chemical fertilizers.
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Land Restoration: Applying bio-fertilizers to improve poor and infertile soils
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The Harmful Effects of Bacteria on Plants
Bacteria are among the most harmful microorganisms that affect plant health and agricultural
productivity. They cause various diseases that weaken plants, reduce crop quality, and, in
severe cases, lead to plant death. In this paper, I will discuss how bacteria affect plants, how
they spread, the most common bacterial diseases, environmental factors that contribute to their
spread, and methods of prevention and control.
Bacterial Diseases and Their Impact on Plants:
Bacterial Diseases in Agriculture _Bacterial infections can cause a wide range of plant
diseases, affecting leaves, stems, roots, and fruits. These diseases weaken plants, lower yields,
and spread rapidly if not controlled properly. Some of the most common bacterial plant diseases
include:
Bacterial Wilt_ (Ralstonia solanacearum): a disease that blocks water transport in
plants like tomatoes and potatoes, causing sudden wilting and death.
Fire Blight _(Erwinia amylovora): it affects fruit trees like apples and pears, making
branches look burnt and blackened.
Bacterial Leaf Spot _ (Xanthomonas sp.): it causes dark, water-soaked spots on
leaves, which eventually dry out and fall off, reducing photosynthesis.
The Impact of Bacteria on Crop Productivity:
When plants get infected with bacteria, their productivity is significantly affected in several ways:
Damage to leaves: Reduces photosynthesis, which is essential for plant growth.
Root infections: Make it difficult for plants to absorb water and nutrients.
Fruit and seed damage: Some bacteria cause fruit rot, making them unsuitable for consumption
or sale.
If bacterial infections spread widely, entire fields can be affected, leading to major economic
losses for farmers.
How Bacteria Spread Among Plants:
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Bacteria can be transmitted in different ways, making it easy for infections to spread. Some
common methods include:
Contaminated water and soil: Bacteria can enter plants through irrigation water or infected soil.
Insects and animals: Some insects, like aphids, carry bacteria from one plant to another.
Wind and rain: Bacteria can travel through water droplets and reach new plants.
Human activities: Farm tools, hands, and machinery can transfer bacteria if not properly
cleaned.
Understanding these transmission methods is crucial for preventing bacterial infections.
When is Bacteria Harmful to Plants?
Not all bacteria are bad for plants—some, like Rhizobium, actually help plants grow by fixing
nitrogen in the soil. However, harmful bacteria cause damage in several ways:
Invading plant tissues: They enter through wounds or natural openings.
Producing toxins: Some bacteria release chemicals that kill plant cells.
Blocking water transport: Some bacteria clog plant vessels, leading to wilting.
Distinguishing between harmful and beneficial bacteria is important for developing effective
disease control methods.
Environmental Factors That Increase Bacterial Infections
Certain environmental conditions make it easier for bacteria to infect plants. These include:
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High humidity and moisture: Bacteria thrive in wet conditions.
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Warm temperatures: Many plant-pathogenic bacteria grow rapidly in warm climates.
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Poor air circulation: Increases the spread of bacterial spores.
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Overcrowding of plants: Allows bacteria to spread more easily from one plant to another.
By controlling these factors, farmers can reduce bacterial infections in crops.
Major Bacterial Diseases in Crops
Some of the most damaging bacterial diseases include:
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Soft Rot (Pectobacterium spp.) – Affects vegetables like potatoes and carrots, causing
tissue breakdown.
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Crown Gall Disease (Agrobacterium tumefaciens) – Causes tumor-like growths on
plant stems and roots.
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Bacterial Canker (Clavibacter michiganensis) – Affects tomatoes and peppers,
causing lesions and fruit rot.
These diseases demonstrate how devastating bacterial infections can be in agriculture.
How to Prevent and Control Bacterial Infections in Plants.
Chemical and biological methods for protecting plants
Conclusion
References
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McCutcheon, J. P. (2021). The Genomics and Cell Biology of Host-Beneficial intracellular
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Hall 2008, p. 145. βακτήριον. Liddell, Henry George; Scott, Robert; A Greek-English Lexicon at
the Perseus Project. βακτηρία in Liddell and Scott. Harper D. "bacteria". Online
Etymology Dictionary. Krasner 2014, p. 74.
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