The Living Soil: The Basis of Ecologically Sustainable Agriculture*

A compilation of the lecture notes of Dr. T.C. Mendoza , Professor of Crop Science , Crop Science Cluster, College of Agriculture, UPLB. August 2012

1.0. What is soil ?

2.0. Natures Principle relevant to the soil

3.0. Functions of Soil

4.0. What is Soil quality ?

5.0. Composition of soil – the Living Organism

5.1. SOM and its importance

5.2. Functions of soil organisms

5.3. Major groups soil organisms

5.4. Organic Matter and the functions of humus

5.5. Differentiating organic matter and humus

6.0. Building up soil organic matter/humus ( separate lecture module on nutrient cycling )

7.0. Natural plant nutrition

8.0. Nitrogen Fixation

Annex A. Review of Major elements required for plant growth

References:

Alexander, M. 1977. Introduction to Soil Microbiology. 2d ed. John Wiley & Sons. New York, NY.

Bargyla and Gylver Rateaver. The Organic Method Primer.

Carter, V. G. and Dale, T. Top Soil and Civilization (Rev. Ed)

Hendrix, P.F., M.H. Beare, W.X. Cheng, D.C. Coleman, D.A. Crossley, Jr., and R.R. Bruce. 1990. Earthworm

effects on soil organic matter dynamics in aggrading and degrading agroecosystems on the Georgia

Piedmont. Agronomy Abstracts, p. 250, American Society of Agronomy, Madison, WI.

Magdoff F & RR Weil.2004.Soil Organic Matter in Sustainable Agric.CRC Press LLC 398 p.

Paul, E.A. and F.E. Clark. 1996. Soil Microbiology and Biochemistry. 2d ed Academic Press. San Diego, CA.

Scheewe, W. Nurturing the Soil: Feeding the People. Rev., updated & Expd. Ed.

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* This is a compiled lecture notes of T.C. Mendoza , Professor of Crop Science , Crop Science Cluster, College of Agriculture, UPLB. August 2012

1

1. What is soil?

… where you and me or all of us came from (biblical)

… is the transformation product of mineral and organic substances on the earth’s surface under the influence of environmental factors operating over a very long time and having defined organisation and morphology (technical)

….. is a natural medium on the surface of the earth where plants grow.

… growing medium for plants

… bases of life for all plants, animals, humankind

… where our FOOD actually comes…

FOOD = NUTRITION = HEALTH

… where our nutritious food comes from

… the basis of human health

Health is wealth

… soil is the basis of our wealth

… soil is the basis of our happiness

Health is happiness

Soil as the basis of life

FOOD = nutrition = health = wealth = hapiness

How is soil formed?

Soil formation is long and complex, it can take

anywhere from 100 to 10,000 years to create one inch

of topsoil! Soil formation is driven by factors such as

climate, topography, living organisms and the type of

parent materials. Parent materials come from the

break down of underlying rock or from deposits by

streams and rivers, seas and gulfs, hills, wind and

glaciers or organic plant residues. Over time, these

materials are weathered by the effects of freezing,

thawing, wetting, drying, heating, cooling, erosion,

plants, and animals and from chemical reactions with

water, oxygen, organic and inorganic acids, and

organic matter. Eventually the parent material is

divided into smaller and smaller particles and forms

layers called "horizons". The top layer of soil is the

A-horizon is the one containing most of the organic

matter and biological activity. The B-horizon is the

zone of maximum accumulation of materials, and the

underlying C-horizon is mainly the parent material,

but slightly altered. The younger the soil is, the less

developed are these underlying horizons and the

thinner the top horizon.

Evolution of the concepts or misconcepts about soil

Soil is alive -> the living soil. Soil is a living, dynamic matrix that feeds and recycles liquids, gases and solid matter. Hence it is food for microbes, insects, animals and plants.

Soil is not simply a physical object or dust (indicative of non-life). A gram of fertile soil housed….

o 2.5 M – bacteriao 4000,000 – fungio 50,000 – algaeo 30,000 – protozoao 25,000 – nematodeso 500+ - spring tails, worms, insects, mites

Soil as the basis of healthy life

healthy soil -> healthy plant

-> healthy human beings

-> healthy society

Why? Sick soil -> sick plant -> sick society

Impoverished soil

-> impoverished human being

(sick individual, family, society)

Soil as the basis of nations wealth not only health

When soil is gone so is the wealth of the nation !

2

2.0. Nature’s Principle Relevant to the Soil

Principle One: In nature, soil is always covered.

Principle Two: There is always a diversity of

plants.

Principle Three: There is always a cycle of energy

and nutrients.

Principle Four: Plants regulate the uptake of

nutrients on their own.

Principle Five: The vegetation absorbs a maximum

of sunlight.

Principle Six: The soil “plows” itself.

Principle Seven: Life is interconnected.

3.0. Importance/Functions of Soil

Soil is the medium that enables us to grow food

for people or animals, natural fiber, and timber, and

supports wildlife. Around 99 % of global food

supplies (calories) for human consumption come

from land-based food production (FAO, 2007).

Soil is a natural filter that neutralizes certain

pollutants by transforming them or accumulating and

absorbing their toxicity. In addition, soils are a major

factor in purifying water supplies and are a critical

component for regulating flooding through

the storage of rainfall. The sealing and compaction of

permeable soils results in a more rapid delivery of

rainfall to the river network. These are just examples

of the critical ecosystem services provided by soil.

Soil is a biological engine where dead plant

and animal tissues, and other organic wastes, are

decomposed to provide nutrients that sustain life.

Soil plays a crucial role in regulating a

number of life-sustaining natural biological and

chemical cycles (ecosystem services). Carbon,

nitrogen and a range ofessential nutrients are

continuously recycled between the soil and plants,

geological deposits, groundwater and the atmosphere.

The intensity of these biogeochemicalexchanges

varies from place to place and is regulated by soil

characteristics.

Soil protects our buried heritage of

archaeological and historic remains from damage and

depletion. Much of the evidence of past habitats and

human heritage remains buried, awaiting discovery

and study by archaeologists and palaeo-ecologists.

The degree of

preservation of such remains depends on the local

soil characteristics and conditions [2]. Soils that

preserve cultural heritage should also be regarded as

valuable.

Soil provides the foundation on which we

construct our buildings, roads and other

infrastructures. In addition to providing the support

for the vast majority of human infrastructure, soil

provides a range of raw materials such as clay for

pottery and

peat for fuel.

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Soil has important ecosystems functions

as follows ……..

(a) recycling of organic materials in soils to release

nutrients for further synthesis into new

organic materials;

(b) partitioning of rainfall at the soil surface into

runoff and infiltration;

(c) maintaining habitat diversity of pore sizes,

surfaces, and water and gas relative

pressures;

(d) maintaining habitat stability, including a stable

structure, resistance to wind and water

erosion and buffering of habitat against rapid

changes of temperature, moisture, and

concentration of potentially toxic materials;

(e) storage and gradual release of nutrients and

water

(f) the partitioning of energy at the surface, which

is important in global circulation processes.

(g) sequestering carbon through the humus

cycle.Under organic management, soils can

provide carbon sequestration of 2 ton/

hectare per year

Cycling of carbon and nutrients is probably

the best known soil function in ecosystems. Carbon

and nitrogen cycles have been measured and

modeled. Nutrient cycling has been studied more in

non cultivated soils (e.g., forests or rangeland). The

levels of cycling activity that can be expected in

specific ecoregions are known.

The partitioning of water at the soil surface is

an equally important function in ecosystems. This

partitioning determines both quantity and quality of

surface and groundwater. Water running over the

surface can carry sediment and other pollutants, and

quickly reaches drainages. Water that infiltrates into

the soil and moves (Source: Warkentin, 1995.

JSWC). Top soil serves as biofilter. It purifies the

water before it infiltrates deep into the ground.

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4. What is soil quality?

One soil scientist defined soil quality as “the

integration of different chemical, physical, and

biological properties of soil interacting in complex

ways that determine its potential fitness or capacity to

produce healthy and nutritious crops. The concept is

now expanded to include not only soil productivity

but also food quality/safety, environmental quality

and human/animal health.(Fig. 1). Thus, with these

concept, we can now describe a relationship given us:

Healthy soil = healthy crop = healthy society

Healthy animals

The backward arrow depicts a healthy

society nurturing a healthy soil. A healthy crop grows

in a healthy soil. But what is a healthy soil? This

leads us to the characterization of healthy soil. One

soil scientist (Haberern, 1992) introduced the idea of

“Soil Health Index”. Soil Health Index (SHI)

characterize soils capability to produce healthy and

nutritious crops in a sustainable way. SHI explores

the components of soil quality as relate to sustainable

agriculture. How soil quality can be quantified to

indicate the status of soil health and provide an early

warning of soil degradation and the need for remedial

measures.

But exactly, what is a healthy or quality soil

for crop production?

Can we list easily distinguishable physical,

chemical, biological properties?

Physical - thick top soil (> 30 cm)

- Dark brown to black color (red soils are

associated with acid soils and low P) is

associated with high organic matter.

- Friable, loose, porous (low bulk density)

These physical characteristics translate easily to the

following:

high water holding capacity

well-drained and well-aerated

easy to prepare/till for planting

walking on it gives no harm for bare feet, it

is walking on a foam

Chemical - near neutral pH (pH 5.5-6.8)

- High cation exchange capacity (C.E.C.)

or nutrient retention

- Low electrical conductivity (Eo = < 4) or

low saltiness

- contains adequate amount of all the

essential nutrients

- High soil organic matter (OM > 3%).

Singularly, it is one important soil quality

indicator. High SOM is always equated to

fertile or quality soil for crop production.

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Chemical

NPK

Micronutrients

pH, Salinity

Physical Structure

Air, Water, Tilth,

Biological

Organic Matter

Roots/Weeds/Fertility/Insects

Bacteria, Fungi, Insects, Earthworms

Listing all indicators of healthy/quality soil is important as it gives us a picture on the status of the soil

currently use for crop production as shown in the simple illustration below.

Degraded fertile/healthy

poor quality soil quality soil

|__|__|__|__|__|__|__|__|__|__|

0 1 2 3 4 5 6 7 8 9 10

It maybe difficult now to find a soil which has 10

maximum points in the spectral line. Most soils are

perhaps between 3-6 points. What is the relevance of

describing soil as to its quality status? It is related to

the amelioration needed, or management and/or crop

species that must be planted and the adaptive farming

practices that must be done.

Some farmers in Bondoc Peninsula, Quezon no

longer plant corn in adversely eroded/degraded soil,

instead, they plant trees (mahogany, narra, madre de

cacao, coconut) and are seeded with cover crops.

They select the more “fertile” soils for planting

ginger, corn, upland rice and vegetables.

Is Soil health = Soil quality ?

Soil health is used synonymously with soil

quality . The relationship is drawn between and

health and the health of animals and humans eating of

animals and humans eating the crops produced by the

soil (Haberern,1992). The components of soil health

are the biological processes that produce a balance of

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macro and micro nutrients, traces organics that have

enzymatic functions, and the freedom from plant

diseases and from various pests that attack unhealthy

crops growing in unhealthy soils. Soil health is

achieved by promoting biological activity in the soil

through additions of organic matter, and by avoiding

addition of potentially toxic materials. These ideas

were largely the concern of organic farming as we

learn more about the dependence of our health on the

foods we eat.

. The use of biological activity in concepts

of soil quality or soil health has been a relatively

minor theme in soil science in the last 50 years. Soil

productivity has been related more to additions of

nutrients and management of water. Soil biology was

more prominent in the previous half century, after the

discoveries of soil bacterial functions and nitrogen

fixation by symbiotic and free living bacteria.

Biological processes were not understood until the

latter part of the 1800s, well after physical and

chemical properties of soils were investigated in the

mid years of the century.

In the last 15 years there has been increased

interest in measuring biological parameters to

characterize soil functions. Measurements of

biomass activity measured by respiration, enzymatic

activity, and diversity of organisms are all becoming

much more important (Doran et al.). These

biological parameters are being related to soil

management – to determine the effects, for example,

of different tillage practices on soil biota.

Fig.1 Attributes of Soil Quality

Soil Productivity

Human/ Animal Food Quality/

Health Safety

Environmental

Quality

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Fig.2 Interrelationships of principal factors Affecting Soil Quality

SOIL ATTRIBUTES

Physical

Chemical

Biological

CLIMATE SOIL QUALITY LAND

Rainfal l Vegetation

Temperature Geology

Storms Drainage

Run-off

HUMAN

MANKIND

Land use

Mgt. Practices , Costs of inputs , Ownership

Marketability , Farm policy

Indicators of Soil Quality:

Soil Quality Index (SQI)

SQI = f (SP, P, E, H, ER, BD, FQ, MI)

Where: SP = Soil Properties (Physical, Chemical, Biological), ER = Erodibility

P = Potential Productivity BD = Biological Diversity

E = Environmental Factors FQ = Food Quality/ Safety

H = Health (Human, Animal) MI = Management Inputs

3.0. Composition of Soil - the Living Organism

Lady Eve Balfour coined in 1943 the notion

of “the living soil” and concluded that one has to

“feed the soil and let the soil feed the plants.” The

tradition of organic agriculture sees the soil as an

organism, which contains countless organisms. Soil

is alive: decomposition processes are driven by a

mass of soil microorganisms.

A living soil contain around 50 percent clay

and sand particles (solids), 25 percent water, and 25

percent air. The solids can contain around 5 percent

(but often less) organic matter that is composed

largely of humus. Humus originates from various

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forms of organic matter and is essential for the

fertility and structure of a soil. Although it represents

only a little share of the soil, it determines how the

soil looks like and its corresponding fertility. (Humus

will be discussed in more detail later).In a good or

fertile soil, a huge variety of micro-animals and

microorganisms are active in making up humus, to

convert it later into plant nutrients, and to provide

additional services to the plants growing on the

surface of the soil. There are earthworms, termites,

nematodes, and many other micro-animals (about 50

to 100 different species and varieties) involved in

these activities. Further, there are algae, fungi

(similar to molds), bacteria, actinomycetes, and

protozoans. A handful of soil may contain more than

10 billion microorganisms (Torsvik and Ovreas,

2002), the majority of which are bacteria —

comparable to the number of people on Earth! In

addition to the huge amounts of bacteria, 1 m3 of

fertile topsoil will contain hundreds of kilometers of

fungal hyphae, tens of thousands of

protozoa,thousands of nematodes, several hundred

insects,spiders and worms, and hundreds of metres of

plant roots. The total weight of microorganisms in the

soil below a hectare of temperate grassland can

exceed that of a medium-sized elephant — five

tonnes — and often exceeds the above-ground

biomass. This biota is involved in most of the key

functions of soil, driving fundamental nutrient

cycling processes, regulating plant communities,

degrading pollutants and helping to stabilise soil

structure. Soil organisms also represent a crucially

important biotechnological resource, with many

species of bacteria and actinomycetes providing

sources of antibiotics and other medicines.

It is difficult to see soil biological features.

But many living organisms thrive in

soil as in .

. .

2.5 million Bacteria

1 gram of fertile 400, 000 fungi

agri-soil

(Erlich, et. Al. 1977) 50, 000 algae

30, 000 protozoa

These organisms compete but the prevailing

mode of existence is mutual dependence. One

member of the ‘soil community’ is in one way or

another dependent on many other members. Most

members of the soil community are living either from

dead organic matter or depend on energy provided by

plants through their roots. The interrelations between

the soil organisms are so manifold that it is

impossible to understand them completely. We know

very little about the control and adjustment processes

between the different soil organisms. (Winfried

Scheewe, 2000. Feeding the People: An Introduction

to Sustainable Agriculture)

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4. Soil Organisms and their Functions

Organisms and the soil animals can be

distinguished according to their respective functions

in the soil.

1. The first group is

composed of the decomposers or ‘humus

makers.’ Many soil animals belong to this

group as well as many species of bacteria,

fungi, and actinomycetes - food preparers.

2. Another group breaks

down the soil humus making the nutrients

accessible for the plant roots done by bacteria,

actinomycetes, and fungi food cookers.

3. Several species of

bacteria, algae, and actinomycetes fix gaseous

nitrogen and make it available to plants - food

synthesizers

4. Many soil animals and

microorganisms improve soil structure through

their natural activities - soil structural builders

5. Many organisms

discharge some kind of enzymes, which can

stimulate plant growth, and the activities of

other organisms. Some organisms secrete

substances like antibiotics that inhibit the

development of various organisms.

6. Several organisms and

soil animals also exude substances in the soil

environment adverse to some crops and other

plants.

Major Groups of Soil Organisms

A diverse biological community in soils is

essential to maintaining a healthy environment for

plants. There may be over 100,000 different types of

organism living in soils. Of those, only a small

number of bacteria, fungi, insects, and nematodes

might harm plants in any given year. Diverse

populations of soil organisms maintain a system of

checks and balances that can keep disease organisms

or parasites. Some fungi kill nematodes and others

kill insects. Still others produce antibiotics that kill

bacteria. Protozoa feed on bacteria. Some bacteria

kill harmful insects. Many protozoa, springtails, and

mites feed on disease-causing fungi and bacteria.

Beneficial organisms, such as the fungus

Trichoderma and the bacteria Pseudemonas

fluorescens, colonize plant roots and protect them

from attack by harmful organisms.

Microorganisms - are very small forms of life that

can sometimes live as single cells, although many

also form colonies of cells. A microscope is usually

needed to see individual cells of these of these

organisms. Many more microorganisms exist in

topsoil, where food sources are plentiful, than in

subsoil. They are especially abundant immediately

next to plant roots, where sloughed off cells and

chemicals released by roots provide ready food

sources. These organisms are important primary

decomposers of organic matter, but they do other

things, such as providing nitrogen through fixation to

help growing plants. Soil microorganisms have had

another direct importance for humans - they are the

origin of most of the antibiotic medicines we use to

fight various diseases.

1

Considering the biomass that each group in the

soil presents, microorganisms are the most abundant.

The following groups are common in the soil:

a) Bacteria.

One of the simplest and smallest forms

of life known. They possess an unlimited

capacity to increase their numbers in the soil by

growth and division as they are single-cell

organisms

Many bacteria are able to produce

spores or similar resistant bodies that allow

them to endure unfavorable conditions. Soil

bacteria are either autotrophic or heterotrophic.

Autotrophs obtain their energy from the

oxidation of mineral parts in the soil. Most

bacteria are heterotrophic; their energy and

carbon requirements come directly from

organic matter.

Bacteria live in almost any habitat. They

found inside the digestive system of animals, in

the ocean and fresh water, in compost piles

(even at temperatures over 130oF), and in soils.

They are very plentiful in soils; a single

teaspoon of topsoil may contain more than 50

million bacteria. Although some kind of

bacteria live in flooded soils without oxygen,

most require well-aerated soils. In general,

bacteria tend to do better in neutral soils than in

acid soils.

Bacteria as a group participate in all of

the organic transactions in support of higher

plants. They dominate processes like nitrogen

oxidation, sulfur oxidation and nitrogen

fixation. In addition to being among the first

organisms to begin decomposing residues in

the soil, bacteria benefit plants by increasing

nutrient availability. For example, many

bacteria dissolve phosphorous, making it more

available for plants to use.

Bacteria are also very helpful in

providing nitrogen to plants. Although

nitrogen is needed in large amounts by plants,

it is often deficient in agroicultural soils. You

may wonder how soils can be deficient in

nitrogen when we are surrounded by it - 78

percent of the air we breathe is composed of

nitrogen gas. Yet plants as well as animals

face the dilemma of the Ancient Mariners, who

was adrift at sea without fresh water: "Water,

water, everywhere nor any drop to drink."

Unfortunately, neither animals nor plants can

use nitrogen gas (N2) for their nutrition.

However, some types of bacteria are able to

take nitrogen gas from the atmosphere and

convert it into a form that plants can use to

make amino acids and proteins. This

conversion process is known as nitrogen

fixation.

b) Fungi.

Similar to most bacteria, they depend

on the soil organic matter for their energy and

carbon needs or relieve it from growing plant

roots. The most common group of fungi in the

soil are molds which can grow in all kinds of

soil environment; acidic neutral, or alkaline,

but have a preference for slightly acidic soil

environment. The diameter of fungal hyphae

ranges from two to ten micrometres. In one

gram of dry soil, one can find 100,000 up to

one million individuals. This would result in

biomass of 800 to 8,000 kg/ha.

1

Fungi are very versatile in their

ability to decompose organic residues. They

decompose cellulose, starch, gums, lignin, and

other substances. In decomposing plant

residues, fungi are usually more effective than

bacteria. They turn more biomass into humus

and produce less “by-products” like carbon

dioxide and ammonium. Up to 50 percent of

the substances decomposed by molds become

organic tissue compared to 20 percent in the

case of bacteria. Fungi can, however, not

perform some tasks which the bacteria can, like

fixing nitrogen or oxidizing metals.

Many plants develop a beneficial

relationship with fungi that increases the

contact of roots with the soil. Fungi infect the

roots and send out root-like structures called

hyphae. The hyphae of these mycorrhizal

fungi take up water and nutrients that can then

feed the plant. This is especially important for

phosphorous nutrition of plants in low-

phosphorous soils. The hyphae help the plant

absorb water and nutrients and in return the

fungi receive energy in the form of sugars,

which the plant produces in its leaves and

sends down to the roots. This symbiotic

interdependency between fungi and roots is

called a mycorrhizal relationship. All things

considered, it's pretty good deal for both the

plant and the fungus. The hyphae of these

fungi help develop and stabilize soil aggregates

by secreting a sticky gel that glues mineral and

organic particles together.

c) Soil Algae are generally chlorophyll-bearing

organisms and, like higher plants, are

capable of performing photosynthesis.

They are largely restricted to the parts of

the soil penetrated by sunlight. Thus, the

soil surface and larger cracks in the soil

are the major zones of algae activity.

Among the four groups of algae, it is the

blue-green algae that is abundant and of

ecological importance in tropical soils.

Algae release carbonic acids that can

accelerate the weathering of minerals. They

also produce large amounts of extra cellular

polysaccharides which can act as soil

aggregating agents. This may be especially

important on bare soils. Some algae have the

capacity to carry out non-symbiotic and

symbiotic nitrogen fixation. This ecological

role is important in flooded rice fields where

algae form a symbiosis with the fern azolla.

d) Actinomycetes resemble molds in their

morphology as they are filamentous,

often profusely branched, and produce

fruiting bodies in the same way. On the

other hand, they are similar to bacteria:

they are composed of one cell and are of

similar size. Actinomycetes produce

reproductive spores that allow them to

endure adverse situations. They develop

best in moist, well-aerated soil but can

stand also drier conditions. They are

relatively sensitive to acid soil condition.

At pH values below 5.0, their activities

cease. Most actinomycetes are free-

1

living saprophytes and are able to

decompose a tremendous array of carbon

rich substrates, like lignin, chitin, and

cellulose. Some actinomycetes produce

quickly evaporating substances called

geomins which contribute to the soil

much of its earthy smell, especially

apparent during and soon after rainfall.

Many actinomycetes exude antibiotics

like streptomycin in support of their

species. Antibiotics also possibly

hamper pathogens in general. Ironically,

some soil borne pathogens come from a

group of actinomycetes. One example is

the sweet potato pox caused by

Streptomyces ipomoeae.

Soil macrofauna

a) Earthworms (oligochaetes) and

the smaller ‘pot’ worms (belonging to the

family of the enchytraeid) are the most cited

members of the soil fauna. They present the

bulk of the soil animals. They are actively

decomposing soil organic matter. They

increase soil aeration and penetrability as well

as the aggregation of soil particles. The

channels created may also influence the

movement of nutrients and enable greater

infiltration of rainwater. Their most important

contribution, however, is the mixing of soil

materials. Worms need a moist but well-

aerated environment to thrive. They need

rough organic matter like leaves as their feed.

Normally in arable soil, their number can vary

from 30 to 300 per square meter.

Earthworms are important as Charles Darwin

believed more than a century ago. They are

keepers and restores of soil fertility. Different

types of earthworms, including the night-

crawler, field (garden) worm, and manure (red)

worm have different feeding habits. Some feed

on plant residues that remain on the soil

surface, while other types tend to feed on

organic matter that is already mixed with the

soil.

The surface-feeding night-crawlers fragment

and mix fresh residues with soil mineral

particles, bacteria, and enzymes in their

digestive system. The resulting material is

given off as worm casts. Worm casts are

generally higher in available plant nutrients,

such as nitrogen, calcium, magnesium, and

phosphorous than the surrounding soil and,

therefore, make an important contribution to

the nutrient needs of plants. They also bring

food down into their burrows, thereby mixing

organic matter deep into the soil. Earthworms

feeding on debris already below the surface

continue to decompose organic materials and

mix them with the soil minerals.

A number of types of earthworms, including

the surface-feeding night-crawler, make

burrows that allow rainfall to easily infiltrate

into the soil. These worms usually burrow to

three feet or more under dry conditions. Even

those types of worms that don't normally

produce channels to the surface help loosen the

soil, creating channels and cracks below the

1

surface that help aeration and root growth. The

number of earthworms in the soil ranges from

close to zero to over a million per acre. Just

imagine, if you create the proper conditions for

earthworms, you can have 800,000 small

channels per acre which conduct water into

your soil during downpours.

They aerate the soil pores for water passage by

tunneling through its depth, mixing in organic

materials as they go. The castings in the soil or

on its surface, are enriched by humus extra

minerals: 5 times as much nitrate nitrogen

surrounding soil, 2 times as much calcium, 2

½ times as available magnesium, 7 times as

much available phosphorus, and

exchangeable potassium..

An earthworm can produce in 24 hours enough

castings of its own weight, up to ½ pound a

year. 10 millions of 5 tons of castings a day,

and 12 tons of topsoil per year. Castings are

not affected by rain because they are colloidal.

The digestive processes of the earthworms kill

many harmful microorganisms of the soil,

while not destroying the useful actinomycetes

multiplying the content of the latter 7 times as

they pass through the worm.

Earthworms multiply very rapidly. There are

many and each type prefers a certain habitat

and cannot be induced to stay at home

anywhere else. It is best to transfer eggs so

when they hatch, the new worms will consider

their current location as home and will be

willing to stay there. Mature worms tend to go

back from where they came. It sometimes

helps to take them up with some of the soil

around them. They leave when organic matter

diminishes, but come from all directions when

there is a good supply of garbage, manure or

sludge, especially attracted to coffee grounds,

cornmeal, mash, and all kinds of carbohydrates.

Cold and heat earthworms cannot take; they

simply go far down into the soil or move away

to a more comfortable spot. Light hurts their

sensitive skins, so when exposed to it they

make every effort to squirm back into the soil.

To sound waves also they are sensitive,

vibrations and noises make them move far

down into the soil.

b) Nematodes or eelworms are

well known for their parasitic role in some field

crops. These non-segmented worms, usually

about one millimeter long and less than 50 mm

in diameter, can often reach population

densities of millions per square meter.

Nematodes need an aerobic habitat and feed off

the tissue of plants (under certain

circumstances they can become a pest) as well

as algae and other decomposing

microorganisms. Thus, they are affecting

primary production and decomposition in the

soil as well. A number of nematodes are

parasites as they feed on other members of the

soil microfauna, particularly protozoa and also

other nematodes. The activities regulate

secondary decomposition in the soil.

Nematodes live mostly in water films which

allow them high mobility. They can survive as

cysts in adverse conditions for longer times.

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Some types of nematodes feed on plant roots

and are well known plant pests. Diseases such

as pythium and fusarium, which enter feeding

wounds on the root, sometimes cause more

damage than the feeding itself. However, most

nematodes help in the breakdown of organic

residues and feed on fungi, bacteria and

protozoa as secondary consumers. In fact, as

with the protozoa, nematodes feeding on fungi

and bacteria also helps convert nitrogen into

forms for plants to use. As much as 50 percent

or more of mineralized nitrogen comes from

nematode feeding.

c) Termites represent another

group of decomposers in tropical soil. The

quantities of materials they deposit often

compare to the surface casting of earthworms.

The effect of termites on soil productivity,

however, I less beneficial than that of

earthworms chiefly because of the organisms in

the guts of the termites. These organisms

require energy in the form of carbon which

could otherwise serve different soil organisms

or be turned to humus. Termite deposits

commonly have a lower organic matter content

than the surrounding topsoil because termites

mix subsoil with low organic content into their

mounds. They accelerate the decomposition of

dead areas and grasses but disrupt crop

production by the fast growth of their nests or

mounds.

d) Springtails or Collembola are wingless

insects that live near or on the surface of soils.

The species living on the surface posses

springing organs, compound eyes, and

elongated antennae. None are more than a few

millimeters in length and those normally living

beneath the soil surface are even smaller. Like

mites, springtails are very numerous. They

show varying degrees of tolerance to different

environmental factors. Springtails feed on

leaves and other organic matter as well on the

microflora.

d) Arthropods composed another

large family among the soil animals and is

composed of many classes and species of

invertebrate animals, like insects, arachnids,

and crustaceans. They include saprophagous

animals like millipedes which feed on dead

plant materials as well as the centipedes which

are preying on soil animals. It is unclear if the

species decompose organic matter with their

own enzymes or if they depend on the

microflora in their guts. In general, arthropods

comprise a small part of the soil animal

biomass. Ants play an important role in

aerating the soil. They help improve the crumb

structure of the soil and transport a lot of

biomass. In many forest sites, ants represent

50 percent of the arthropods found in the soil.

5.0. Organic Matter and the Formation of Humus

All organic matter that remains in the field

will eventually fall to the ground and decay. The first

decomposers rapidly invade the organic debris. The

useful substances are converted into the body

materials of the decomposers. Larger soil animals

also produce feces or excrements which serve as

feeds for other life forms. Additional waves of

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decomposers follow and feed on whatever remained

from the debris.

Under the participation of many different

species and innumerable individuals of soil animals

and microorganisms, organic matter is turned into

humus. In a natural systems, it is an ever-repeating

process: leaves, straw, or stems of plants fall on the

soil after they have died and are decomposed. The

following illustrations provide a brief description of

the formation of humus.

1. Usually, the dead organic matter

already contains microorganisms like

fungi (molds) on its surface when it falls

down to the ground. The withering

continues on the surface of the soil. The

microorganisms make the leaves or straw

soft in texture.

2. After some weeks it becomes

digestible to various soil animals which

start feeding on it. Among these soil

animals are millipedes, mites, insect

larvae, springtails, and worms.

3. By passing through the intestines

of the soil animal, like earthworms, the

organic matter is turned into a medium

that is suitable for the growth of certain

bacteria, fungi, and algae.

4. The leaf or straw litter and the

feces of the animals are now suitable for

the growth of other microorganisms.

The microorganisms create the feed for

other species of springtails, mites, and

small worms.

5. The feces of these soil animals

and the remaining fragments of leaves

and straw are providing the feed for

algae, nematodes, and other

microorganisms that decay further the

organic matter. Near the end of this

cycle, the original organic matter is no

longer visible. Everything is converted

into humus. In this stage, humus can

persist for a long time.

The roles of the soil animals and microorganisms in

decomposing organic matter are complementary and

interrelated. The conversion of organic matter into

humus is a gradual process. It relies on the activities

of many different organisms and soil animals. The

intensity of this process depends mainly on the

quantity and quality of organic matter, the

temperature and the level of moisture in the soil. 5.1.

Organic matter and its importance

Soil organic matter, and the soil organisms

that live on it, are critical to many soil processes.

Organic matter allows high crop yields and reduced

input costs. Up to 15% of soil organic matter is fresh

organic material and living organisms. Another third

to one half is partially and slowly decomposing

material that may last decades. This decomposing

material is the active fraction of soil organic matter.

The active organic matter, and the

microbes that feed on it, are central to nutrient

cycles. Many of the nutrients used by plants are held

in organic matter until soil organisms decompose the

material and release the nutrients to plants. Organic

matter is especially important in providing nitrogen,

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phosphorus, sulfur, and iron. A soil with 3% organic

matter contains about 3,300 kg of nitrogen per ha

(225 kg/mu). Depending on the rate of

decomposition, 10 to 50 kgs may become available to

plants in a year.

The Changing Forms of Soil Organic Matter

1. Additions. When roots and leaves die, they

become part of the soil organic matter.

2. Transformations. Soil organisms

continually consume plant residue and other

organic matter, and then create by-products,

wastes, and cell tissue.

3. Microbes feed plants. Some of the wastes

released by soil organisms are nutrients that

can be used by plants. Organisms release

other compounds that affect plant growth.

4. Stabilization of organic matter. Eventually,

soil organic compounds become stabilized

and resistant to further changes. This

compound is knows as “humus”, is the end

result of organic matter decomposition by

microbes.

5.2. Functions of Organic Matter

1. Nutrient cycling Increases the nutrient holding

capacity of soil (CEC). Is a pool of nutrients for plants. Binds nutrients, preventing them

from becoming permanently unavailable to plants.

Is food for soil organisms from bacteria to worms. These organisms hold on to nutrients and release them in forms available to plants.

2. Water dynamics Improves water infiltration.

Decreases evaporation. Increases water holding capacity.

Stabilized organic matter acts like a sponge and can absorb six times its weight in water. Water held by organic matter can make the difference between crop failure or success during a dry year

3. Structure

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Reduces crusting, especially in fine-textured soils.

Encourages root development. Improves aggregation,

preventing erosion. Prevents compaction, allowing

air to access the roots.

4. Other effects of soil organic matter Dark, bare soil may warm more

quickly than light-colored soils, but heavy residue may slow warming and drying in spring.

Many of the effects of organic matter are related to the activity of soil organisms as they use soil organic matter.

Plant residues and other organic material may support some diseases and pests, as well as predators and other beneficial organisms.

5.3 Determinants of Soil Organic Matter Levels

The amount of organic matter in soil is changed through:

the addition of organic matter (roots, surface residue, manure, etc.),

and the loss of organic matter through decomposition.

Five factors affecting both additions and losses:

1. Management. Practices that increase crop yield will increase the amount of roots and residue added to the soil each year. On the other hand, intensive tillage increases the loss of organic matter by speeding decomposition. While tillage primarily burns younger organic matter, older, protected organic compounds can be exposed if small aggregates are broken apart. In addition to changing the amount of soil organic matter, tillage practices also affect the depth of soil organic matter.

2. Vegetation. In prairies, much of the organic matter that dies and is added to the soil each year comes from grass roots that extend deep into the soil. In forests, the organic matter comes from leaves that are dropped on the surface of the soil. Thus, farmland that was once prairie will have higher amounts of organic

matter deep in the soil than lands that were previously forest.

3. Soil texture. Fine-textured soils can hold much more organic matter than sandy soils for two reasons. First, clay particles form electrochemical bonds that hold organic compounds. Second, decomposition occurs faster in well-aerated sandy soils. A sandy loam rarely holds more than 2% organic matter.

4. Climate. High temperatures speed up the degradation of organic matter. In areas of high precipitation (or irrigation) there is more plant growth and therefore more roots and residues entering the soil.

5. Landscape position. Low, poorly-drained areas have higher organic matter levels, because less oxygen is available in the soil for decomposition. Low areas can accumulate organic matter that erodes off hill tops and steep slopes.

Differentiating Organic Matter and Humus

Humus is the product of the decomposing and synthesizing activities in the soil and exists in a dynamic state. Humus is composed of relatively stable organic substances. It can endure in the soil for longer time, but microbes continuously convert humus to provide energy and nutrients for plants. In natural systems there would also be a more or less continuous creation of new humus from plant debris.

Basically, three kinds of humus or humic compounds can be distinguished. They are differently resistant to degradation and solubility through acidic and alkali substances.

a) Fulvic acid has the lightest color and the lowest molecular weight. It is soluble in both acid and alkali and most susceptible to microbial attack.

b) Humic acid is medium in molecular weight and color. It is soluble in alkali but not in acids and is much more resistant to degradation.

c) Humin is highest in molecular weight and darkest in color. It is insoluble in both acid and alkali and is most resistant to decomposition by microbes. Even fulvic acid can last for several years or decades in the soil, depending on the environmental

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condition. The humus forming compounds are much more resistant to microbial decomposition than freshly applied crop or plant residues.

A similar distinction can be made between stable humus and friable humus (fertile mould). The former is long lasting and mainly found in the clay-humus complex and supports the soil structure. The latter can easily be decomposed by soil organisms and serves as plant nutrients.

Humus has distinct properties that make it different from the mineral soil material and from the less complex substances that emerge during its synthesis:

The presence of humus gives the topsoil a dark or brownish color. If the soil looks yellow or red, the humus content in the soil and the fertility is most likely very low.

Humus contains usually about 55 percent carbon and about four to five percent nitrogen. The ratio between carbon and nitrogen (C:N) is about 10:1.

Humus content in topsoils varies usually between 1.5 and 4.5 percent. Soils in rainforests contain 3 to 5 percent humus, tropical soils under annual cropping with no special measures have only 1 to 1.6 percent humus. The higher the clay content of a soil the greater usually is the humus content.

Humus serves as a stock of nutrients for higher plants. The higher the content of humus in the soil, the better the nourishment of the plants on it’s surface. Humus based plant nutrition makes inappropriate dosages impossible and losses of nutrients are negligible. Below a level of 1.5 percent, however plants can no longer be adequately nourished. Humus is not necessarily degraded to minerals, as the adherents of the mineral theory believe. Organic substances can be directly absorbed by plants and play an important role in their nutrition. Besides, humus provides several active agents, plant hormones, antibiotics, and increases the biological activity. This limits adverse organisms.

A high humus content enables an adequate supply of nitrogen, partially released from the humus. Besides, energy from humus supports nitrogen-fixing microorganisms that supply additional nitrogen to the crop.

Humus enhances the physical and chemical properties of soil. Its cation exchange capacity is higher than that of most silicate clays. This property is very important for poor soils.

The water holding capacity of humus exceeds that of clay four to five times (on weight basis). Humus can absorb water in equivalent of 80 to 90 percent of its weight.

Stable humus forms are involved in the formation of soil aggregates with day particles. The humus particles are very small and have a consequently high surface area. Thus, they act like glue linking mineral soil particles to so-called clay-humus complexes. Humus contributes greatly to the stability of soil aggregates of various sizes. Ideally, the soil consists of many small crumbs that allow plant roots to grow through. A soil with a good structure is well aerated and acts like a sponge that can absorb plenty of water. This is also very important for sandy soils. In clay soils, humus improves the aeration.

Humus reacts with metal cations to form complexes. Some are soluble, others not. Complexes involving iron (Fe3+) and aluminum (Al3+) are firm. Humus interacts also with oxides of iron and aluminum to form stable aggregates. Thus, an increased humus content can reduce toxic metal concentrations.

Humus serves as a buffer system for the pH value in the soil. The higher the humus content the more the soil tends to have an optimal pH value (between pH 6-7). This enhances the activities of bacteria and actinomycetes which are hampered in an acidic environment. Mot plant nutrients are also more readily available compared to acidic conditions.

Humus gives soil optimal condition and structure. The humus content of the soil influences the activities of the soil flora and fauna to a large extent. The higher the humus content of the soil the greater the dynamics of microbial processes. The more biologically active the soil, the higher is its fertility, the better is its structure. Humus enhances the capacity of the soil to supply mineral nutrients since the nutrients are stored in compounds which bacteria can break up to make them available to plant roots. Minerals contained in inorganic soil compounds are more difficult to access.

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One can consider humus a stock of nutrients. Taking into account that humus is constantly decomposed or degraded to provide nutrients to crops and energy or soil organisms, it is obvious that some agricultural practices have to replenish the reserves. Research results show that tropical soils lose about 4,000 kg humus per hectare within three years of cultivation. An average of fallow would replenish 250-600 kg per hectare, thus it would take 7 to 16 years to compensate for the losses.

Some years ago, German scientists suggested to keep a humus inventory or balance sheet for each field. Through long-term experiments they found out that different crops deduct differently from the humus

reserve. Organically grown crops draw 30 to 50 percent more humus than crops raised with synthetic fertilizer that substitutes humus to some extent. Several root crops, like potatoes, and vegetables like squash, cucumber and cabbage, for instance, use up more humus than carrots or tomatoes. Cereals, radish, and onions belong to the group of ‘low humus contents.’ The latter would require about one ‘humus unit’ (HU) per hectare. One humus unit is equivalent to one ton humus containing 50 kg nitrogen and 580 kg carbon. Potatoes require almost three HU while tomatoes, for example, need two HU per hectare in organic farms.

5.5. Building up soil organic matter / Humus

To build organic matter levels in topsoil, more

organic matter must be added than is lost to

decomposition and erosion. Increasing organic matter

is about changing the balance between how much

energy goes in and how much is burned off.

Another way to think of soil is like a giant wood

stove. You continually add organic matter (wood),

and it burns to release energy and nutrients that will

be used by plants and microorganisms. Ideally, you

want a slow, steady burn that releases nutrients to

plants as needed.

Intensive tillage aerates the soil and is like

opening the flue or fanning the flames.

Decomposition is desirable because it releases

nutrients and feeds soil organisms. But if

decomposition is faster than the rate at which organic

matter is added, soil organic matter levels will

decrease. It is just as important to increase the

amount of organic matter added into the soil.

Building organic matter is a slow process.

First, the amount of residue and active organic matter

will increase. Gradually, the species and diversity of

organisms in the soil will change, and amounts of

stabilized organic matter will rise. It may take a

decade or more for total organic matter levels to

significantly increase after a management change.

Fortunately, the beneficial effects of the changes

appear long before organic matter levels rise.

Why does it take so long for organic matter

levels to increase? An acre of soil six inches deep

weighs about 1000 tons, so increasing the proportion

of organic matter from two to three percent is

actually a 10 ton change. However, you cannot

simply add 10 tons of manure or residue and expect

to measure a one percent increase in soil organic

matter. Only ten to twenty percent of the original

material becomes part of the soil organic matter.

Much of the rest is converted over several years into

carbon dioxide.

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Figure 4. An illustration of soil organic matter losses and gains in response to tillage.

Most organic matter losses in soil occurred in the first

decade or two after land was cultivated. Native levels

of organic matter may not be possible under

agriculture, but many farmers can increase the

amount of active organic matter by reducing tillage

and increasing organic inputs.

Steps in Building up soil organic matter / Humus

Step # 1. Add organic matter

Grow more organic matter. Plant a high

residue rotation that includes sod crops that

leave lots of roots in the soil (small grains or

forages), crops that leave a lot of surface

residue (e.g., grain corn) or cover crops that

supply both.

Apply livestock manure. Manure is an

excellent way to build organic matter.

Step # 2. Reduce organic matter losses

Reduce tillage. Merely maintaining soil

organic matter levels is difficult if soil is

intensively tilled (such as with annual use of

a moldboard plow.) Reducing tillage means

leaving more residue, and tilling less often

and less invasively than conventional tillage.

No-till is the most extreme version of

reduced tillage, but is not easy to practice for

some farmers. As you reduce tillage, some of

the nutrients in manure or legumes will go

into building soil organic matter levels and

not into your crops.

Control erosion. The soil that erodes from

the surface of your land is the soil with the

highest concentration of organic matter.

Erosion is especially detrimental where

topsoil organic matter is shallow.

To maintain fertility and soil structure in a

sustainable organic farming system:

Recognize and respect soil as a

complex living system in which soil

organisms play an important role in digesting

organic matter, leaving soil soluble minerals

and CO2.

Identify farming practices that either

impair or enhance soil life.

Recognize soil life as the focus of

our efforts to practice good management.

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6.0. Natural Plant Nutrition

Under natural conditions, plants direct their

nutrition themselves in a manner quite different from

the concept of agricultural chemistry. During the last

decades, research revealed that the so-called

rhizosphere (root zone) is a zone of complex

interactions between plant root and soil organisms.

The growing roots constantly discharge various kinds

of exudates (basically carbohydrates) which supply

many soil organisms near the roots with humus or to

produce acidic substances that help to dissolve

nutrients from minerals.

During their growth plants continue to extend

their roots. Through the tips of their roots, plants

secrete mucus (slime). This serves as energy source

for bacteria and other organisms and encourages

them to break down humus into substances that

plants can absorb.

During their growth plants establish new

roots, while older roots die. Thus, during its growth

plants produce organic matter that is available to the

soil biota. Cereal plants, for example produce around

four times more roots during their development than

are left at the end of their cycle.

The microorganisms in the soil work together

with the roots of the plants for the growth of the

vegetation. The mucus secreted by the tips of the

roots encourages soil organisms to convert organic

substances (humus) into nutrients for the plants. The

plants absorb minerals like nitrogen and phosphate,

and other more complex substances. This natural

process is only possible by the interaction of plant

roots and soil organisms. This process provides the

plants with the proper quantities of nutrients. The

application of chemical fertilizer cannot replace this

system. It will disturb or destroy many soil

organisms. Further, the plants will suffer from

unbalanced nutrition which makes them susceptible

to pests and diseases.

7.0. Nitrogen fixation

Nitrogen is the most abundant gas in the

atmosphere of the earth. Since the first occurrence of

life, it has been essential for plant growth, as it is

necessary in synthesizing protein molecules. In

natural systems, most of the nitrogen is recycled

through the organic matter. Agricultural products

take considerable quantities of nitrogen out of the

system. Thus, nitrogen is usually the most limiting

factor for plant growth. Besides, even soils covered

with natural vegetation lose some nitrogen tot e

atmosphere which has to be replaced by other

mechanisms. For agriculture and related sciences,

there is still q question not fully solved: how does

atmospheric nitrogen become available to plants and

especially to crops in the fields? Plants themselves

lack the capacity to absorb nitrogen directly from the

air. They depend on other organisms to supply it in a

form they can incorporate into their metabolism.

Farmers knew that planting leguminous

plants improved the growth of other crops as well.

The Romans used to sow lupines in rotation with the

main crops around 2,000 years ago. In the 15 th

century Dutch farmers rediscovered this method.

Chinese and Japanese farmers are using clover and

soybeans to improve the fertility of their fields for

almost 4,000 years.

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The wisdom of these practices fell into

oblivion with the development of modern sciences

that paved the way for agricultural chemistry. With

the introduction of synthetic nitrogen, nature’s ways

of providing the essential nutrient seemed outmoded.

That natural systems and optimized cropping systems

can supply sufficient nitrogen to achieve yields

similar to those obtained by use of synthetic inputs.

Biological nitrogen fixation is mediated by

organisms that can use atmospheric nitrogen as their

sole source of nitrogen. They are called diazotrophs:

‘Diazo’ refers to dinitrogen, the form of nitrogen

which occurs usually in the atmosphere. Gaseous

nitrogen occurs as a molecule consisting of two

nitrogen atoms (N2) connected by triple bond.

Because of the triple bond, it requires relatively high

amount of energy to break up the dinitrogen

molecule.

Scientists distinguish basically between

symbiotic nitrogen fixation and nonsymbiotic

nitrogen fixation. Both ways have in common that

bacteria or actinomycetes incorporate nitrogen, or

more exactly dinitrogen, from the air. Plants as well

as all other organisms need nitrogen either bound

with oxygen (NO2) or hydrogen (NH4). The nitrogen

fixing organisms require energy in the form of

carbohydrates derived from plants and organic matter

to break up the N2 molecule. The energy requirement

differ significantly among the various species and

genera. An important factor in the process is the

enzyme nitrogenase which the organisms has to

protect against oxygen. As energy source glucose is

converted into adenosine-triphosphate (ATP). The

glucose molecules are either derived from

photosynthetic products of the host plant or from

decomposed organic matter. An exception is the

group of cyanobacteria, which are capable of

photosynthesis.

7.1. Symbiotic Nitrogen Fixation

Symbiotic nitrogen fixation in nonleguminous

plants. Several kinds of shrubs and trees as well as

many grasses including rice and sugarcane varieties

possesses root nodules with nitrogen fixing capacity.

The Frankia symbiosis is common among

nonleguminous shrub and trees. It can also be found

in rice. Frankia is a filamentous organisms closely

related to actinomycetes. It infects root hairs or

invades cells where it forms nodules. The nodules

are perennial, modified lateral roots with lobes up to

five centimeter in length.

Another symbiotic relationship exists

between the aquatic fern azolla and the bacteria

Anabaena. The bacteria occur mainly in

specialized cells called heterocysts. The aquatic

fern azolla is a common green manure used in

Vietnam and China for rice production (see

section: Nitrogen fixation in flooded rice fields).

Symbiotic nitrogen fixation in leguminous plants

Nitrogen fixation in legumes depends

upon a highly coordinated sequence of

interactions between plants of the family

Leguminosae and soil microorganisms belonging

to the genera Rhizobium and Bradyrhizobium.

The symbiosis results in the formation of

nodules, usually on the roots. Most of the

leguminous plants form nodules. An exception is

Sesbania rostrata, a green manure crop that can

grow in flooded area. It develops nodules also on

the lower stem. The plants supply carbohydrates

2

from their leaves for the bacteria which in turn

fix atmospheric nitrogen and supply amino acids

for both organisms. The root nodule bacteria

may become antagonistic to the plant if the plant

experiences stress due to drought or at the time of

flowering or setting of seed.

Nodules can only fix nitrogen actively if the

plant is adequately supplied with all nutrients for

active growth. Obviously, the plant must be in good

condition to benefit optimally from the symbiosis.

Of the total respiration of soybean plants, for

example 57 percent was from the top, 18 percent

from the roots and 25 percent from the nodules. The

tolerance of acidity depends on the Rhizobium strain.

Rhizobium nodules appear to be more

efficient fixers of nitrogen than the nonsymbiotic

bacteria. The latter needs 2.5 times more

carbohydrates than the former to fix one gram of

nitrogen.

7.2. Nonsymbiotic nitrogen fixation

To the group of free-living organisms belong

the cyanobacteria that resides on the soil surface.

Microbes like Azotobacter, Azospirillum, and

Beijerinckia associate loosely with the roots of

certain plants. The last mentioned group depends on

carbon supplied from either decomposing organic

matter or from plant roots. There are genera of

bacteria that live in aerobic condition. Other genera

prefer the anaerobic environment, like the genera

Clostridium and Enterobacter. Some genera relate

only to one plant species like the Azobacter paspali

which associates with the tropical grass Paspalum

notatum (Bahia grass). Bahia grass shows good

growth even on N-poor soils. Several sugarcane

varieties contain in their internal tissues the

bacterium Acetobacter diazotrophicus. Due to its

location, the organisms captures a significant part of

the sugar to drive nitrogen fixation. It is, however,

free of competition from other organisms. Some

cultivars may derive 100 to 150 kg per hectare from

this symbiosis. The contribution of the free living N-

fixers to the N reserve of the soil varies between 10

and 90 kg per hectare per year.

7.3. Nitrogen fixation in flooded rice fields

Of great agricultural importance is the

Azolla-Anabaena symbiosis. Azolla is a floating fern

that has long been used as nitrogen source for

lowland rice. Anabaena, a blue-green algae is

contained in ‘pockets’ of the fern. The rate of

nitrogen fixation (83-125 kg/ha) is comparable with

that of legumes.

Most kinds of nitrogen fixation occurring in

rice fields, however, are non-symbiotic. Usually,

they contribute most of the nitrogen. Nitrogen

fixation is associated with the decomposition of straw

and can take place in the root zone (rhizosphere) of

the rice plant. In addition, blue-green algae and

various heterotrophic organisms fix nitrogen.

Rhizosphere associated fixation

Among the bacteria which settle on the

root surface are also diazotrophs. They comprise

about 10 percent of the microbial activities in the

rhizosphere and obtain their energy mainly from

root exudates. Their contribution to nitrogen

supply is relatively low with estimates ranging

between 1 to 7 kg per hectare and crop. Several

nitrogen-fixing bacteria have also been found to

colonize in the interior of the roots of rice and

other grass plants. They persist within or

between the cells of the plant tissue. Rhizobium

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which enters into symbiosis with legumes has

been found to associate with rice. The bacteria-

rice relationship, however, does not lead to the

formation of nodules.

Decomposition of straw

The application of straw to the surface or

subsurface layers of flooded soils result in

intense microbial activity. This creates a

conducive condition for various nitrogen-fixing

bacteria. They use the carbohydrates from

decomposed straw as their source of energy. The

nitrogen-fixing bacteria include the

heterotrophic. Azotobacter, Azospirillum

lipoferum, and Pseudomonas diazotrophicus a

well as phototrophic bacteria which can utilize

light energy. It is estimated that straw-associated

nitrogen fixation can contribute 2-4 kg nitrogen

per ton of rice straw. Given a supply of five tons

rice straw, 20 kg could be fixed. Another source

estimates the possible nitrogen fixation of about

25 kg nitrogen per hectare within 30 days.

Blue-green algae (Cyanobacteria)

Free-living nitrogen fixing cyanobacteria

are abundant in flooded rice fields. Due to the

photosynthetic nature of these organisms, the

quantity of fixed nitrogen is independent from

the supply of energy from the soil. Some species

liberate extracellular ammonia (NH4), Blue-green

algae can fix up to 70 kg nitrogen per hectare per

cropping. The inoculation with cyanobacteria

increased rice yields by 337 kg grains per

hectare, indicating a gain of about 10 kg nitrogen

per hectare. The activities of the blue-green

algae appear to decrease if the ammonium

content in the water is increased.

Heterotrophic nitrogen fixation

This group is comprised of free-living

bacteria. Some of these live in association with

roots and other submerged portions of the rice

plant. Most members of this group, however,

depend on the supply of organic matter. They

live predominantly on organic debris. The

bacteria need between 19 to 117 gram of carbon

to fix one gram of nitrogen. They can add an

average of 7 kg nitrogen per hectare per

cropping. The quantity, however, varies

significantly among varieties. The ability of the

rice plant to optimize this associated is controlled

by several genes.

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Annex A. Review of Major elements required for plant growth

Nitrogen (N), phosphorus (P), and potassium (K) are the 3 most important soil nutrients required for plant growth. In all, plants require sixteen elements, each of which has one or more special function in the plants growth and development. Some elements like calcium, magnesium and sulfur (macronutrients) are required in relatively large amounts.

Element Function Symptom of Deficiency

Nitrogen (N)

Essential for plant growth. Necessary for protein production

by the plant. Necessary for many critical plant

functions (photosynthesis, cell division and plant growth).

Adequate N produces a dark green color in the leaves, caused by a high concentration of chlorophyll. Nitrogen deficiency causes a yellowing of the leaves, which first starts on older leaves. Nitrogen deficient plants tend to be stunted, grow slowly, and produce fewer tillers than normal.

Phosphorus (P)

Essential for plant growth and is especially vital to early growth.

Promotes early root formation and growth

Improves the quality of many fruits, vegetables and grain crops.

The first sign of P deficiency is an overall stunted plant. A purple or reddish color is often seen on young plants especially at low temperatures. With severe P deficiency, dead areas may develop on the leaves, fruits and stems.

Potassium (K)

Essential for protein synthesis and cell division.

Decreases water requirement of plants

Important in fruit formation. Helps plants survive winter Helps improve stalk strength and

resistance to lodging

Potassium deficiency symptoms show up as scorching or firing along the margins of older leaves in most plants, especially grasses. The leaves may later turn brown. Deficient plants grow slowly and have poorly developed root systems. Stalks are weak, lodging is common and seed and fruits are small and shriveled. In grass/legume forages the legume will not persist in the mixture when K is deficient.

What are the important sources of nutrients?

Table 2: Macronutrients required by plants and their sources*Supplied by Air and Water Supplied by Soil Supplied by Precipitation

Carbon (C) Nitrogen (N2)Hydrogen (H2) Phosphorous (P4) Sodium (Na)Oxygen (O2) Potassium (K) Chlorine (Cl)

Calcium (Ca)Magnesium (Mg)

Sulfur (S8)Silicon (Si)Iron (Fe)

Aluminium (Al)*Other nutrients are required in small amounts (known as micronutrients) and are obtained from the soil.

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Nitrogen: Animal and human manures, nitrogen-fixing plants (clover, alfalfa, peas, etc.) and soil microbes are the major sources of N on ecological farms. N can also be supplied by chemical fertilizers and small amounts are dissolved in rainwater or produced by lightning. Nitrogen mineralization is a major source of nitrogen to the soil. Mineralization is the process of decomposition of organic matter. The rate of nitrogen mineralization depends largely on the temperature and moisture content of the soil. Soil tillage accelerates the mineralization process because it accelerates soil warming and increases aeration. Efforts to build up soil organic matter in the cropping rotation need to be made to support mineralization processes to release N for crops that require a N supply.

Phosphorus: The most common source of P outside of farm manures, is phosphate rock from which various commercial fertilizers are made. Most ecological farmers prefer to rely on natural decomposition and soil processes to recycle P and make insoluble P fertilizers and fixed soil P become available. This

process is more efficient on ecological farms that have a “living” soil where soil microbes, earthworms fungi and root acids work to make P available to the plant.

Potassium uptake in plants is also greatly enhanced through the development of a “living” soil. Most ecological farmers emphasize strategies that make the vast natural reserves of potassium in soil become available for plant growth especially on loam and clay soils. Deep rooted green manure crops, soil microorganisms, earthworms and root acids play a major role in making potassium more available to plants. Improving soil structure and the soil organic matter content improves potassium uptake by improving the soils cation exchange capacity (CEC) (see below) and enabling more extensive and deeper rooting of plants. Farmers then need to manage the supply of potassium in the farm cycle to optimize its availability for crops with high demands. For example many farmers will apply manure to potatoes because it has a high potassium demand.

Manure/compost is an excellent way to supply trace elements to crops and will generally prevent deficiencies from occurring!

Common Soil Amendments having minimal negative impact on soil life these include:

Calcitic limestone Increases pHCompost Storehouse for plant nutrientsDolomitic limestone increases pH (may cause excessive magnesium imbalance)Gypsum Adds CalciumLeaves & Leaf Mold Humus, Ca, Mg, N,P,KManure N,P,K (varies with type)

Rock PhosphatePhosphorus and Trace Minerals

Sawdust Mulch, High Carbon for CompostSeaweed Potassium and Trace MineralsSul Po Mag Adds PotassiumStraw Carbon source for compost, aerates soil

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How nutrients move within the soil?

Nitrogen:

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Figure 2. the cycling of nitrogen in the environment. Nitrogen comes from organic matter => NH4 (ammonium) => NO2 (nitrite)=> NO3 (nitrate)=> and then back into the plant, or organic matter. (http://muextension.missouri.edu/xplor/envqual/wq0252.htm)

In the nitrate form, nitrogen is the most mobile nutrient in the soil and subject to leaching. N in the organic ammonium form is not subject to leaching and will stay stuck to the soil particles. The availability of N to crops depends on the conditions for the breakdown of organic matter. Urea fertilizer converts to ammonium when it is applied to the soil, and then is converted to nitrate. The silty and porous loess soil with low organic content cannot hold or bind nitrogen fertilizer and it can be readily leached into ground water and water courses. http://www.geog.ouc.bc.ca/physgeog/contents/9s.html

Phosphorus: Phosphorus sticks so tightly to the soil, that it is safe to say that it doesn't move unless the soil does. Unfortunately large losses of P through erosion can occur because the concentration is highest on the soil surface.

Potassium: It also sticks to soil particles, although not quite as tightly as phosphorus. In some very coarse sandy or gravelly soils with low organic matter, there may have been some loss of potassium through leaching.

Micronutrients: A healthy soil microbial community is essential for release of nutrients from organic matter. “Nutrient cycling” ensures that, when a plant dies, all its nutrients end up recycled back into the soil. Bacteria and fungi break down the plant tissue and make available the nutrients which can be once

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