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Author(s): A. M. Child
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Source: Studies in Conservation, Vol. 40, No. 1 (Feb., 1995), pp. 19-30
Published by: International Institute for Conservation of Historic and Artistic Works
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MICROBIALTAPHONOMY OF ARCHAEOLOGICALBONE
A.M. Child
Summary-Taphonomy is the study of all changes that occur within an animal or plant following death. Bone
is the predominant material of animal origin to survive within the archaeological environment.It is the source
of a wealth of information concerning the relationships, diets, disease and ages of people (and animals) in
past cultures. For this information to be extracted and interpreted, there is a need for conservators and
archaeological scientists to be aware of the processes of taphonomic change which may occur in bone. These
changes are legion; this paper attempts to define some of the major changes seen in bone which may be attributable to the various actions of microorganisms.
Introduction
Taphonomy is the study of all changes occurring
within a substrate following death. These changes
are many and varied, and it is not the aim of this
article to present a comprehensive list. The main
factors involved in the taphonomic changes of bone
in the burial environment will be discussed below.
Bone is the predominant material of animal origin to survive within the archaeological environment. It is a composite material, comprising both
inorganic and organic fractions. Its study reveals
considerable information to the conservator, the
bone specialist and the archaeological scientist. For
this information to be retrieved, the conservator
must be aware of the likely mechanisms of decomposition and the state of preservation of the excavated bone.
One of the major problems confronting analysts
and conservators of archaeological bone is the
assessment of its integrity, since conservation treatments will be dictated by degree of preservation.
Both the inorganic and the organic phases of bone
can be changed by taphonomic processes, and estimation of the degree of preservation of these phases
based upon external morphology has been proved
to be unreliable [1].
Definitions
For clarity, some of the terms used in this paper
have been defined here. Other definitions exist,
however; the definitions given here have been
selected because they represent the most common
usage.
Biodegradation: any change in the properties of a
material caused by the activities of organisms.
Bone structure
Bone is a highly specialized composite material
comprising both inorganic (mineral) and organic
(mostly protein) phases. Its inorganic fraction (90%)
is calcium hydroxyapatite. The remaining 10% is
organic, made up of collagen, non-collagenous proteins (NCP), lipids, mucopolysaccharides and other
carbohydrates [4]. There are two types of bone,
cancellous bone (spongy bone) and compact bone
(cortical bone), and their distribution within the
body is dictated by biomechanical considerations.
Both compact and cancellous bone are formed by
the deposition of collagen fibrils in layers. In compact bone, these layers are laid down in rings
around the osteone, their alignment changing by
approximately 90? in each layer [5].
Bone mineral
19
A.M. Child
lesser quantities of pyrophosphate, magnesium,
sodium and potassium [6]. Strontium and lead,
ingested as part of the diet of an individual, are
stored in the skeleton. Fluoride ions have a high
affinity for bone mineral, converting hydroxyapatite
to fluorapatite, and fluoride analyses have been
used to check provenance [7].
Bone proteins
The organic fraction of bone comprises 10-15% of
the total bone weight. There is one major protein
component, collagen, and a group of proteins
termed collectively non-collagenous protein (NCP).
Collagen
20
Palaeopathology
The gross morphology of archaeological bone can
be changed by the burial environment, but physical
measurements of skeletal bone dimensions will still
yield information on growth, health and incidence
of some diseases within human populations. Similar
examination of animal bone produces information
relating to butchering methods, diet, hunting and/or
farming techniques practised by ancient populations
[14]. Microscopic examination of archaeological
bone (and the related surviving soft tissues) will
yield more information on disease [15].
Archaeological science
The preservation of bone depends not upon the
length of burial but upon the environment of burial. If bones are sufficiently well-preserved, they still
contain indigenous organic macromolecules. These
can be used to provide information on:
-the age of the bone by radiocarbon dating
[16-18] or by amino acid racemization [19-22];
-the diet of the animal by stable isotope analysis
[23-26];
-genetic relationships [27-29].
This information is only reliable where the proteins
used have survived unchanged by biological, physical or chemical degradative processes [30].
40 (1995) 19-30
Studiesin Conservation
Microbialtaphonomyof archaeologicalbone
Bone protein is unusual in that it survives over
archaeological, even geological, time scales.
Generally, protein loss from unmineralized substrates is considered to be exponential, so that the
amount which survives depends upon the initial
concentration [31]. The protein loss within archaeological bone does not follow this pattern and, as a
result, archaeological bone can contain only 1-2%
nitrogen [26]. Indeed, the carbon to nitrogen ratio
in archaeological bone collagen does not change
from that of modem bone until almost all of the
collagen (97%) has been lost [23]. Where 98% of
the original bone protein has been lost, the amino
acid content is enriched in aspartic and glutamic
acid residues [26, 32]. The original source of these
residues is uncertain; however, three possibilities
exist:
-contamination of the bone proteins with soil proteins [33];
-survival of the NCP, rich in these residues, whose
presence is masked when collagen survives well
[32];
-selective decomposition of the collagen helix, to
leave acidic amino acids of collagen origin.
The degree to which proteins survive intact in
bones from archaeological contexts can be measured using immunochemical means. Although
these methods are well established for application
to modem materials, they have only recently been
applied to archaeological ones [34-39]. Results must
be viewed with caution [40]; however, they show
that indigenous proteins (i.e., apohaemoglobin and
osteocalcin) survive in an immunologically recognizable form in bones.
Proteins (both collagens and NCP) are thought
to survive in bone because of their close association
with the mineral phase, which protects against
enzyme attack. The collagens are further preserved
because of their innately protective structure and
chemistry (see 'Collagen' above).
40 (1995) 19-30
Studiesin Conservation
A.M. Child
the environment in which the decomposition
occurred.
Anaerobic and aerobic decomposition
Microorganisms can be divided into three categories, depending upon their metabolism: they may
be either obligately aerobic, facultatively anaerobic
or obligately anaerobic [50].
In aerobic environments, complete decomposition
of the protein to carbon dioxide, water, nitrogen
dioxide and sulphur dioxide occurs without a considerable reduction in pH; therefore the proteins in
bone are more likely to survive. All the fungi and
some of the bacteria have an obligately aerobic
metabolism, degrading complex proteins with proteolytic enzymes. Rapid aerobic growth will promote
anaerobic conditions; this occurs when the rate of
oxygen consumption exceeds the rate of oxygen diffusion into the system. When anaerobic conditions
have been achieved, the obligate aerobic microorganisms will stop growing, but the bacteria that
have the facility for both anaerobic and aerobic
decomposition will switch to anaerobic pathways.
The obligate anaerobes will start to flourish.
Anaerobic fermentation uses substances other
than molecular oxygen as a terminal electron acceptor [50]. Microbial decomposition of protein under
anaerobic conditions leads, initially, to a drop in
pH. This is due to the generation of acidic compounds such as low molecular weight fatty acids
and amino acids, which are by-products of anaerobic metabolism. Their presence will result in the
demineralization of hydroxyapatite and the exposure of collagen to collagenolytic enzymes. Extrapolating from work on dental caries [51], an
increase in proton concentration will result in the
partial demineralization of hydroxyapatite, because
it will buffer the changes in pH at its own expense.
Microbial fermentation of bone proteins by
anaerobic pathways could lead to the total loss of
the organic fraction of bone since the products of
the reaction perpetuate the reaction; total loss of
the organic fraction, however, is not likely. As the
rate of anaerobic decomposition slows due to the
lack of metabolites, oxygen will diffuse into the system. Eventually, the rate of anaerobic degradation
will be surpassed by the rate of oxygen diffusion
and the system will return to its aerobic state, when
the rate of aerobic degradation will be determined
by the concentration of bio-available organic matter [52].
Catalyzing bone decomposition
To decompose bone, a microorganism must be able
to obtain energy from the collagen and mineral.
22
For the microbial enzymes to gain access to the collagen, the microbe must also be able to demineralize the bone, or grow in an environment where
demineralization occurs (e.g. a low-pH soil).
Enzymes
Enzymes are proteins which can increase the rate of
(catalyze) biological reactions between 106- and 108fold. As well as increasing rate, enzymes are specific
in the reactions which they will affect. An individual enzyme will catalyze a specific reaction with a
unique substrate or group of substrates. Enzymes
that disrupt proteins are called proteolytic enzymes
or proteases, and enzymes that are unique in their
ability to hydrolyze efficiently the triple-helical
regions of collagen under physiological conditions
(i.e., moderate temperature and around neutral pH)
are called collagenases. Collagenases are complexes
of several different enzymes, each of which has a
different catalytic function. There are two accepted
types of collagenase [53].
Collagen degradation by vertebrate collagenases
Vertebrate collagenases (tissue collagenases) disrupt
unmineralized collagen into only two fragments by
action at a specific site within the al(I)-chain, a single glycine-isoleucine bond between residues 772
and 773 [54]. The enzyme appears, therefore, to recognize the whole collagen molecule configuration.
Collagen degradation by microbial collagenases
On the other hand, microbial collagenases recognize
small amino acid sequences. All microbial collagenases examined so far appear to have the same
amino acid sequence requirements for cleavage
[55-59]; hence examination of the action of a wellcharacterized bacterial collagenase can be included
here.
The anaerobic bacterium Clostridiumhistolyticum
produces a collagenase complex of six enzymes. All
are highly active against collagen and devoid of
other proteolytic activities. Study of their amino
acid sequence requirements for cleavage is challenging, since purification of these enzymes is difficult;
however, the requirement for one of them (,3-collagenase) has been demonstrated [60]. Unlike vertebrate collagenases, 3-collagenase does not have a
rigid sequence requirement, but will cleave between
the X- and the glycine- residues in any of the
sequences below:
-glycine-Y-X-glycine-proline-hydroxyproline-glycine-Y-X-glycine-alanine-arginine-glycine-Y-X-glycine-Z-alaninewhere X-, Y- and Z- can be any of the amino acids
which constitute collagen, except glycine. Microbial
Studies in Conservation40 (1995) 19-30
23
A.M. Child
Autolysis usually follows very rapidly after death;
even in the short interval between death and burial,
the osteocytes, marrow and neuro-vascular bundles
undergo autolysis [72]. Autolysis is self-limiting
and, after a certain stage is reached, the cells
remain stable for long periods of time [73]. The
majority of changes in bone, however, affect the
extracellular matrix proteins (i.e., collagen) which
are not amenable to autolysis.
Microbial changes
Augmenting the processes of autolysis is microbial
decomposition: autolysis opens up the soft tissues,
thus increasing access for microorganisms.
Decomposition of whole bodies involves the loss of
both soft and hard tissues, and both aerobic and
anaerobic environments will be achieved within the
rotting flesh.
Due to the presence and high numbers of gut
flora (which include some microorganisms capable
of inducing dental caries [74]), the bones within the
abdomen and thorax will suffer the demineralizing
effects of putrefaction for longer than the long
bones or the skull. This is borne out in some studies, but not in others [75, 76]. Laboratory studies
using bones inoculated with microorganisms [77]
support the premise that soft tissue destruction augments hard tissue loss.
Biostratinomic changes
Autolytic and microbial changes appear very soon
after death. Autolytic destruction can occur within
10 seconds following death of the cell [73]. The
types and degree of microbial destruction will be
dictated by the environment in which the corpse
lies. If burial does not immediately follow death,
the growth of microorganisms which would normally be prohibited by the low burial temperatures
will be promoted (e.g. Cl. histolyticum). Once the
body has cooled, these microorganisms are unlikely
to grow, but it is possible that the temperature of
the decaying body may increase sufficiently to allow
for their growth.
It is probable that Cl. histolyticum has its most
important role in the breakdown of collagen in the
pre-burial stage. Collagen breakdown will occur as
the bones and associated tissues lie on (or slightly
below) the surface of the soil. Cl. histolyticum is
present in the soil, but also in the gut of humans
and some animals as normal flora.
Diagenetic changes
Janaway [41] considered that soil was less important in the initial stages of decomposition, arguing
that the body will create its own environment which
in turn will modify the effects of the surrounding
soil. Studies in soil microbiology have shown that
24
Microbialtaphonomyof archaeologicalbone
every 10?C rise in temperature[80]. The concomitantincreasein oxygen concentrationwill promote rapid aerobic decomposition of organic
components.Fast-growingfungi, previouslyheld in
check by burial conditions,tend to flourishat the
expense of other organisms.With the presence of
metabolitesfrom fungal action, the rate of decomposition of the bone will, to a certain extent, be
controlledby the interactionof the inherentmicrobial species (see 'Microbial interactions' below)
until physicalconditions(e.g. storage at controlled
relativehumidity)performthis function.
Chemical hydrolysis
If the mineral phase of bone retains its integrity,
then collagen can only be lost following chemical
alteration.A number of chemical transformations
will occur and will continueafter death, such as the
process of non-enzymiccrosslinking,but the most
significantchange will be hydrolysisof the peptide
bond.
A simple, conceptualmodel of collagen peptide
bone hydrolysishas been suggested.This model still
requires much work before it can be usefully
appliedto mineralizedcollagen,but it fits well with
many observedphenomena[81]. The rate of collagen loss from the bone will dependupon the rate of
peptide bond hydrolysis, the rate of diffusion of
these small fragmentsout of the bone and the rate
of post-mortemcrosslinking.
Crosslinkswill form as a result of the continued
non-enzymic process. 'Vegetable tannates' in the
burial environmentwill bond to the collagen [82].
The degree of bonding by these tannates will
depend upon the rate of diffusion of these chemicals into the bone. This diffusionwill be enhanced
following demineralizationof the bone. It is likely
that the presenceof these compoundsin the bone
will physically inhibit the action of collagenolytic
enzymes.
Limitations of microbial decomposition
25
A.M. Child
Conclusion
The various pathways for the microbial taphonomy
of archaeological (and historical) bone have been
defined here and, even though an exhaustive list has
not been given, it can be seen that a bewildering
range of reactions is possible. These include demineralization of the bone, damage due to the action
of microbial enzymes (both collagenases and proteases), the microbial production of MFD (microscopical focal destruction) and the alteration of the
proteins following decomposition.
Acknowledgements
The author would like to thank Professor R.D.
Gillard, Dr Matthew Collins, Dave Watkinson,
Susan Hardman and Naomi Earl-Turner for their
helpful comments during the preparation of this
manuscript. Thanks are also due to Dr J. Morgan
and the staff of the Cardiff Royal Infirmary,
Bacteriology Department, for their kind permission
to use the laboratory facilities for the microbial isolation work. The project was funded by the Science
& Engineering Research Council (Science-Based
Archaeology Committee).
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Author
ANGELA M. CHILD studied microbiology at the
Resum--La taphonomie est l'etude de tout changement qui intervientsur un animal ou sur -uneplante apres sa
mort. Les os sont les principaux materiaux d'origine animale d survivre dans l'environnementarcheologique.
C'est une source importante d'informations sur les relations, les regimes, les maladies et les dges des peuples
(et des animaux) des anciennes cultures. Pour trouver et interpreter ces informations, il est besoin de conservateurs et d'hommes de sciences archeologues qui connaissent les processus de changements taphonomiquesqui
peuvent advenir aux os. Ces changements sont nombreux: ce papier tente de definir quelques-unsde ces principaux changements, qui peuvent etre attribues a l'action variee des microorganismes.
Zusammenfassung-Taphonomie bezeichnet das Studium aller Veranderungenan Lebewesen und Pflanzen
nach dem Tod. Knochen sind das vorherrschendeMaterial lebenden Ursprunges, das sich im archaologischen
Rahmen erhalt. Sie sind die Quelle fir eine Vielzahl von Informationen uiber Beziehungen, Nahrung,
Krankheiten und Alter von Menschen und Tieren vergangenerKulturen. Damit diese Informationengesammelt
und interpretiertwerden k6nnen, miissen Konservatorenund archdologische Wissenschaftlerein Bewujftseinfur
taphonomische Veranderungen entwickeln, die sich in Knochenmaterial abspielen konnen. Die vorliegende
Arbeit versucht, wichtigste in Knochen feststellbare Veranderungenzu definieren, welche den zahlreichen
Aktivitdten von Mikroorganismenzuzuschreibensind.
Resumen-Tafonomia es el estudio de todos los cambios efectuados en las sustdncias animales y vegetales
despues de la muerte de las mismas. De los restos de origen animal, el hueso es el principal material perStudies in Conservation40 (1995) 19-30
29
A.M. Child
durable dentro del dmbito arqueol6gico. El hueso es una abundantefuente de informacion acerca de las relaciones sociales, dietas, enfermedades y edades de gentes (y animales) de culturas pasadas. Para extraer e
interpretaresta informacion, es necesario que los conservadoresy cientificos arqueol6gicos esten conscientes de
los procesos de cambio tafonomicos que pueden ocurir en el hueso. Estos procesos de cambio son numerosisimos. Este trabajopropone la definicion de algunos de los principales cambios observados en hueso y atribuibles
a las acciones varias de los microorganismos.
30