FTIR, DNA, AND THE FUTURE OF ARCHAEOLOGICAL SOIL ANALYSIS

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FTIR, DNA, AND THE FUTURE OF ARCHAEOLOGICAL
SOIL ANALYSIS
FTIR Spectra and Analysis Although the purpose
of this study was to compare rather than
characterize the spectra from the different
land-use areas, a bit of FTIR geography is useful
in getting our bearings in the spectra. The
broad peak seen in all three figures at 3500-3200
cm-1 is due to O-H stretching vibrations in
alcohols, phenols, and water (Ellerbrock et al.,
1999). Because an alcohol was used in the
preparation of soil samples for analysis, and
because water content can vary between samples
even after careful preparation, this peak is not
as informative as it seems. The tall peak seen
around 1600 cm-1 represents unsaturated ketones
or amides, and the second tall peak around 1400
cm-1 is due to carboxylic and carbonylic groups
(Ellerbrock et al., 1999). In many of the
spectra, a smaller peak can be seen at 1081 cm-1
which represents certain groups found in
cellulose (Chapman et al., 2001). Interestingly,
bands at 1690 cm-1 and 1710 cm-1 commonly
associated with manure amendments were not
observed in these spectra, suggesting that
these peaks are not long-lived enough to be
archaeologically informative. Comparisons of
peak presence/absence and peak height between
spectra from different land-use types suggests
that the region between 1600 and 1400 cm-1,and
the region between 100 and 800 cm-1 may be the
most informative for differentiating soils having
different land-use histories. The inter-area
variance in these regions can be seen in Figure 1
below.
FTIR and DNA Analysis at the Harvard Forest The
purpose of our fieldwork at the Harvard Forest
was to develop and implement methods to
differentiate archaeological soils according to
land-use history. Our primary technique was
phosphate analysis, but we have also begun
preliminary work in developing alternative
methods for characterizing soil organic matter
(SOM). A protocol for using FTIR (Fourier
Transform Infrared Spectroscopy) to distinguish
soil samples having different archaeological
land-use histories is in preparation. FTIR can be
used to produce visual representations of soil
composition, a potentially useful analytical
tool. We have also extracted DNA from the
microbial biomass of the soils from the study
site in the Harvard Forest. This DNA will be
further analyzed in order to characterize the
microbial complements of soils having different
land-use histories.
FTIR as an Analytical Tool in the Field The
primary goal of this study was to determine the
effectiveness of FTIR spectroscopy as a field
technique for the chemical analysis of
archaeologically interesting soils. Modern FTIR
equipment can produce rapid-non-destructive
analysis of fresh or preserved material, an
advantage over time-consuming laboratory methods
(Chapman et al. 2001,). It is important to
determine, however, whether this method can
reliably differentiate soils that have
experienced different archaeological land-use
patterns. This analysis was performed in
conjunction with a study of the phosphate content
of soils having different land-use histories, and
the resultant phosphate data were checked for
covariance with features of the FTIR
spectra. It should be emphasized that the
purpose of this study was to compare, rather than
characterize, the soils from the different
historical land-use areas. The question
investigated can most neatly be summarized as Do
easily extractable soil organics produce FTIR
spectra that differ according to land-use
type? In this study, we analyzed dried soils
from three different historical land-use areas,
as determined through historical data and
phosphate analysis previously cultivated soils,
improved (manured and plowed) pasture, and
permanent woodlot from the Pierce Farm area of
the 380 ha Prospect Hill tract of the Harvard
Forest in Petersham, Massachusetts. Principles
Evidence from long-term field experiments
indicates that the composition and quantity of
SOM is affected by agricultural management
practices, especially the addition of field
amendments such as fertilizers and manures. These
amendments can produce differences in the
content and spatial arrangement of functional
groups within the SOM (Ellerbrock et al. 1999).
FTIR (Fourier Transform Infrared Spectroscopy)
can be used to analyze the organic fraction of
soils by identifying infrared bands (absorption
peaks) characteristic of various functional
groups Methods Dry soil samples for FTIR
analysis were taken from the 0-10 cm and 15-25 cm
depth intervals of soil cores of three different
land-use areas of the Pierce Farm. It should be
noted that these core intervals do not represent
natural soil depths, as the soils were compacted
during the coring process. 200 µl of EDTA and
100 µl of 2-propanol were added to centrifuge
capsules containing 0.25 g soil samples. The
samples were centrifuged in an Eppendorf
centrifuge for 15 minutes at 10000 rpm, and then
syringe-filtered through a 45 µm PTFE filter.
This process was repeated 3 times. 100 µl of the
supernatant liquid was pipetted onto
Spectra-Tech PTFE (Polytetrafluoroethylene) and
PE (Polyethylene) ST-IR cards. The cards were set
out to dry for 24 hours under a fume hood, and
then analyzed in a Thermo Nicolet IR 100 FTIR
spectral analyzer. Absorbance spectra from
samples on PE and PTFE were compared to minimize
the deleterious effects of the different
intrinsic interference regions of the two ST-IR
card types. PE cards are not useful between
2918-2849 cm-1, 1480-1430cm-1, and 740-700 cm-1.
PTFE cards can show interference in the 1270-100
cm-1 and 660-460 cm-1 regions. These interference
regions are marked by grey bands in Figures 1-3,
which display spectra obtained on PTFE cards.
To Infinity and Beyond Work is continuing on
identifying the organisms represented by the DNA
extracted from the Harvard Forest
soils. Another several waves of subtractive
FTIR analyses are planned using different
extractants in order to attempts to reduce the
intra-landuse area variance seen in the soil
spectra (see Figure 2 above).


DNA Extraction and Analysis
Additional investigation of the variable regions
mentioned above Is also being performed in the
hope of identifying consistent differences in
absorbance peak position or intensity between
land-use areas. These differences should be
consistently greater than intra-landuse area
variation in order to be useful.
Absorbance spectra were also collected for
samples from each land-use area which had been
heated at 650 C for 8 hours In a muffle furnace.
The muffling process destroys organic material,
leaving the inorganic soil fraction behind. These
samples were used to represent the mineral
component of the soil spectrum. Spectra produced
by the muffled samples were subtracted from those
of their non-muffled counterparts from the same
land-use area (after Cox et al., 2000). The
subtracted spectra obtained by this method
represent the organic component of the soils. An
example of a subtracted spectrum is shown in
Figure 3.
References Chapman, S.J. , S.D. Campbell, A.R.
Fraser, and G. Puri. 2001. FTIR Spectroscopy of
peat in and bordering Scots pine woodland
relationship with chemical and biological
properties. Soil Biology and Biochemistry
331193-1200. Cox, R.J., H.L. Petersen, J. Young,
C. Cusik, and E.O Espinoza. 2000. The forensic
analysis of organic soil by FTIR. Forensic
Science International 108 107-116. Ding, G. J.M.
Novak, D. Amarasiriwardena, P.G. Hunt, and B.
Xing. 2002. Soil organic matter characteristics
as affected by tillage management. Soil Science
Society of America Journal 66 421-429.
Ellerbrock, R.H., A. Hohn, and J. Rogasik. 1999.
Functional analysis of soil organic matter as
affected by long-term manurial treatment.
European Journal of Soil Science 50
65-71. Ellerbrock, R. H., A. Hohn, and H.H.
Gerke. 1999. Characterization of soil organic
matter from a sandy soil in relation to
management practice using FT-IR spectroscopy.
Plant and Soil 21355-61.