Microbiology is found every where around us. It can be found in the air we breathe, in water bodies and the ground we walk on. Each person contains trillions of microorganisms, outnumbering human cells by a ratio of 10 to 1.
Apart from human, all other higher organisms existing till- date, including plants, insects, fish, rats, and apes etc, harbor microbiomes. For example, plants are believed to rather live in association with a large variety of microbes. These microbes live either inside (endosphere) or outside (episphere) of plant tissues. Among these microorganisms, bacteria and fungi are predominant. They play important roles such as increased nutrient availability, uptake nutrients by plants and increased plant stress tolerance. Thus, plant fitness (growth and survival) is the result of physical and physiological functions of the plant per se as well as the associated microbiome, which together are known as a plant holobiont.
The most common association between plants and microorganisms is that called root-arbuscular mycorrhizal (AM) and legume-rhizobial symbioses. Both association influence the way roots uptake various nutrients from the soil. Some of these microbes cannot survive in the absence of the plant host (the ‘obligate symbionts’ including viruses, some bacteria and fungi), which inturn provides space, oxygen, proteins, and carbohydrates to the microorganisms.
Soil microbiology and soil health have gained increasing attention in recent years. Both are part of the factors that contribute to agricultural sustainability.
Soil microbiology is the study of microorganisms in soil, their functions, and how they affect soil properties. It’s a subdiscipline of environmental microbiology that study;
a. The functions of microorganisms like bacteria, archaea, viruses, fungi, parasites, and protozoa
b. How microorganisms interact with each other and other soil properties like plants and minerals
c. How microorganisms affect soil structure, nutrient processing, and recycling
d. How microorganisms affect soil salinity and acidity .
In soil microbiology, the microorganisms interact with each other and other soil properties such as plants and minerals. They play important roles in the ecology and physiology of plants. They govern nutrient processing and recycling in soil, and also affects the decomposition of organic matter in soil, soil salinity and soil acidity, thereby impacting soil fertility and crop health.
Key practices in soil microbiology include: composting, earthworms, soil analysis, nutrient cycling, crop rotation, no-till systems, cover crops, agroecosystems, green manures, organic agriculture.
COMMON SOIL MICROORGANISMS
Microbes are found everywhere, in human body, in the air, water bodies, on and in the ground and even in the most extreme environments, like volcanoes and in glaciers in the oceans etc. Microbes are the start of the soil food web as they are consumed by each another and by larger soil fauna like worms and slaters bugs.
There are millions of microorganisms in one gram of soil, including soil fungi, soil bacteria, actinomycetes, algae, archaea, ciliates ,single-celled organisms like protozoa such as amoebae, and animalia species such as nematodes. The biomass and activity of each microbial species varies and evolves throughout the soil’s lifecycle: fungi typically dominate the biomass of a healthy sample, despite their fragility and sensitivity, while bacteria remain the most resistant to changing conditions. Soil microbial biomass can range from several hundred to thousands of pounds per acre. Some of these microorganisms including bacteria, and viruses, perform important beneficial services for soil and plant health. But only a small portion are harmful and detrimental to plant and human. Variations in microbial levels and activity are directly correlated with soil management.
Generally speaking, soils with a high diversity of microorganisms tend to be healthier than those with low levels of diversity.
BACTERIA
Bacteria are a free living, single-celled organisms that are found everywhere, small only 1-3 micrometre long. They come in many different forms and shapes from rod shaped, round, corkscrew, rounded rods and comma shaped, and comma shaped.
FUNGI
Fungi are either single celled or complex multi-cellular organisms. They are mainly found in the soil and on plants. Fungi help to break down plant matter into nutrients and carbon, but they can also cause plant disease including rot, mildew, canker and rust.
Some of the beneficial fungi used to improve soil health and plant productivity include:
a. VASCULAR ARBUSCULAR
The association of AM fungi with plants has been known since 1842, and over 80 % of land plants are found associated with them . It is thought that AM fungi helped in the domestication of plants.
This fungi produce a substance called glomalin (a type of glycoprotein) which glues soil aggregates together and helps to stabilise the soil structure. Structures known as hyphae act like an extension of the plant, accessing water beyond the plant’s roots reach to supply nutrients and water making plants more resilient to droughts. Mycorrhizal fungi form a connection with mycorrhizae found on other plants, creating a chemical signalling link. When a plant is being attacked by an insect, the signalling chain is used to alert surrounding plants so they can take preventative measures to avoid attack. Mycorrhizae fungi are found on most plants except for Brassica and chenopod families of plants.
b. SAPROTROPHIC FUNGI
Saprotrophic fungi decompose dead plant and animal matter and make nutrients available for plants. They also make humus – a valuable resource needed by plants and the soil.
NEMATODES
Nematodes are microscopic round worms that move in the soil like snakes. Nematodes need a relatively damp environment and feed on bacteria, fungi, other nematodes (predatory nematodes) and plant roots. They help to increase nutrients within the soil as by excreting plant available nutrients including nitrogen and potassium. Nematodes can be used as a part of an integrated pest and disease management program as they feed on ground dwelling insects, like slugs, borers, grubs and some snails.
Nematodes exist many different forms, including beneficial and disease causing.
ARCHAEA
Archaea are similar to bacteria but they have a cell wall and a flagella (a tail), with which they use to swim.
PROTOZOAN
Protozoa are unicellular microorganisms and move by using a flagella or cilia. They consume bacteria and can attack fungi. By feeding on bacteria, protozoa help to release nutrients (including nitrogen and phosphorus) back into the soil.
CILIATE
Ciliates promote nutrient cycling in the soil. Compacted and anaerobic soils tend to contain higher levels of ciliates than healthier soils.
The hairlike structures of ciliates are used for movement and food gathering.
AMOEBA
Amoebae are single-celled microbes that move with the aid of pseudopodia.
VIRUS
Viruses transfer genes from host to host, and kill other microbes. They are responsible for the turnover and concentration of nutrients in the soil.
Several cultured microbes have been used for plant-microbe interaction and still, more of these enormous unculturable microbes are still being discovered and will continue to be discovered.
FUNCTIONS OF MICROBES IN THE SOIL
Microbes undertake a range of different roles in the soil. They play crucial roles in plant growth, development, and overall productivity. They perform the following functions;
a. Decomposition of plant matter
b. Making nutrients available to plants.
c. Microbes release vitamins and hormones that can trigger a plant’s immunity
d. Help to reduce plant’s susceptibility to disease, infection or pests.
e. Nitrogen fixing bacteria pull nitrogen out of the atmosphere and make it available to plants.
f. Release oxygen in the atmosphere
g. Solubilize phosphorus in the soil, making it available for plants. They convert phosphates to an inorganic form which is a more plant available format. They also
help address phosphorus deficiency by increasing the soluble phosphorus content of soil.
h. Soil structure and interactions among microorganisms (including soil fungi, soil bacteria and species like nematodes) can impact soil biology and biochemistry and other properties of soil.
As a key components, soil microorganisms impact soil health in various ways. The major organisms involved in the improvement of soil health include; Soil microbes, soil bacteria, and soil organisms.
The microbial structure of soil is proportional to the organic matter content, giving soil microbes, soil bacteria and soil organisms a key role in soil health. This means that soils that have large amounts of regularly added organic residues tend to support more soil microorganisms, which contribute to overall soil health.
In return of the above benefits derived by plants from microbs, plants supply carbohydrates (simple sugars) to attract microbes to compensate for nutrients and water needs of the organisms. The carbohydrates also increase the liable carbon fraction within the soil. These carbohydrates can be noticed in the soil when a plant is pulled out of the ground and the soil washed off, a whiteish foam found around the roots is the carbohydrates or liquid carbon.
SOIL MICROBIAL LIFE CYCLE
The soil microbiome is always in a different state of flux, with microbes ebbing between different stages of their life cycle, from early development to exponential growth to a lag phase before dying. As they die, the microbes release nutrients in a soluble form to the plant. In certain circumstances, the plant actually engulfs the microbe as a source of food, providing the plant with essential nutrients. Dead microbes (known as a necromass) excreted by the plants increase soil carbon and release additional nutrients for plant uptake.
BACTERIA AND FUNGI RATIO
A healthy soils generally have a fungal-dominated community. Both fungi and bacteria play different roles in the soil, but the ratio must not pass the threshold. A highly productive agricultural soils tend to have ratios of fungal to bacterial biomass near 1:1 or somewhat less. Forests tend to have fungal-dominated food webs. The ratio of fungal to bacterial biomass may be 5:1 to 10:1 in a deciduous forest and 100:1 to 1000:1 in a coniferous forest
The fungal to bacterial ratio is important because of the different lifestyles of bacteria and fungi. Bacteria have faster turnover rates (i.e. short life cycles), such that bacterial-dominated communities are linked to faster rates of nitrogen cycling and subsequent N losses from soil. In contrast, fungi have slower life cycles, which result in greater retention of nitrogen in the soil. Due to their extensive hyphal networks, fungi are also thought to be larger contributors to both the production of enzymes involved in decomposition and aggregate formation, and resistant to drought. On a community-level, fungal hyphae are the “internet of the soil” , they facilitate connections among other microbes and plants, helping plants to acquire nutrients and alleviate plant water stress. This does not mean bacteria are not good. It is the balance between bacteria and fungi that seems to be most important.
fungal-to-bacterial ratios are critical to soil health and sustainability. This is because soils with more fungi relative to bacteria (higher fungal to bacterial ratios) are beneficial because fungi are more efficient at breaking down complex organic matter, particularly lignin and cellulose, which are abundant in plant residues, leading to improved nutrient cycling, better carbon sequestration, and healthier plant growth, especially in environments with high levels of organic matter or low nutrient availability. Thus, making degraded soils to regain their structure faster, retain more nitrogen and are more resilient to drought and floods. This is often observed in forests or grasslands compared to intensively managed agricultural soils.
In addition, all bacterial and fungi are not equal. Ideally, a prairie soil has a mix of fast and slow growing bacteria and a diversity of symbiotic fungi so that prairie plants can find an ideal match. Finally, while microbes are the foundation of a healthy soil, they are part of a larger soil food web that must be intact in order to sustain the microbial community.
REASONS FOR MAINTAINING A HIGHER FUNGAL-TO-BACTERIAL RATIO:
a. DECOMPOSITION OF COMPLEX ORGANIC MATTER: Fungi, with their hyphae, can access and break down larger organic particles that bacteria cannot reach, making them key players in decomposing plant litter and woody debris.
b. NUTRIENT CYCLING: Fungi can effectively mineralize nutrients like phosphorus and nitrogen from organic matter, making them available to plants, especially in nutrient-poor soils.
c. IMPROVE SOIL STRUCTURE:
Fungal hyphae can bind soil particles together, creating better soil aggregation and improving water infiltration and aeration.
d. MYCORRHIZAL ASSOCIATIONS:
Many plants form symbiotic relationships with mycorrhizal fungi enhance nutrient uptake, particularly phosphorus, from the soil.
e. CARBON SEQUESTRATION: Fungi can store more carbon in their biomass compared to bacteria, contributing to long-term carbon storage in the soil.
FACTORS THAT CAN INCREASE THE FUNGI-TO-BACTERIAL RATIO:
The ratio between fungi and bacteria can affect the type of plants grown. To get more fungi in the soil, farmers, agronomists,etc carry out composting, buy mycorrhizal fungi and add to the planting hole when planting new plants.
There are many other different ways to increase either the fungi or bacterial ratio in the soil. Such ways include;
a. HIGH ORGANIC MATTER INPUT:
Adding large amounts of organic matter with a high carbon-to-nitrogen (C:N) ratio, like wood chips, straw, leaves litters, or aged manure, favour fungal growth, while minimizing readily available nitrogen sources that promote bacterial dominance.
b. LOW SOIL DISTURBANCE: Minimal tillage or no-till farming practices can preserve fungal hyphae networks.
c. LOWER SOIL pH: Fungi tend to thrive in slightly acidic conditions, where bacteria may be less active.
d. DROUGHT CONDITIONS: In dry environments, fungi can access water more efficiently due to their hyphae, giving them an advantage over bacteria.
e. USE A FUNGAL DOMINATED COMPOST, COMPOST TEA OR SPRAY OUT FISH HYDROLYSATE.
For a more bacterially active soil, use a bacterial dominated compost or compost tea, or spray out a simple sugar like molasses.
f. MULCHING: By applying a layer of mulch on the soil surface, this maintain moisture levels and provide a habitat for fungi. The mulch materials to use must contain high C:N ratio, like wood chips or shredded bark.
g. INCORPORATING MYCORRHIZAL FUNGI INOCULANTS:
Introduction of beneficial mycorrhizal fungi directly into the soil through inoculants will form symbiotic relationships with plant roots and enhance nutrient uptake.
h. AVOID ADDING HIGH-NITROGEN MATERIALS
Avoid adding high nitrogen materials like grass clippings or fresh manure in large quantities, as they promote bacterial growth.
i. NO-TILL PRACTICES:
Minimize soil disturbance to preserve existing fungal hyphae networks.
j. COMPOSTING TECHNIQUES:
Create a compost pile with a higher C:N ratio by adding more woody materials to promote fungal activity during decomposition.
k. PLANT SELECTION: Choose plants known to form strong mycorrhizal associations, as they can indirectly increase the fungal population in the soil. etc
PLANT MICROBIOMES
The plant microbiome refers to all microorganisms associated with a living plant or Plants live in association with diverse microorganisms. These microbes interact closely with plants, influencing their health and performance. They (microbes) live either inside (endosphere) or outside (episphere) of plant tissues. Meaning that they live in different plant environment. Understanding the role of the microbiome in plant health, production, and nutrient cycles is just as important as focusing on the plant itself. Different microbiomes exist within the plant environment:
a. Phyllosphere – Microbes on leaves, stems, and flowers. They are exposed to environmental factors like wind and temperature.
b. Endosphere – Microbes inside plant tissues, such as roots, stems, and leaves, which can enter through root tips or natural openings.
c. Rhizosphere – Microbes surrounding plant roots, aiding nutrient availability and supporting plant resilience.
Maintaining a balanced microbial environment is essential, as not all microbes benefit crops. The interaction between beneficial and harmful microbs varies between annual crops (e.g., maize, wheat, soybeans) and perennial crops (e.g., trees, vineyards).
Microbiomes play a major role in agriculture. They can help make agriculture more sustainable by reducing the need for fertilizers and pesticides. They can also help combate biotic stress that can damage their growth and development.
Some of the organisms found in plant microbiome include: bacteria, fungi, protists, nematodes, and viruses.
HOW PLANT MICROBIOMES BENEFIT PLANTS
a. PLANT GROWTH: Microbiomes can help plants grow and develop.
b. NUTRIENT UPTAKE: Microbiomes help plants take in nutrients from the soil.
c. STRESS TOLERANCE: Microbiomes help plants tolerate stress factors like drought.
d. PATHOGEN RESISTANCE: Microbiomes help plants defend themselves against pathogens.
TYPES OF MICROBIOMES
1. RHIZOSPHERE MICROBIOME
The rhizosphere comprises the 1–10 mm zone of soil surrounding the roots that is under the influence of the plant where root exudates, mucilage and dead plant cells are deposited . A diverse array of organisms specialize in living in the rhizosphere, including bacteria, fungi, oomycetes, nematodes, algae, protozoa, viruses, and archaea. The most frequently studied beneficial rhizosphere organisms are mycorrhizae, rhizobium bacteria, plant growth promoting rhizobacteria (PGPR), and biocontrol microbes. Among the prokaryotes in the rhizosphere, the most frequent bacteria are within the Acidobacteria, Proteobacteria, Planctomycetes, Actinobacteria, Bacteroidetes, and Firmicutes. Certain bacterial groups (e. g. Actinobacteria, Xanthomonadaceae) are less abundant in the rhizosphere than in nearby bulk soil.
Mycorrhizal fungi are abundant members of the rhizosphere community, and have been found in over 200,000 plant species, and are estimated to associate with over 80 % of all plants. These mycorrhizae–root associations play profound roles in land ecosystems by regulating nutrient and carbon cycles. Mycorrhizae are integral to plant health because they provide up to 80 % of N and P requirements. In return, the fungi obtain carbohydrates and lipids from host plants.
2. PHYLLOSPHERE MICROBIOME
The aerial surface of a plant (stem, leaf, flower, fruit) is called the phyllosphere and is considered comparatively nutrient poor when compared to the rhizosphere and endosphere. The environment in the phyllosphere is more dynamic than the rhizosphere and endosphere environments. Microorganisms also live in this above-ground parts of plants. These microbial colonizers are subjected to diurnal and seasonal fluctuations of heat, moisture, and radiation. In addition, these environmental elements affect plant physiology (such as photosynthesis, respiration, water uptake etc.) and indirectly influence microbiome composition. Rain and wind also cause temporal variation to the phyllosphere microbiome. Overall, there remains high species richness in phyllosphere communities. Fungal communities are highly variable in the phyllosphere of temperate regions and are more diverse than in tropical regions. There can be up to 107 microbes per cm2 present on leaf surfaces of plants, and thus the bacterial population of the phyllosphere on a global scale is estimated to be 1026 cells. The population size of the fungal phyllosphere is likely to be smaller. Phyllosphere microbes from different plants appear to be somewhat similar at high levels of taxa, but at the lower levels taxa there remain significant differences. This indicates that microorganisms may need finely tuned metabolic adjustment to survive in phyllosphere environment. Proteobacteria seems to be the dominant colonizers, with Bacteroidetes and Actinobacteria also predominant in phyllospheres. Although there are similarities between the rhizosphere and soil microbial communities, very low similarity has been reported between phyllosphere communities and those in open air.
3. ENDOSPHERE MICROBIOME
Some microorganisms, such as endophytes, penetrate and occupy the plant internal tissues, forming the endospheric microbiome. The AM and other endophytic fungi are the dominant colonizers of the endosphere. Bacteria, and to some degree Archaea, are important members of endosphere communities. Some of these endophytic microbes interact with their host and provide obvious benefits to plants. Unlike the rhizosphere and the rhizoplane, the endospheres harbor highly specific microbial communities. The root endophytic community can be very distinct from that of the adjacent soil community. In general, diversity of the endophytic community is lower than the diversity of the microbial community outside the plant. The identity and diversity of the endophytic microbiome of above-and below-ground tissues may also differ within the plant.
In addition to the rhizospheric and endophytic microbiomes, phyllosphere community composition also depends on plant identity. Plant community influences phyllosphere microbiomes by directly shaping the composition of microbial species present on leaves through factors like leaf chemistry, morphology, and developmental stage, which are determined by the plant species present, thus influencing which microbes can successfully colonize and thrive on the leaf surface; essentially, different plant species will attract different microbial communities to their phyllospheres due to their unique characteristics. For example, the leaves of plants produce chemical compounds including waxes, sugars, and phenolic compounds, which influence and attract microbes to adhere to and colonize the leaf surface.
Factors like leaf shape, size, and surface texture can affect the microenvironment on the leaf, impacting the types of microbes that can establish themselves.
Lastly, the different stages of plant growth (seedling, flowering, senescence) do result in changes in leaf chemistry and morphology, causing shifts in the phyllosphere microbiome composition. And the diversity in plant community can provide a wider range of microhabitats for different microbial species, leading to a richer and more complex phyllosphere microbiome.
DRIVERSITY OF PLANT MICROBIOME COMPOSITION
Plant microbiome structure is influenced by complex interactions between hosts, microbes, and associated environmental factors such as climate, soil, cultivation practices etc.
a. HOST FACTORS THAT INFLUENCE PLANT MICROBIOME COMMUNITY COMPOSITION
i. PLANT SPECIES
The genetic make up of the host plant has a significant influence on the identity of its microbiome. The plant determines which microbes can colonize its tissues, through the production of specific root exudates and phytohormones, and by regulating its immune response, thus shaping the composition and abundance of microbial species that can thrive on or within the plant.
Genetically, different plant genotypes naturally attract different microbial communities due to variations in their genes controlling root exudates, cell wall composition, and immune responses, which can selectively favor certain microbial taxa.
ii. PLANT DEVELOPMENT STAGE:
As a plant grows and develops, its microbiome composition changes, with different microbial communities being present at different stages like seedling, flowering, and fruiting.
Different plant species growing adjacent to one another can harbor distinct microbiomes. They release different chemical compounds from their roots, including sugars, amino acids, and organic acids, which act as signals to attract specific microbes and influence their colonization patterns. For example, a comparative survey carried out on the microbiomes around different cereal roots of maize, sorghum, and wheat showed that different community composition of microbs colonized these plant’s root zones. This was supported by a research carried out to determine the microbiome compositions of grapevines and some weed species roots and rhizospheres using 16S rRNA gene from the plants grown in the same field, it was discovered that these species hosted significantly different microbiomes in the roots and rhizosphere, with the more pronounced difference in the root communities. Plants that are distantly-related phylogenetically show greater variation in associated microbiome compositions, suggesting a role of plant phylogeny in structuring root microbiomes .
Plant species also influences the identity and diversity of endophytic communities.
A plant community influences endophytic microbiomes by shaping the composition and diversity of microbes present within the plants through factors like host plant species, root exudates, surrounding plant species, and environmental conditions, which ultimately determine which microbial communities can successfully colonize and thrive within the plant tissues, impacting the plant’s overall health and resilience. For instance, plant’s immune system plays a crucial role in recognizing and interacting with microbes, either allowing beneficial microbes to colonize or actively defending against potential pathogens, thus shaping microbiome composition.
In summary, different plant species naturally attract different microbial communities due to variations in their root exudates, which act as chemical signals to specific microbes, leading to a unique endophytic microbiome for each plant species. This had been supported by a research study where differences in endophytic community composition in potato and Eucalyptus plants were determined. The most abundant bacterial root endophytes were rare in the potato or absent in Eucalyptus and vice-versa. This suggest that the host plant selects its endophytic microbes.
Apart from this, the presence of neighboring plants can impact the endophytic microbiome of a focal plant by influencing the availability of nutrients, competition for space, and potential exchange of microbes through the soil.
The life stages of a plant, like seedling, flowering, and senescence, can also affect the composition of the endophytic microbiome as the plant’s physiological needs change. And lastly, abiotic conditions like soil type, moisture content, nutrient availability, and temperature can influence the overall microbial community in the soil, impacting which microbes are able to colonize the plant roots and become endophytes.
THE EFFECTS OF HOST PLANT SPECIES IN RECRUITING MICROBES FROM THE SURROUNDING ENVIRONMENT
The effect of pant species in recruiting microbs from the surrounding environment indicate that plants have evolved traits that govern root microbiome assemblages . For example, endosphere, rhizosphere community composition are correlated with host taxonomy. Researchers have discovered that the rhizosphere and root microbiomes are mostly influenced by soil type, and the nodule while root endophytes are influenced by plant species.
Apart from the factors that influence the microbiomes above, plant traits such as leaf permeability, wettability and topography and physicochemical properties, cuticle chemistry, root exudates, antibiotic production, and inherent plant immunity to invasion by microbes may also play a major role in influencing plant microbiomes.
iii. PLANT GENOTYPES
The genotype of a plant is a word used to describe the genetic make – up of the plant. It can be described as the whole genome, the DNA sequence of individual genes or a collection of scores at different genetic markers.
Plant genotype plays a crucial role in shaping the structure and composition of plant microbiomes associated with roots, leaves, fruits, and seeds; influencing diversity, community structure, and even co-occurrence networks, especially in fruits, leaves, and soil.
Plant root produce exudates. These exudates are specific to the host plant, can modulate the rhizosphere community and select specific root microbiomes, contributing to host-specific plant microbiomes. Apart from this, plants can cope with biotic and abiotic stresses based on their genotype which influences the plant metabolome (e.g., exudates, VOCs). This can affect microbiome assembly.
The effects of plant genotype on microbiomes can vary depending on the environment, with genotype effects being strong in some environments but absent in others. The genotype of a particular plant specie also influence the difference in microbe community composition. For examples: Studies have shown that plant genotype influences the bacterial and fungal communities associated with different plant species, including Boechera stricta, Medicago trunculata, Glycine max, and Olea europaea. Genetics of the host also shape the plant-microbiome structure. For example, OTUs in three different potato varieties were cultivar-specific. Similarly, cultivar-dependent effects have been reported for the bacterial communities in young potato rhizospheres. It has been reported in a study that genotype contributed to about 6% of the variation of the microbiome composition in the rhizosphere region. A larger influence of host genotype on community composition has also been reported. Genotype-dependent microbiome community structuring has been reported for sweet potato, wheat, pea, and oat. Bacteria such as Acinetobacter, Chryseobacterium, Pseudomonas, Sphingobium, and Stenotrophomonas were more abundant in low-starch cultivars than those having high-starch contents. Within-species genetic variability can influence microbiome composition in leaf tissues. To support this, a field experiment was carried out to unravel driversity in community composition of bacteria associated with leaves and roots of Boechera stricta. The findings suggested that the host genotype influences leaf community, but the root microbiome was variable at different collection sites.
iv. PLANT ORGAN
Different plant tissues host distinct microbiome communities. The plant-microbiome interaction occurs at the rhizosphere, endosphere, and phyllosphere where different tissues and organs lies.
Root exudates can favor the recruitment of a beneficial microbiome in the rhizosphere.
While plant topology and phytochemistry influence the recruitment of the phyllosphere microbiome etc. With these, diverse plant strategies selectively recruit beneficial microbiomes.
Plant organs, such as roots, stems, leaves, and flowers, each harbor distinct microbial communities (microbiomes) that are influenced by the plant’s own characteristics and the surrounding environment, impacting plant health and development. The rhizosphere (root environment) for example, where roots are found releases root exudates (substances released by roots) which attract specific microbes, influencing the composition of the rhizosphere microbiome.
At the endosphere (internal tissues) where endophytes are found, microbes that live within plant tissues, are influenced by plant species, genotype, and developmental stage.
And at the Phyllosphere (leaf surface), plant topology, phytochemistry, and environmental factors like rain and wind influence the phyllosphere microbiome.
A study reported that each surface and internal tissue of plants may harbor distinct microbial communities and that the role of tissue-type was greater than host type and the microbiome of the soil. This may be because the adaptation strategies of various tissues may affect the microbes in colonizing them for community composition.
For instance, surface tissues at the phyllosphere are exposed to constant fluctuations of weather and have relatively poor nutritional status compared to the root or internal tissues at the rhizosphere and endosphere. Therefore, microbes colonizing the leaf surface need to be adapted in these conditions.
Fungi in the rhizosphere are directly influenced by plant roots, play a crucial role in plant health by promoting growth, enhancing nutrient uptake, and protecting against pathogens and abiotic stresses. Fungi, like Arbuscular mycorrhizal fungi (AMF), form symbiotic relationships with plant roots, enhancing nutrient and water uptake.
Rhizosphere fungi can produce plant growth-promoting substances like phytohormones (e.g., auxins, gibberellins) and stimulate root development. They can also solubilize and make available nutrients like phosphorus and iron, which are often unavailable to plants in the soil.
Rhizosphere fungi can outcompete or inhibit the growth of plant pathogens, reducing the risk of root diseases. Some fungi produce antimicrobial compounds that can directly harm pathogens.
They can also induce systemic resistance in plants, making them more resilient to various stresses.
Rhizosphere fungi can also help plants tolerate abiotic stresses like drought, salinity, and heavy metal contamination. They can improve nutrient uptake under stress conditions and help plants adapt to changing environmental conditions.
Fungi within the plant endosphere (the interior of plant tissues), can have various effects, ranging from mutualistic to pathogenic, and influence plant health, growth, and resistance to stressors.
Some of these fungi enhance nutrient uptake by plants, particularly phosphorus and nitrogen, which are essential for plant growth. Some endophytes can improve plant tolerance to abiotic stresses like drought, salinity, and heavy metals. While Some fungal endophytes produce compounds that protect plants against pathogens, acting as a natural defense mechanism. Apart from all these, some
endophytes are growth promoter. They produce plant hormones like auxins and cytokinins, which stimulate root and shoot development. Some can bioremediate
pollutants and toxins in the soil, thus improving soil health and promoting plant growth etc.
And lastly, The phyllosphere microbiome, including fungi, plays a crucial role in plant health, influencing growth, stress tolerance, nutrient acquisition, and disease resistance, with interactions ranging from mutualism to antagonism. Some phyllosphere fungi play a mutualists role by promoting plant growth and development by enhancing nutrient uptake and providing hormones. Some of them can help plants cope with environmental stressors like drought, salinity, and heavy metals. While some contribute to plant defense mechanism against pathogens. They achieve this by competing with the pathogen for resources, production of antimicrobial compounds, and induction of plant dwfencw response. They also facilitate nutrient uptake by plants, making essential elements more available and influence seed germination and seedling establishment, contributing to plant survival and reproduction.
It should be noted that as microbs within the three microbiomes perform a beneficial role, so also some have negative effects.
ENVIRONMENTAL FACTORS AFFECTING SOIL MICROBIOMES
These factors may include soil pH, salinity, soil type, soil structure, soil moisture and soil organic matter and exudates, which are most relevant for below-ground plant parts, whereas factors like external environmental conditions including climate, pathogen presence and human practices influence microbiota. These external environmental factors are physical factors including: temperature, osmotic pressure, pH, and oxygen concentration. They determine the survival of the microbs within the microbiota. In nature, where many species coexist, fluctuating environmental conditions cause dramatic population shifts due to the varying growth rates of different microorganisms. Every microbial species has a set of optimal conditions under which it flourishes. However, because the conditions in natural environments fluctuate widely, microbes have adapted tolerance to a range of environmental conditions. For example, many microbes have an optimum growth temperature of 30°C, but will still grow, albeit slower, at 4°C. In the laboratory, where conditions can be controlled, it is possible to achieve optimal growth conditions for a given microorganism that is cultured for use.
TESTING SOIL MICROBIAL ACTIVITY
Soil test can help understand better the level of microbial activity and type (bacterial or fungal) useful to improve soil health.
Some of the test used to determine microbial activities include numerous approaches like phospholipid fatty acids (PLFAs), substrate-induced respiration, or quantitative PCR (qPCR), Chloroform fumigation–extraction, chloroform fumigation–incubation, arginine ammonification, ATP, microscopic method, plate culture , microBIOMETER and DNA analysis etc, all used to determine F:B ratios. Laboratory testing is also used. Each has its own drawbacks and advantages. These quantification techniques have been extensively used, but also compared. Despite differences, they have altogether showed good repeatability. However, there is a clear need to standardize methods like the DNA extraction procedure for qPCR.
The drawback of these methods is that many of the methods carry large and tedious procedures making them unsuitable as rapid estimates of microbial biomass. In addition, most of these techniques have not been applied to study microbial biomass dynamics in composting and vermicomposting processes, being only widely used fumigation–extraction, with some studies using ATP measurements and PFLAs profiles , although the use of molecular techniques is increasing.
1. THE SOLVITA CO2 BURST TEST: This test provides a cheap and easy way to assess microbial activity on-farm without the use of laboratory testing. Once sampled, the test takes 24 hours to complete and provides an indication of soil health based on the volume of carbon dioxide produced by soil microbes.
2. THE MICROBIOMETER TEST: This type of test is available for home testing. It takes just 20 minutes and provides an idea of both microbial biomass and the fungal to bacteria ration of a soil sample. This helps landholders better understand how their soil health is responding to land management practices and adopt management decision to suit the soil.
3. There are also a number of laboratory scale tests that can be undertaken to assess soil microbiology.
a. A phospholipid fatty acid (PLFA) test measures microbial biomass and identifies missing microbes.
b. DNA SEQUENCING: This is gaining momentum as a way to understand the composition of a microbiome at a genetic level. While the testing itself is relatively cheap, interpreting the results requires the expertise of a soil scientist which makes the process more expensive. Future advances may automate next generation sequencing services and therefore make this a more realistic option for landholders.
4. PHOSPHOLIPID FATTY ACID ANALYSIS (PLFA)
PLFA method provides an easy to use and robust measure of changing soil microbial condition. The method provides data on both the quantity and composition of the soil microbial community- critical knowledge because the community is an important component of soil health.
The method is a widely used technique due to the sensitive, reproducible measurement of the dominant portions of the soil microbiota and the fact that PLFA does not require cultivation of the organisms.It is not cost effective and results in biased results due to the differing ease of culturing of some organisms. The main drawback of PLFA has been that the extraction time is very long and cumbersome
5. SUBSTRATE- INDUCED RESPIRATION TECHNIQUES
The substrate-induced respiration (SIR) asists in the measurement of microbial respiration of samples after amending them with an excess of a readily nutrient source, usually glucose, to trigger microbial activity. The microbial population in soil is activated by the addition of readily decomposable respiratory substrate.
The initial maximum respiratory response, which has to be optimized for every new kind of sample, is related with the current size of living microbial biomass.
6. MICROSCOPY TECHNIQUE
The Gold Standard for estimating individual fungal and bacterial biomass separately is microscopy. It calculates both fungal and bacterial biovolume separately.
Note that microBIOMETER detects the same range as microscopy.
