Lectures 12 and 13
Soil Microbial Population Ecology

Lecture Structure
Definition and Introduction
Why should we look at this ?
Food webs
4 Phases of microbial growth
Succession and competition
Substrates, Microbes and the Environment
Substrate quality
Substrate quantity
C:N ratio
Case Studies

1. Conifer Needle decomposition
2. Cereal Shoots
3. Mycorrhizas
4. Dutch Elm Disease

Definition of Ecology:
Ecology is the study of the relationships between organisms and their environment.

Soil population ecology:
is the interaction between the following 3:

1. Organisms (microbes, plants and animals)
2. Substrates (dead roots, leaves, dead organisms, pesticides)
3. Environment (water, air and soil particles)

The interaction of these three groups can be shown diagramatically in the following schematic figure. The arrows denote one factor influencing another. In summary all the factors can influence one another making the study of soil population ecology very difficult and complex. Examples for each of the arrows are given underneath.

1. e.g. Pesticide adsorption by clay particles preventing breakdown and movement
2. e.g. Plant mucilage binding soil particles together (improves the soil's water retention and structure)
3. e.g. Decomposition of the substrate
4. e.g. Some chemicals are toxic to organisms (e.g. pesticides)
5. e.g. Predation
6. e.g. Mutualism, symbiosis
7. e.g. Earthworms increasing soil porosity and aeration
8. e.g. Compaction preventing earthworm burrowing

Why is microbial population ecology important ?

Basically because few soil processes are carried out by a single organism alone. Most are carried out by a group of microbes living together within a dynamic community. Examples of soil processes involving more than one organism are:

Inorganic nutrient cycling (N, P, S)
Substrate decomposition (plant litter)

Food Webs

There are rarely clear successions in cycling pathways e.g. the succession of organisms involved in oak leaf decomposition is different in the UK from that of the USA, and, decomposition is different in a Cambisol compared to a Podzolic soil. There is no one specific decomposition pathway just generalisations.

Food webs are normally interconnected and extremely complex

We know that there are 1000's of species in soil so the food webs must implicitly be complex.

In addition the pathways are not simple i.e. fungi are not predated only by nematodes (i.e. can be defined by a single one way arrow).

e.g. one fungi can attack another fungus
e.g. a fungus can trap and eat nematodes
e.g. nematodes can eat fungi
e.g. nematodes can eat nematodes

Food webs are very environment dependent (its not the same for all soils)

e.g. there are no termites in the UK
e.g. the pH, O2 status, water content may inhibit some organisms
e.g. the substrates are different depending on environmental conditions

They are very dynamic (they change depending on substrate type and availability)
e.g. after manure addition

Here is a classic food chain where CO2 is fixed by plants which then die and are degraded by bacteria which are eaten by protozoa which are eaten by worms. At each trophic level energy is being lost as CO2 (normally > 60 % of the C taken into an organism is respired). This means that there is less and less C available as you go down the chain. This is why there are lots of bacteria in soil and few earthworms (see Lecture 1-2).

The 4 Phases of Microbial Population Growth

1. Lag phase

This is the time needed to switch on the necessary cell machinery to (a). transport the substrate into the cell, and (b), process the substrate once inside. It normally requires the de novo synthesis of new enzymes and therefore requires gene transcription and translation which will take at least a few hours.

2. Exponential phase

The necessary machinery for substrate use are now in place (the enzymes required to transport the substrate into the cell and the enzymes required to turn this into energy or new cell material). The substrate is in plentiful supply. Growth is very rapid and goes in the following exponential pattern

1 cell…. 2 cells...4 cells….8 cells….16 cells….32 cells

3. Stationary phase

At this point either the substrate or another nutrient (e.g. P or N) has become limiting so that growth is now slowing rapidly as it becomes harder and harder to obtain the limiting factor.

4. Death phase

The cell starts to run out of energy so they start to die.

Example calculation (to put things in perspective)
If a single bacterium kept dividing exponentially every hour this is how many microbes (clones) you would have after 4 days:

Time (hours) Bacteria Population Size
0 1
24 16 million
48 280000000 million
72 4700000000000000 million
96 79000000000000000000000 million

If a bacterium dimensions are 2Ám by 0.5Ám then its volume is 3.14 x 10-12 m3
So after 96 h you have 2.48 x 1017 m3of bugs
This is equal to 2.48 x 1011 cubic kilometres
i.e. nearly a million times a million km3

Therefore as microbes have not taken over the earth and sunk us into a black hole, the amount of substrate in soil must be limiting

Now we will talk about two important concepts: Succession and Competition


Below is a graph showing succession of three groups of organisms. Substrate has been added as time = 0 and bacteria have responded by growing (in 4 phases as described above). As protozoa are triggered into action by bacteria, they don't start growing until the bacteria are in exponential phase. They then go through four phase growth. This is followed similarly by protozoal predators mites. Note that all go through 4 phases of growth and that the population numbers are lower at each stage. Secondly note that the curves start and finish at different times. i.e. the time of death is not the same for bacteria and mites. The 3 curves represent from left to right, bacteria, protozoa and mites repectively


Here we have on the surface similarly looking graphs for two fungal species. However, it is subtly different and is characteristic of competition. Fusarium is the top curve and Pisolithus the botton curve. Here the substrate has been added at time =0 and Fusarium has reacted first. Pisolithus, however, can also use this substrate but it takes longer to turn on the necessary apparatus for transport (maybe it has only a few membrane receptors for this substrate). The important point to note, however, is that they both go into stationary phase and death phase at the same time. This indicates that they are both using the substrate and that Pisolithus is not using Fusarium as a substrate. Basically Fusarium has out-competed (higher population) Pisolithus for the substrate.

This leads us onto two soil microbiolgical terms to describe fast and slow growers in soil. These are

Organisms which grow extremely rapidly when a new substrate arrives
The are 'boom' and 'bust' (i.e. big fluctuations in pop'n numbers)
They are not long lived
They spend most of their time in hibernation (waiting for substrate)
They are more adapted to taking up substrate at high concentrations
They are uncommon in soil (as soil is normally substrate limiting)
They are analogous to 'r strategists'

Organisms which grow slowly when new substrate is added
Their populations tend to be more stable
They are longer lived
They are more adapted to taking up substrate at low concentrations
They are common in soil
They are analogous to 'K strategists'

Below is a graph of the population numbers versus time for each group

Substrates, microbes and the environment

Inputs of Substrate to the Soil

Example: Mixed Temperate Forest Ecosystem

Leaves and needles constitute 25-60 % of the net primary production
Roots constitute 40-75 % of net primary production
Over 60 % of most fine tree roots die each year

Tropics Temperate
Net Primary production (g/m2) 2200 1200
Soil Organic Carbon (g/m2) 1900 7000
Total Microbial Carbon (g/m2) 80 90
Active Microbial Biomass Carbon (g/m2) 8 9

Substrate Quality

Most substrates are 90 % water (10 % dry matter)
Substrate quality determines how fast it's broken down
Generally the more nutrients the substrate contains - the faster it is broken down
Microbes need not just C but other nutrients as well

Here is a table of the typical macronutrient content (% of dry weight) of two groups of organisms and two substrates.

Bacterial cells Fungal cells Green Shoots Cereal Straw
C 50 40 40 40
N 6.25 2.5 1 0.4
P 3 0.6 0.2 0.1
S 1 0.4 0.2 0.1
C:N Ratio 8 16 40 100

Oxygen and Hydrogen makes up most of the rest.

One important point is the carbon to nitrogen ration (C:N ratio). These are the two nutrients most needed by microbial cells for growth as they are used to make proteins, cell walls etc. From the C: N ratio we can guess at which organisms might decompose it

Note the C:N ration of fungi (16) is much greater than that for bacteria (8), and that both are lower than that of crop residues (40-100).

C:N of microbe > C:N substrate = Excretion on N into soil
C:N of microbe < C:N substrate = Uptake of N from soil

N- rich residues (e.g. dead animal cells C:N =10)
Bacteria will rapidly degrade these as they have a low C:N ratio (the C:N ratio of the substrate is still greater than that of the microbe so the bacteria may still need to take up a small amount of external N from the soil)
Fungi will also rapidly degrade these. As the C:N ratio of fungi is greater than the residue they will excrete the excess N into the soil.

N- poor residues (e.g. cereal straw C:N = 100)
Bacteria will be poor at degrading this as they will be N starved
Fungi will be OK (they will still need to take up some external N from the soil)

Population Ecology Case Studies

CASE STUDY 1: Decomposition of Conifer Needles


Generally the substrate quality is poor for the following reasons
The substrate is dry needles with waxy cuticles
The waxy cuticle covers the stomata to prevent fungal spores getting in
They contain antibiotic resins
N and P contents are <1 % (low)
C:N ratio is about 40
major components

cellulose = 30 %
lignin = 30 %
hemicellulose = 20 %
protein = 3 %
polyphenols = 2 % *

This is a phenol ring - Lots of these joined together make a polyphenol

Needles constitute about 75 % of the total surface litter inputs (other inc. cones, branches etc)
About 20 % of the needles fall off a tree each year
There may be 10 times as many needles on the floor as on the trees
Needle drop is often seasonal - this affects decomposition rate
Pinus sylvestris Needles fall off in autumn
Picea abies Needles fall off all year round

Microbial decomposition

It takes about 7-10 years to degrade 70 % of the needle
It takes about 30 years to degrade 98 %
The remaining 2 % is made of highly recalcitrant organic matter which can last for up to 10,000 years (often complex phenolic material)
Over 150 fungi are involved in the decomposition process
Many bacteria, actinomycetes, protozoa and mesofauna are also involved
Decomposition probably involves more than 300-500 individual species
Decomposition starts on the tree not on the ground
There is no definite species succession (for the reasons given above)

Below is an indication of some of the stages of pine needle decay (You don't want all 300 do you ?). I have split it into two sections. Decomposition on the tree and Decomposition on the ground.

A. Infection on the tree
(normally starts as a result of insect or abrasion damage as otherwise needles are well protected)

Stage 1. Auereobasidium pullulans (fungus which just lives on the surface of the needle)
Stage 2. Lophodermella sulcigena (strong pathogenic fungus which infects the inside of the needles)
Stage 3. Lophodermium pinastri (weak pathogenic fungus which enters wound sites (some started by fungus in stage 2))
Stage 4. Flavobacterium (opportunistic bacteria which enters after 2 and 3)
Stage 5. Naemacyclus niveus (fungus which invades inside and causes needles to finally fall off)

B. Infection on the ground (some of the fungi stages)

Stage 5. Hyphae from Stages 1-4 are eaten by mesofauna (e.g. mites)
Stage 6. The 4 fungi from above plus Fusicoccum bacillare sporulate
Stage 7. Desmazierella acicola moves in (Fungi from stages 3 and 6 die out)
Stage 8. Helicoma monospora replaces Aureobasidium on surface
Stage 9. Desmazierella acicola takes over on the inside
Stage 10. Mites, worms and springtails eat the fungal hyphae
Stage 11. Trichoderma and Penicillium colonize the outside
Stage 12. Mortierella and Chaetomium move into the inside

This is only a fraction of the stages but it can be seen that it is both succession and competition a the same time.

Decomposition nearly always follow the schematic below where the easily degradable compounds are used first with the substrate becoming harder to break down with time (i.e. lignin is often left till last).

(simple carbohydrates, fats)

(cellulose, hemicellulose and protein)

(phenolics, waxes and lignin)

Many compounds are protected by lignin and phenolics e.g. Phenolic-protein complexes


Characteristic of Podzolic soils
Low pH favours fungi
Low N status of soils favours fungi
Often cold temperatures slow breakdown

CASE STUDY 2: Decomposition of Cereal Shoots

This time we will not talk about the microbial succession, but some more important features such as environment.

Substrate quality
They contain few antibiotic resins
P and N concentration are quite high
C:N ratio is 30-60 (low)
Major components

cellulose 30 %
lignin 15 %
hemicellulose 25 %
protein 30 %
polyphenols <1 %

Decomposition follows epidermis-cortex-endodermis-phloem-xylem

Again decomposition starts when the shoot is alive (e.g. rust fungi)


Decomposition rate depends largely on whether the shoots are buried or on the surface (this is important when ploughing in crop residues)

Decomposition of rye leaves over a 12 month period.

decomposition is dependent on nutrient concentration. Look at the following graph which plots decomposition rate as a function of shoot macronutrient concentration (N + P)

CASE STUDY 3: Ectomycorrhizae

This isn't really decomposition population ecology (as above) but more the interaction of organisms in the environment. Here are two examples which I will use to illustrate the interaction between large animals and fungi. Here we can see that we can go from the bottom of the trophic ladder to the top in one step (compared to via 300 organisms and trophic levels in the conifer needle example).

Case Study 3A from New Mexico

Some mycorrhizae sporulate (produce toadstools) on the soil's surface
There is little wind penetration at the soil's surface so there is poor wind dispersal of spores
> However, squirrels are attracted to the brightly coloured sporocarps
They climb trees with the sporocarp where there is more wind so spore dispersal is increased (the squirrel gets food out of the bargain)
They squirrels also excrete the spores

Case Study 3B from France

Some mycorrhizae sporulate underground (e.g. truffle)
Thus good spore dispersal is very difficult
To overcome this they then release pheromones
This attracts animals who dig them up and carry them away (e.g. pig)

Adapted from a page on Microbial Ecology.