Microbiology of decomposition is the study of all
microorganisms (mainly bacteria and fungi) involved in decomposition
the chemical and physical processes during which organic matter is broken down
and reduced to its original elements.
Decomposition microbiology can be divided between two fields
of interest:
The decomposition of plant materials is commonly studied in
order to understand the cycling of carbon within a given environment and to
understand the subsequent impacts on soil quality. Plant material decomposition
is also often referred to as composting. The decomposition of cadavers and
carcasses has become an important field of study within forensic taphonomy.
Decomposition microbiology of plant materials
The breakdown of vegetation is highly dependent on oxygen
and moisture levels. During decomposition, microorganisms require oxygen for
their respiration. If anaerobic conditions dominate the decomposition
environment, microbial activity will be slow and thus decomposition will be
slow. Appropriate moisture levels are required for microorganisms to
proliferate and to actively decompose organic matter. In arid environments,
bacteria and fungi dry out and are unable to take part in decomposition. In wet
environments, anaerobic conditions will develop and decomposition can also be
considerably slowed down. Decomposing microorganisms also require the
appropriate plant substrates in order to achieve good levels of decomposition.
This usually translates to having appropriate carbon to nitrogen ratios (C:N).
The ideal composting carbon-to-nitrogen ratio is thought to be approximately
30:1. As in any microbial process, the decomposition of plant litter by
microorganisms will also be dependent on temperature. For example, leaves on
the ground will not undergo decomposition during the winter months where snow
cover occurs as temperatures are too low to sustain microbial activities.
Decomposition microbiology of cadavers and carcasses
The decomposition processes of cadavers and carcasses are
studied within the field of forensic taphonomy in order to:
- aid in the estimation of post-mortem interval (PMI) or time since death;
- aid in the location of potential clandestine graves.
Decomposition microbiology as applied to forensic taphonomy
can be divided into 2 groups of studies:
- microorganisms from within the body;
- microorganisms from the decomposition environment.
Microorganisms in the body
When considering cadavers and carcasses, putrefaction
is the proliferation of microorganisms within the body following death and also
encompasses the breakdown of tissues brought upon by the growth of bacteria.
The first signs of putrefaction are usually the discolorations of the body
which can vary between shades of green, blue, red or black depending on 1)
where the color changes are observed and 2) how far along within the
decomposition process the observation is made. This phenomenon is known as
marbling. Discolorations are the results of bile pigments being released
following an enzymatic attack of the liver, gallbladder
and pancreas
and the release of hemoglobin breakdown products. Proliferation of bacteria
throughout the body is accompanied with the production of considerable amounts
of gases due to their capacities of fermentation. As gases accumulate
within the bodily cavities the body appears to swell as it enters the bloat
stage of decomposition.
As oxygen is present within a body at the beginning of
decomposition, aerobic bacteria flourish during the first stages
of the process. As the microbial population increases, an accumulation of gases
changes the environment into anaerobic conditions which is consequently
followed by a change to anaerobic bacteria. Gastro-intestinal bacteria
are thought to be responsible for the majority of the putrefactive processes
that occur in cadavers and carcasses. This can be in part attributed to the
impressive concentrations of viable gastro-intestinal organisms and the
metabolic capacities they possess allowing them to use an array of different
nutrient sources. Gastro-intestinal bacteria are also capable of migrating from
the gut to any other region of the body by using the lymphatic
system and blood vessels. Furthermore, we know that coliform
varieties of Staphylococcus are important members of the
aerobic putrefactive bacteria and that members of the Clostridia
genus make up a large part of anaerobic putrefactive bacteria.
Proposed evolution of microorganisms within the body during
decomposition. As oxygen is available at the beginning of decomposition,
aerobic microorganisms flourish and quickly deplete the oxygen. Anaerobic
bacteria can then proliferate in the body. Later in the decomposition process,
fungi and bacteria from the environment will also become involved in the
process.
Microorganisms outside the body
Cadavers and carcasses are usually left to decompose in
contact with soil whether through burial in a grave or if left to decompose on
the soil surface. This allows microorganisms in the soil and air to come in
contact with the body and to take part in the decomposition process. Soil
microorganism communities also undergo changes as a result of decomposition
fluids leaching in the environment. Cadavers and carcasses often show signs of
fungal growth suggesting that fungi use the body as a source of nutrients.
The exact impacts that decomposition may have on surrounding
soil microbial communities remains unclear as some studies have shown increases
in microbial biomass following decomposition whereas other have seen decreases.
It is likely that the survival of microorganisms throughout the decomposition
process is highly dependent of a multitude of environmental factors including
pH, temperature and moisture.
Skeletonized pig carcass showing the production of a cadaver
decomposition island surrounding the remains as a result of leaching of
decomposition fluids into the surrounding environment.
Decomposition fluids and soil microbiology
Decomposition fluids entering the soil represent an
important influx of organic matter and can also contain a large microbial load
of organisms from the body. The area where the majority of the decomposition
fluid leaches into the soil is often referred to as a cadaver decomposition
island (CDI). It has been observed that decomposition can have a favorable
influence on the growth of plants due to increased fertility, a useful tool
when trying to locate clandestine graves. The changes in the concentration of
nutrients can have lasting effects that are still seen years after a body or
carcass has completely disappeared. The influence that the surge in nutrients
can have on the microorganisms and vegetation of a given site is not well
understood but it appears that decomposition initially has an inhibitory effect
for an initial stage before entering a second stage of increased growth.
Decomposition fungi
Fungal mycelia (white) on hoof of a deceased pig
It is well known that fungi are heterotrophic for carbon
compounds and almost all other nutrients they require. They must obtain these
through saprophytic or parasitic associations with their hosts which implicates
them in many decomposition processes.
Two major groups of fungi have been identified as being
linked to cadaver decomposition:
- ammonia fungi
- post-putrefactive fungi
Ammonia fungi are broken-down into two groups referred to as
"early stage fungi" and "late stage fungi." Such a
classification is possible due to the successions that are observed between the
types of fungi that fruit in or around a burial environment. The progression
between the two groups occurs following the release of nitrogenous products
from a body in decomposition. Early stage fungi are described as being ascomycetes,
deuteromycetes
and saprophytic basidiomycetes whereas late stage fungi consisted of
ectomycorrhizal basidiomycetes.
Decomposition fungi as PMI estimators
Considering the amount of forensic cases in which
significant amounts of mycelia are observed is quite high, investigating
cadaver associated mycota may prove valuable to the scientific community as
they have much forensic potential.
Only one attempt at using fungi as a PMI marker in a
forensic case has been published to date. The study reported the presence of
two types of fungi (Penicillium and Aspergillus) on a body found
in a well in Japan and stated that they could estimate PMI as being
approximately ten days based on the known growth cycles of the fungi in
question.
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