Chapter 9
Decomposition is breakdown of chemical bonds formed during the construction of plant and animal tissue.
It is the end product of the energy pathway begun with photosynthesis.
Decomposition involves respiration: the release of the energy fixed by photosynthesis, CO
2
and
H
2
O.
Decomposition involves several processes: fragmentation, ingestion, egestion, and concentration.
All heterotrophs are decomposers to some extent, but the concept of decomposers is reserved for those organisms that feed on detritus.
Decomposers include bacteria, fungi and detritivores.
Decomposer bacteria may be aerobic or anaerobic .
Anaerobic bacteria use inorganic compounds such as sulfate or nitrate as oxidant that is a molecule that accepts electrons other than oxygen.
 For example, some bacteria called sulfate reducers can transfer electrons to sulfate
(SO
4
2) reducing it to H
2
S. Other bacteria, called nitrate reducers, can transfer electrons to nitrate (NO
3
) reducing it to nitrite (NO
2
). Other nitrate reducers can reduce nitrate even further to nitrous oxide (NO) or nitrogen gas (N
2
).
 NO
3
+ 2e-
+ 2H+ →NO
2
- + H
2
O
 Sulfate (SO
4
2 is reduced to sulfide (S 2), typically in the form of hydrogen sulfide
(H
2
H). Eight electrons are add to sulfate to make sulfide:
 acetate + SO
4
2 + 3H + → 2CO
2
+ H
2
S + 2H
2
Fermentation produces organic acids and alcohol.
Some decomposer bacteria are...

Facultative anaerobes : they use oxygen if available; if not, they shift to fermentation.

Obligate anaerobes: they die in the presence of oxygen.
Bacteria are the main decomposers of dead animal matter.
Fungi are the main decomposers of plant material.

After one group of decomposers has exploited the material to the extent of its ability, a different group of bacteria and fungi moves in and continue the process of extracting nutrients.
A succession of microflora occurs in the decomposition of organic matter until the material is finally reduced to inorganic nutrients.
Invertebrate detritivores are involved in the fragmentation of dead organic matter. There are four major groups:
1. Microfauna and microflora : protozoans, rotifers and nematodes living in the water film of soil pores.
2. Meiofauna : animals whose body falls within 100μm - 2 mm, e.g. mites, springtails, some worms.
3. Macrofauna : between 2 mm - 20 mm long; e.g. woodlice, spiders, earthworms, beetles, centipedes, slugs, snails, ants, and harvestmen.
4. Megafauna : over 20 mm, e.g. moles, rabbits, rodents, and earthworms, snails on land, crabs and mollusks in water.
Microbivores are organisms living in the soil that feed on bacteria, fungi and other small forms.
 Amebas, springtails, larvae of beetles, and mites.
Microbivores control the population of decomposers.
"The invertebrates that feed on detritus are a taxonomically diverse group. In terrestrial environments, they are usually classified according to their size. This is not an arbitrary basis for classification, because size dictates their access to resources, as they burrow and crawl among the cracks and crevices of the litter layer. The microfauna (animals with body widths less than
0.1 mm) includes protozoans, nematode worms and rotifers. The principle groups of the mesofauna (body widths between 0.1 mm and 2 mm) include litter mites (Acari), springtails
(Collembola), and pot worms (Enchytraeidae). The macrofauna (body widths between 2 mm to
20 mm) and megafauna (body widths greater than 20 mm) include woodlice (Isopoda), centipedes (Chilopoda), millipedes (Diplopoda), earthworms (Megadrili), snails and slugs
(Mollusca), and the larvae of certain flies (Diptera) and beetles (Coleoptera). The larger animals are mainly responsible for the initial shredding of plant remains. Soil bacteria and fungi complete the cycle, consuming the fragmented material. By their action, detritivores promote a large-scale redistribution of organic material, and thus contribute directly to the development of soil structure ." http://www.albany.edu/natweb/fsdetr.html
George Robinson, Assistant Professor, Biological Sciences.
Interesting sites: http://www.deathonline.net/decomposition/corpse_fauna/index.htm
Animal decay: http://everything2.com/index.pl?node_id=1478719 http://adipocere.homestead.com/chemistry.html

1. Leaching is the removal of soluble substances by water, e.g. sugars.
2. Fragmentation involves the breaking of the material into smaller pieces; this may be done physically or chemically.
These two abiotic processes result in the loss of mass and change in the chemical composition of the detritus.
3. Mineralization is the release of organically bound nutrients into an inorganic form available for plants and microbes. Detritivores oxidize organic compounds into smaller and simpler products.
4. Nutrient immobilization is the incorporation of mineral nutrients into microbial biomass.
Those nutrients not taken up by microbes become available to plants.
In nitrogen mineralization, organic nitrogen from decaying plant and animal residues (proteins, nucleic acids, amino sugars, urea) is converted to ammonia (NH
3
) and ammonium (NH
4
+) by the mechanisms listed below. This process is also called ammonification. The resultant ammonia can be converted back to organic N (immobilization) where it is taken up by microbes and plants (assimilated), or nitrified to nitrate (NO
3
).
Once NH
4
+ has been formed, there are numerous possible fates:
1. It can be assimilated (or immobilized) by microbes and plants.
2. It can be held on exchange complexes in soil.
3. It can be fixed in the inner layer portions of clays.
4. It can be volatilized as NH
3
in decaying vegetation or manure.
5. It can be nitrified by the autotrophic nitrifying bacteria.
Living leaves produce exudates that are washed off by rain and support. Microorganisms feed on the exudates and cells that slough off the surface of the leaf.
Once on the ground, bacteria and fungi attack the leaves. The leaves are broken down into smaller pieces. The macro and megafauna are involved in the fragmentation of organic material.
 Their fecal material is rich in microorganisms that continue the chemical decomposition process.
 Earthworms release vitamin B
12
into the soil. Others bury and mix organic matter with the soil particles. Earthworms can process up to 10% of the A horizon.
 In the absence of detritivores, decomposition is slowed down significantly. Wood decomposition is slowed down by half.

The soil region immediately surrounding the roots, is known as the rhizosphere and, and the root surface itself is the rhizoplane .
The rhizoplane supports a large number of microorganisms.
Root exudates consist of simple sugars (10), fatty acids (11), amino acids (21), vitamins (10), nucleotides (4), and miscellaneous compounds (11). The number indicates those identified so far.
Animals decomposed faster than plant matter.
Scavengers (crows, foxes, vultures, etc.) consume most of the flesh and some bone material.
What is left is attacked by bacteria rather than fungi.
Maggots can consume a small mammal carcass in about 10 - 11 days in the summer time.
Bacteria and maggots can consume about 70% of the body of an animal. The remaining 30% is mostly hair and bones.
The fecal matter of large herbivores contains abundance of partially digested organic matter that provides a rich resource for specialized detritivores in addition to bacteria, fungi and earthworms.
Some of the coprophagous detritivores are dung beetles and the larva of certain fly species.

Nonhumic substances :
Carbohydrates, proteins, peptides, amino acids, fats, waxes, resins, pigments, and other low-molecular-weight organic substances.
Labile, easily to be utilized and degraded by microorganisms, exibit rapid flux rates; low instantaneous concentrations in water

Humic substances (80% of the organic matter):
Humic acids, fulvic acids, humin; the formation of humic substances occurs during the degradation of higher aquatic and terrestrial plant material (celluloses, hemicelluloses, and lignin) by fungi and bacteria.
Loss: photolysis, microbial decomposition, aggregation and sedimentation, and outflows.
Humic acids chelate cations, and help detoxify the soil.
The major factors that influence the rate of decomposition are:
1. Quality of the dead organism as a food source.
2. Physical environment, particularly temperature and moisture.
LITTER QUALITY

The nature of the chemical bonds present and the size of the three-dimensional structure of the molecules in which the bonds are formed contribute to the quality or lack of quality of the litter.
Not all carbon compounds are of the same quality as energy source.
Glucose , simple sugars and soluble proteins are very high quality sources of carbon and energy. These compounds decompose very quickly.
Cellulose and hemicellulose are difficult to break down. They are of moderate quality, and are next to being consumed.
Lignins are more complex and variable chemicals. Lignins are a class of chemicals. Their long molecular structure is much folded into complex three-dimensional structures that shield much of the internal structure from attack by enzymes

Lignin is a major component of wood and one the slowest components of plant tissue to decompose.

As carbohydrates and proteins are removed, the proportion of lignin increases and the remaining litter becomes of a lesser quality as energy source.

The proportion of lignin in the leaves of certain trees makes them less desirable to decomposers, e.g. oak and pine.

Species with less lignin and higher carbohydrate and protein content, support a large number of detritivores, e. g. aspen, basswood, elm, white ash, and birch.

The Actinobacteria or Actinomycetes are a group of Gram-positive bacteria. Most are found in the soil, and they include some of the most common soil life, playing an important role in decomposition of organic materials, such as cellulose and chitin. This replenishes the supply of nutrients in the soil and is an important part of humus formation
Polyphenols in the litter interfere with the decomposers metabolism and enzyme function slowing down the process of decomposition.

Polyphenols are a group of chemical substances found in plants, characterized by the presence of more than one phenol group per molecule. The polyphenols are responsible for the coloring of some plants, anthocyanins, e.g. the color of leaves in the autumn.
MEASURING LITTER BREAKDOWN
The loss of mass through time is expressed by the following negative exponential function:
% original mass remaining = e -ek e = natural logarithm t = time unit used (years, months, etc.) k = decomposition coefficient.

The larger the value of k , the faster the rate of decomposition and the steeper the curve.
The most consistent characteristic accounting for variations in the observed rates of decay is the percentage of the total carbon content that is made up of lignin compounds.
The greater the amount of carbon tied up in lignin, the lower the consumption rate by decomposers.
“A substantial fraction of the mass of the humic acids is in carboxylic acid functional groups, which endow these molecules with the ability to chelate positively charged multivalent ions
(Mg++, Ca++, Fe++, most other "trace elements" of value to plants, as well as other ions that have no positive biological role, such as Cd++ and Pb++.) This chelation of ions is probably the most important role of humic acids with respect to living systems. By chelating the ions, they facilitate the uptake of these ions by several mechanisms, one of which is preventing their precipitation; another seems to be a direct and positive influence on their bioavailability. Many organisms can exploit dissolved organics to some degree if they are present, and humic acids may be taken up by this mechanism. Another paradoxical effect of humic acids is the detoxification of heavy metals. One might expect them to be made More, not less toxic by humic acids, but the studies that I've seen seem to indicate a detoxifying effect.
”
Craig Bingman, Science Editor, AFQ http://www.thekrib.com/Chemistry/humic.html
Additional information about humic acids: http://www.phelpstek.com/clients/humic_acid.html
http://www.ar.wroc.pl/~weber/humic.htm#start http://aggie-horticulture.tamu.edu/extension/newsletters/hortupdate/jun02/art4jun.html
A study showed that the percentage of nitrogen in absolute terms increased when the mass decreased during decomposition.
Organisms that decompose organic matter use carbon as a source of energy and nitrogen for building cell structure.
They need more carbon than nitrogen. If there is too much carbon, decomposition slows when the nitrogen is used up and some organisms die. Other organisms form new cell material using their stored nitrogen. In the process more carbon is burned. Thus the amount of carbon is reduced while nitrogen is recycled. Decomposition takes longer, however, when the initial C:N ratio is much above 30.
In the soil, using organic matter with excess carbon can create problems. To complete the nitrogen cycle and continue decomposition, the microbial cells will draw any available soil nitrogen in the proper proportion to make use of available carbon. This is known as "robbing" the soil of nitrogen, and delays availability of nitrogen as a fertilizer for growing plants until some later season when it is no longer being used in the life-cycles of soil bacteria.
When the energy source, carbon, is less than that required for converting available nitrogen into protein, organisms make full use of the available carbon and get rid of the excess nitrogen as ammonia. This release of ammonia to the atmosphere produces a loss of nitrogen from the compost pile and should be kept to a minimum.
A C:N ratio of 20, where C and N are the available quantities, is the upper limit at which there is no danger of robbing the soil of nitrogen. If a considerable amount of carbon is in the form of lignin or other resistant materials, the actual
C:N ratio could be larger than 20. The C:N ratio is a critical factor in composting to prevent both nitrogen robbing from the soil and conserving maximum nitrogen in the compost.”

Washington State University, Whatcom County
Extension.
http://whatcom.wsu.edu/ag/compost/fundamentals/needs_carbon_nitrogen.htm
The optimum ratio in soil organic matter is about 10 carbons to 1 nitrogen, or a C:N ratio of
10:1.
The nitrogen content reflects the nitrogen remaining in the plant tissue as well as...
 In the biomass of the microbes, fungi and bacteria feeding on the plant.
 Excreted products of detritivores.
Bacteria and fungi breakdown proteins into amino acids.
↓
Amino acids are oxidized into carbon dioxide, water and ammonia.
↓
Some bacteria groups transform ammonium to nitrates.
↓
Available for plants
The availability of any particular nutrient to decomposers depends on the ration of energy supply to nutrient supply, expressed as the carbon:nutrient ratio, C:X
When the C:X ratio of the litter material is high, the supply of that nutrient relative to the energy source is low.
If the litter does not meet the demand for nutrient, the microbes than obtain the nutrient from other sources, e.g. soil, and immobilize it in microbial biomass. These nutrients are then unavailable to plants.
Mineralization and immobilization are taking place at the same time. The supply rate of mineral nutrients to the soil during the process of decomposition, the net mineralization rate , is the difference between the rates of mineralization and immobilization.
In nitrogen immobilization, ammonia and nitrate are taken up by microbes and is largely immobilized, or made unavailable to plants, depending on the C:N ratios. When N is abundant, both microbes and plants assimilate ammonia and nitrate. The nitrate undergoes nitrate reduction by a four-step process and is converted to ammonia by reactions that are similar to those that occur in denitrification. The ammonia is then incorporated into Kreb's cycle intermediates to form amino acids. For example, pyruvic acid plus ammonia becomes the amino acid alanine. http://www.ent.iastate.edu/Ipm/Icm/1997/6-23-1997/nitfert.html
Temperature and moisture influence the rate of microbial activity.
Low temperature and dry conditions inhibit microbial activity.

Microflora population and activity is reduced by constant dry conditions and by alternate wetting and drying.
Decomposition in aquatic systems follows the same pattern of leaching, fragmentation, colonization of detritus by bacteria and fungi, and consumption by invertebrates.
 Aquatic fungi attack twigs and leaves in flowing water.
 Shredders, aquatic arthropods, break organic matter into pieces in the process of eating bacteria and fungi from the surface.
 Grazers and scrapers feed on algae, bacteria, fungi and organic matter collected on rocks and large debris.
 Algae take up nutrients and dissolved organic matter from the water.
 Other organisms filter particles and fecal matter from the water.
In ponds, lakes and oceans, dead organisms and other organic material, called particulate organic matter (POM) drift to the bottom.
POM is ingested, digested and mineralized on its way to the bottom. Much of the organic matter settles on the bottom in the form of humic compounds.
I shallow water much of the organic matter arrives in large packages to be digested by benthos like crabs, snails, and mollusks.
Bacteria on the surface sediment can carry aerobic respiration, but a few centimeters below, the oxygen supply is deplete and anaerobic respiration is used.
NO
3
is used as the electron acceptor instead of oxygen resulting in denitrification, the conversion of nitrate to molecular nitrogen.
When nutrients are not limiting, most phytoplankton has the following molar ratio of elements: C:N:P = 106: 16: 1
Denitrification is the microbial reduction of nitrate to di-nitrogen gas. Denitrification is sometimes referred to as 'dissimilatory' nitrate reduction because it occurs in association with the dissimilation (decomposition) of organic matter.. The denitrification reaction for the oxidation of organic matter with Redfield molar proportions is as follows]:
106(CH
2
O) + 16(NH
3
) + H
3
PO
4
+ 94HNO
3
= 106CO
2
+ H
3
PO
4
+ 177H
2
O + 55.2N
2 http://www.ozestuaries.org/indicators/Def_decomposition.html
Bacteria can use sulfate and Fe 3+ in the middle mud resulting in their reduction.
The bacteria require: organic matter; an anoxic environment (or microenvironment); and dissolved sulfate. Hydrogen sulfide gas (H
2
S) and alkalinity are generated in the process:

SO
4
2 + 2(CH
2
O) = H
2
S + 2HCO
3
2-
Dissolved organic matter (DOM) in the water column provides a source of fixed carbon for decomposition.
Macroalgae, phytoplankton and zooplankton are a source of DOM.
Bacteria biomass and large number of phytoplankton are heterotrophic and important in the recycling of organic matter
A major difference involves dissolved organic matter in the water column, excreted by phytoplankton and zooplankton.
Algae and phytoplankton excrete large amounts of organic matter during certain stages of their life cycle, e.g. reproduction.
When phytoplankton and zooplankton die, a large amount of organic matter becomes available.
Zooplankton and phytoplankton play a major role in releasing nutrient that is going to be converted into biomass.
Bacteria take up this dissolved organic matter, which is not broken down into inorganic forms, and convert it into bacterial biomass that in turn becomes food for zooplankton.
Only bacteria can assimilate the large amounts of organic matter that is dissolved in water and convert it into biomass.
Dissolved organic matter is the substrate for the growth of bacteria. DOM and colloidal matter condense on the surface of air bubbles in the water, forming organic particles on which bacteria flourish.
Ciliates and zooplankton eat bacteria and in turn excrete nutrients in the form of exudates and fecal pellets in the water.
If there is enough food, zooplankton will eat more than it needs and excrete in fecal pellets the excess ingested food, which will form part of the suspended material.
Microbial loop is a term used to explain the role of microbes in marine ecosystems.
What is the microbial loop?
The microbial loop is a micro-food chain that works within (or along side) the classical food chain. In the microbial loop the smallest organisms, the heterotrophic bacteria and pico-plankton use dissolved inorganic material directly (as carbon and energy sources). These organisms are grazed by flagellates and ciliates. The flagellates and smaller phyto-plankton are too small to be preyed on directly by copepods, long considered to be a major predator of micro-organisms.
Improved detection methods have demonstrated that ciliate organisms provide an intermediate predator level in the microbial loop. These are then consumed by copepods and the process continues up the classical food chain. http://www.uib.no/ums/magazine/updates/Loop/loop.htm