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SLM 514
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SOM. BIOCHEMISTRY.
Soll Biochemistry sa dacipline in sol eofence tat i closely related with sil microbiology (4
‘major discipline in sol siete). 14s the science that deals with he cHemical ature and behaviour
{tis somtimes refered to as biological chemistry b
‘of biological living matter in the soil alas such,
or chemical biology,
Importance of Soil Biochemistry in Agriculture
Soll biochemistry i of great importance in ‘sgriculture in the sense that itis the beckbone of soit
‘icobial functioning and without it microorganisms eannat function effectively in the soil, it
involves the chemical compounds that make Up part of the organism living cell or produced by or
in the organisms itself: Some of the biochemical compounds produced by soil microorganisms:
‘have been observed tobe of great importance in agriculture. Examples are:
* Enzymes - catalyse chemical reactions during organic matter degradation (decomposition) and
transformations of cyeles in soil.
+Protcin synthesis, Soil microorganisms and the biochemical compounds they produce play important role in nutricat
transformations and use thus; it improves soil quality and soil produetivity, The biology of the soil
helps to determine the characteristics of the soil, while microbial decomposition of soil organic
maiter enhances soil fertli
/, growth of plants and microorganisms, improves or sustains the
carbon storage of soil and improves soil structure,
SOIL MICROBIAL BIOMASS
Soil microbial biomass is the measure of the mass. of living components of soil organic matter. It
consists mainly of Racterie, Fungi and Protozoa which decompose crop residues and omanic
‘matter in the soil. This process releases nutrients such as nitrogen into the soil that are available
for plant uptake, About half of the microbial biomass js located in the surface 10 cm of the soil
Profile and most of the nutrients released also occur there. Generally speaking. up to 5% of the
total organic carbon and Nitrogen in soil is in the microbial biomass. When microorganisms die,
‘these nutrients are released in forms that can be taken up by plants.
Measures of Microbial biomass usually measure either the weight of carbon or nitrogen in the soil
biomass usally starved bectse the soil might bs too
dry or does not have enough organic carbon 50 the amount of labile carbon is of panicuer
importance as this provides readily availible earbon source Tor ierobal dscomposiion. Soils
organisms, In some soils, the microbial ‘same time, thereby suggesting a state of equilibrium almost all the time. However, increase in
microbial biomass over time are considered beneficial. They may indicate an increase in biological
‘beneficial function in soil and future increase in organic carbon content in the sci. In contrast,
decrease over time is considered to have a negative effect on soil quality.
‘Microbes interact ivith each other whether in a mutualistic, symbiotic or suppressive relationship,
they all coexist in the eco-system. The interaction between microbes and plants oceurs in the
Rhizosphere which isthe root zone in close vicinity with the soll. This the zone where complex
biochemical and biological activities between "Microbes and Microbes’, ‘Microbes nd Plants’
‘and ‘Plants end Plants’ are continuously going on to influence the biodiversity in the soil.
The complex soil biodiversity reflects the greet variability among the living entities in the soil
ranging ftom the large number of invisible microbes; bacteria, fungi, protozoa, nematode to the
familiar macro-fauna such as earthwomn and termites. Soil microorganisms play fundamental roles
in soil, they facilitate most, if not all biochemical processes in soil such as carbon and nitrogen
‘eyele, the degradation of organic pollutants, the retention of organic pollutants: action on soil
communities of microorganism are also likely to integrate all the environmental
stresses that affect the soil. In this respect, they Seu i ri ae
structure, est Soil Micro fatina and Micro flora and fungi,
* Soil Meso fina,
© Soil macro fauna,
Soll Mega fauna [based on the recent classification].
Micro fauna, micro flora and fungi whose sizes are between 1-10ym include, Protozoa,
Roundworm, Rotifers, Bacteria and some species of Fungi,
Meso fauna range from 100 - 200um, they include Mites and sptingtails.
Macro fauna are organisms that ae visible to the naked eyes.
11 FACTORS AFFECTING SOIL MICROBIAL BIOMASS
The soil microbial biomass is affected by factors that changes the water or carbon content of the
soil. These inclide;
* Soil properties; Soil type, clay, Soil pH, organic. carbon, soil moisture ¢,t,0,
* Atmospheric properties; Climate
‘+ Management practices
Rainfall is usually the limiting eli CLAY
cee SUPPLIES NUTRIENTS TO
PLANTS
nae SOIL MICROBIAL
BIOMASS (BACTERIA .
orcs |b, tteseses
cate ies encenecs
ORGANICMATTER
Figure 1. The main properties affecting microbial biomass and factors influenced by it
ASSIGNMENT 1
Discuss how the following soil factors affect microbial | TYPES OF MICROBES AND THEIR DISTRIBUTION PATTERN IN THE SOIL,
BACTERIA
‘They are composed of single cells and they are the simplest form of plant life in the soil. Their
cells. are usually Spm in size. They lack nuclear membrane and therefore, their nucleopiasm is not
separated fiom the eytoplasm which is why they are called Prokaryotic organisms. They are the
‘most nunterous organisms in the soil with a population ranging from one hundred million to three
hundred million (100,000,000 - 300,000,000) in a gram of soil. A Bacterium is capable of
producing sixteen million (16,000,000) more in just twenty-four hours (24hirs). Majority of the
beneficial soil bacteria need oxygen and they are thus termed * Aerobic Baeteria’, while those that
do not require oxygen are termed *Anaerobic Bacteria’. This class cause putrefaction of dead
organic matter.
Various species of Bacteria thrive on different food source and in different environment. In
general, Bacteria are more competitive when labile substrates are present. These include, fresh
‘young plant residues and the compounds found near living roots. On the other hind, Autotrophie or Lithotrapie Bacteria are Bacteria that. utilize inorganic
paterials such as NH, Fe, S, and COs as sources of food and enerey
‘There are two categories of autoirophs, namely:
hs or photolithottophis, They obtain energy from sunlight
ithotrophs. They obtain energy needed for growth and
+ Photoautotropt
+ Chemoautotrophs or Chemoli
biosynthesis from the oxidation of inorganic material ot organic eatbon,
Obligate chemonutotrophs are specific for their elemental sources and silize only one or small
soup of lated compounds e.g. Nirobdcter oxidizes nitrite Nitrosomonas oxidizes ammonia and
Thtobacittus oxidizes certain inorganic sulphur compound,
Facultative Chemoautotrophs depend on the oxidation of inorganic ‘material or organic carbon.
‘The chemoautotrophic Bacteria may be subdivided on the bases
provides the energy for growth and cell synthesis, They. ‘include;
+ Nitrite is oxides to Nitrate by
Jnorgenic Sulphur is oxidized te ‘Therefore, Chemoautotrophs are important becabse of the high energy reaction they catalyze and
‘several of the processes for which they are responsible are significant in erop production, Pur
example:
‘+ The formation of niirate in nitrification is catalyzed by Nitrosomonas and Nitrobacter to
provide plant with Inorganic mutrients in an easily assimilated form
‘+ Fiemental Sulphur has been used to control potato scab disease and to bring alkaline soils
into production,
Finally, Bacteria eolls arc often distinguished into Gram positive (+ye) and Gram negative (-ve).
> Gram +ve Bacteria are Bacteria cells that become crystal violet after treatment with gram staining
solution containing Potassium Jodide, Whereas, Gram -ve cells are distained readily.
Symbiotic
; <<
roe sombiotc
Aerobic N fixers: ENVIRONMENTAL AND ALLELOPATHIC SIGNIFICANCE OF BACTERIA.
Bacteria take part in many if not all organic transformations of importance to soil fertility and
growth of higher plants, They are responsible for a number of enzymatic reactions eg. Rhizobium
can be inoculated into legume seeds to fix Nitrogen in the soil. The Nitrogen fixing Bacteria lives
in the root nodules of legumes such as Clover, Beans, etc.
Autotrophic bacteria by oxidation can convert Ammonia, ‘Sulphur, Manganese and Iron, toNitrate,
Sulphate, Manganese (IIT) ion and Ferric ion respectively. These oxidation process is also believed
10 have some side effects by causing rust formation on metal surfaces.
Some Bacteria are capable of detoxifying carbon monoxide gas into carbon dioxide gas (more
harmless) by similar oxidation process whereas some are reported to be capable of reducing carbon
dioxide gas to methane gas by anaerobic reaction. Several scientists believe that these reactions
have a significant role in maintaining the quality of our environment in view of the decrease in
emission of COz into the atmosphere.
It must be stated that Bacteria can be of good benefit and also harmfil to some other organisms.
Several of them are capable of causing diseases in plant. Forexample, the Bacteria wilt disease in
tomato and Bacteria blight disease in Rice. E. coli and Bacillus infections are food poisons
‘Salmonella and are meant 10. oeten nn CHARACTERISTICS OF BACTERIA
Bacteria are deseribed on the bases of Taxonomy and Morphology, their environmental tolerance,
their spatial distribution in the soil and their biotic relationship with other organisms or higher
plants. Some Bacteria species are very fragile and ean be killed by slight changes in the soil
environment while other species are extremely tough and are able to withstand severe heat, cold
‘and drought conditions, Some can remain dommant for decades, waiting for a favorable condition
and others can extract Nitrogen direotly from air or breakdown of some foxie substances, The
population of microbes can boom in a space of few drops in response to changes in soil meistar,
temperature and carbon substances. To gain advantage in the process, many microbes release
antibiotic substances that suppress particular competitor. In this way, some species can suppress:
other disease causing ee
MANAGEMENT OF SOIL BACTERIA
Though largely unaffected by cultivation, Bacteria population are depressed by dry conditions,
salinity, soil compaction and lack of organic matter. It is ‘very difficult to build
acidity, alkalinity,
adesirable condition for Bacteria just by adding them to the soil IF the population of soil Bacteria
is low, it is probably because the soil condition is unfavorable, so any addition of other Bacteria
tty ‘A gram of ganten soll ean contain about Ore mittion (1,000,000) Fungi stich as Yeast and Molds",
‘ince growth can take place from either a spore or Mycelium fragment, itis difficult to estimate
their numbers,
Fungi has no chlorophyll therefore, they are not eble to photosynthesize besides that, they cannot
use atmospheric CO: as a source of Carbon, therefore they are heterotrophic organisms or
sometimes class es Chemo-heterotrophs meaning that, like animals, they require a chemical
souree of energy rather than being able to use light as an energy source as well as an organic
substrate fo get carbon for growth and development.
Fungi function mere effectively than Bacteria because they assimilate into their tissue a bigger
portion of the arganic material they metabolize i.e. they have a high carbon use efficiency than
Bacteria, Another ebility that allows many Funai to greetly outperform Bacteria in Decomposition
of plant litter is the ability to produce lignocellulose degrading enzymes such as laccases, lignin
and Manganese dependent peroxidases and cellulase.
GROUPS OF FUNGI
. ‘The main functional groups of soil fungi are;
1, Decomposers or saprophytic fungi
2. Mutualist 2
|. Mycorchiza and immobilization and retaining nutrients in the soil. The organic acids they produce as by-
Products help create onganié mater that is resistant 1 degradation. However, Fungi are
vapable of degrading Cellulose, Protein and Lignin, some of which arc highly resistant to
breakdown, In other words, fungi are enormously important in Carbon and Nitrogen eycle
because of their ability to degrade complex substrates of plant origin which represent up to
90% of the net primary production in most terrestrial ecosystem.
+ Mutualisis are fungi that develop mutual beneficial relationships with plants, They colonize
plant root and they help the plant obtain nutrient such as Phosphorus from the soil. Their
‘mass hides the roots from pests and Pathogens and provide greater surface area through
which plants can obtain nutrients,
. Mycorthiza are the best known of the mutualist. It means Fungus root and Mycorhiza
fungi grow in plant root. Up to 5 m of living hyphae of Mycorthiza Fungi can be extracted
from 1 g of soil. The four groups of Mycorrhiza fungi are;
‘Arbuscular Mycorthiza Fungi (AME)
Ecto Mycorrhiza
Ericoid
Orchid 4. Pathogens, This group include well known fungi such as Vertilivm, Rhizoerona, and
Pythium. These organisms penetrate the root and decompose the fiving tissues creating
weakened nutrient deficiency in plants and in some eases, it results in the death ‘of the plant.
The pathogenic Fungi are usually the dominant organisms in the Soil, Solls with rich
biodiversity have ee known to suppress soil borne fungi diseases. The suppression
iechanisin includes the native organism out competing the pathogenic organisms by
physically protecting the root and providing a bettor nutrition for the plant, Plant diseases
caused by soil-dwelling fungi include bottom rot, black spot, canker, rust, Rhfzoctonia
disease, root rot and potato wart Pathogenic soil fngi are commonly found at the onset of a.
the cropping season. ;
BENEFITS OF SOUL FUNGI
1. ‘They decompose woody organic matter; Along with Bacteria, Fungi are important
decomposers of hard to digest organic matter. ‘They use Nitrogen in the soil to decompose
woody carbon rich residues low in nutrient and convert the nutrient in the residue to forms
that are more accessible for other organisms, 3. Improves plant resilience; the sheer size and muss of fungi help decrease plant
susceptibility to pests, disease and drought. Mycorrhiza fungi helps improves plant vigor,
decrease plant root hae ‘and can alyo decrease susceptibility to nematode
4, Improves soil structures fungi hyphae bind soil particles together to ereate a water stable
aggregate which in tum creates the pore spaces inthe soil that enhance water retention and
arainage,
MANAGEMENT OF SOIL FUNGI ‘o survive. The lichen fungi share A common ecological strategy of hosting an intemal population
of photosynitiela ces farm Seiichi vey obtain their carbon source in the form of simple suger,
‘ype of organism, Fungi are heterotrophs, ‘teaning that, like animals they require acarbon source
The photosynthetic el'oan either be reen algae (chlorophyta) or cyanobacteria or both |
ENVIRONMENTAL AND ALLELOPATHIC SIGNIFICANCE OF SOM. FUNGI
Fungi are enormously important in ‘carbon and nitrogen cycling because of their ability to degrade
complex substrates Of plant origin Which iepresenia upto 96M of the net primary production in
‘most terrestrial ‘Scosystems, Fungi depend on orgenics matter in soil for food and energy supplies
because unlike bacteria, fungi lack chlorophyll. Since they do not possess chlorophyll, fungi are
either parasites, ‘Pathogens saprophytes or symbionts in nature.
Scrophyvefmel contrat fo demure eying inthe sol together wih Bacteria, they share
the responsibility of decomposing organi residuts in soil, breaking them down into simpler forms
which then become aval i
ne ae slthough this rot process is considered harmful
from a human point of : (on antibiotic) was isolsted originally ftom fungus Penicillium notaram, Aflatoxin produced by
Aspergillus faves is very detriniental to human and animal health. The micro toxin (aflatoxin) is
suspected to be carcinogenic hence very harmful to animals end humans. The organism thrives on