ARTICLE IN PRESS

Soil Biology & Biochemistry 40 (2008) 515–527

www.elsevier.com/locate/soilbio

FTIR spectroscopy can be used as a screening tool for organic matter

quality in regenerating cutover peatlands
Rebekka R.E. Artza,, Stephen J. Chapmana, A.H. Jean Robertsona, Jacqueline M. Pottsb,
Fatima Laggoun-Défargec, Sébastien Gogoc, Laure Comontc, Jean-Robert Disnarc,
Andre-Jean Francezd
a
Soils Group, The Macaulay Institute, Craigiebuckler, Aberdeen AB15 8QH, UK
b
Biomathematics and Statistics Scotland (BioSS), The Macaulay Institute, Craigiebuckler, Aberdeen AB15 8QH, UK
c
Institut des Sciences de la Terre d’Orléans (ISTO), UMR 6113 CNRS/Université d’Orléans, Bt Géosciences, Rue de St Amand, BP 6759,
45067 Orléans Cedex 2, France
d
Interactions Biologiques et Transferts de Matières, UMR CNRS 6553 Ecobio, Université de Rennes 1, 35042 Rennes Cedex, France

Received 22 September 2006; received in revised form 20 September 2007; accepted 24 September 2007

Abstract

Vegetational changes during the restoration of cutover peatlands leave a legacy in terms of the organic matter quality of the newly
formed peat. Current efforts to restore peatlands at a large scale therefore require low cost and high throughput techniques to monitor
the evolution of organic matter. In this study, we assessed the merits of using Fourier transform infrared (FTIR) spectra to predict the
organic matter composition in peat samples at various stages of peatland regeneration from five European countries. Using predictive
partial least squares (PLS) analyses, we were able to reconstruct peat C:N ratio and carbohydrate signatures with reasonable accuracy,
but not the micromorphological composition of vegetation remains. Despite utilising different size fractions, both carbohydrate
(o200 mm fraction) and FTIR (bulk soil) analyses report on the composition of plant cell wall constituents in the peat and therefore
essentially reveal the composition of the parent vegetational material. The accuracy of the FTIR-based PLS models for C:N ratios and
carbohydrate signatures was adequate to allow for their use as initial screening tools in the evaluation of the present and future organic
matter composition of peat during monitoring of restoration efforts.
r 2007 Elsevier Ltd. All rights reserved.

Keywords: Fourier-transform infrared spectroscopy; Peat; Organic matter quality; Carbohydrates; C:N ratio; Organic micro-remains

1. Introduction tion of cut-over peatlands (Gorham and Rochefort, 2003).

Northern Peatlands are composed almost entirely of
decomposing plant material and store approximately a
third of all soil organic matter (Gorham, 1991) even though
their total cover only extends to 3–5% of the global land
area. Peat extraction for fuel and horticultural use has
steadily diminished this carbon stock, with the largest
quantities of peat having been extracted in the mid to late
20th century (Chapman et al., 2003). Various restoration
programs have since been designed to encourage revegeta-
Corresponding author. Fax: +44 1224 498207.
E-mail address: r.artz@macaulay.ac.uk (R.R.E. Artz).
Although some of these programs have demonstrated that
annual gaseous emissions show a return to net carbon
sequestration (Tuittila et al., 1999) or at least reduce net
emissions (Waddington and Warner, 2001), it is not known
how peatland restoration affects the pool of soil organic
matter and hence the long-term regeneration of the carbon
sequestration potential. Increased losses of dissolved
organic carbon (DOC) have been observed from many
peatland ecosystems in the past decades (Freeman et al.,
2001), and some of this can be ascribed to increased
turnover of the soil organic matter (Glatzel et al., 2003).
Currently, monitoring efforts of the evolution of soil
organic matter quality during restoration of peatlands have

0038-0717/$ - see front matter r 2007 Elsevier Ltd. All rights reserved.
doi:10.1016/j.soilbio.2007.09.019
 ARTICLE IN PRESS
516 R.R.E. Artz et al. / Soil Biology & Biochemistry 40 (2008) 515–527
only a limited array of tools. Generally, bulk measures
such as total and soluble organic carbon and nitrogen, and
their ratios, have been most often used to assess restoration
success (Andersen et al., 2006; Comont et al., 2006).
Similarly, a technique often employed in peat organic
matter compositional studies is analysis of the patterns of
carbohydrate monomers derived from plant cellulose and
hemicelluloses as these are indicative of the source plant
composition and the preservation status of these remains
(Cheshire, 1979; Moers et al., 1989, 1990; Bourdon et al.,
2000). Comont et al. (2006) used peat C:N ratios combined
with micromorphological and carbohydrate composition
of peat in a pioneering study to elucidate the evolution
of organic matter with regeneration. These techniques,
however, are expensive and time consuming processes.
Fourier Transform Infrared (FTIR) spectroscopy is a
commonly used technique capable of distinguishing
the principal chemical classes in soil organic matter,
such as carbohydrates, lignins, cellulose, fats and/or lipids
and proteinaceous compounds, through the vibrational
characteristics of their structural chemical bonds. The use
of attenuated total reflectance accessories, in particular
those utilising very hard crystals such as diamond, has
further advanced the use of FTIR in soils and other solid
residues. Dilution with KBr is no longer necessary,
reproducibility is increased and the nondestructive nature
of this analysis allows the sample to be re-used for other
analyses. FTIR spectroscopy has been used successfully on
whole soils to describe the status of decomposition in
different horizons (Haberhauer and Gerzabek, 1999;
Haberhauer et al., 1998; Chapman et al., 2001), for
example through following the reduction of the carbohy-
drate markers with depth. Using multivariate statistics,
FTIR data can be used as quantitative indicators of the
composition of the soil organic matter to distinguish soil
horizons (Haberhauer et al., 1999, 2000). Models utilising
partial least squares (PLS) analysis have been applied to
FTIR data to predict various chemical and physical
qualities of organic materials, including studies of the
lignin and carbohydrate contents of wood and woody peat
(Durig et al., 1988; Tucker et al., 2001; Bjarnestad and
Dahlman, 2002) and the phenolic and carbohydrate
contents of food (e.g. Coimbra et al., 2005). This study
investigated the potential use of FTIR spectroscopy data as
indicators of peat organic matter quality in regenerating
peatlands. We determined various chemical and micro-
morphological characteristics of peat samples from profiles
at sites at different stages of regeneration from five cutover
European peatlands and tested the power of PLS analysis
using FTIR data to predict these organic matter character-
istics. In large-scale restoration projects, it would be
advantageous to be able to use low cost and high
throughput techniques in order to assess the success of
restoration efforts. Our results are therefore discussed with
respect to the utility of FTIR spectroscopy coupled to
predictive PLS in the assessment of organic matter quality
with peatland regeneration.
2. Materials and methods
2.1. Sampling procedure
Nineteen sites within gradients of unaided regeneration
were selected in previously cut-over peatlands in five
countries in Europe (Table 1). Single cores were obtained
from each site with a double-skinned peat corer (to avoid
compaction) and were sectioned into four horizons of
different stages of decomposition. The horizons were
designated horizons 3 (surface layer 0–5 cm), 4 (5–10 cm),
6 (22.5–27.5 cm) and 8 (42.5–47.5 cm). Where horizon 3
samples contained a mixture of new vegetation and cut
surface peat, only the vegetation layer was sampled.
Samples were cut into 1 cm3 subsamples and the sub-
samples mixed to ensure homogeneity. Portions were
shipped on ice packs to partner laboratories for the
relevant analyses contributing to this study. Samples where
not all analyses could be completed due to low sample size
were excluded from statistical analyses, reducing the
dataset for statistical analyses to n ¼ 13 for horizon 3,
n ¼ 18 (horizon 4), n ¼ 18 (horizon 6) and n ¼ 18 (horizon
8; except for carbohydrates, where n ¼ 17).
2.2. FTIR spectroscopy
Spectral characterisation of peat samples was performed
by diamond attenuated total reflectance (DATR) FTIR
spectroscopy using a Nicolet Magna-IR 550 FTIR spectro-
meter (Thermo Electron, Warwick, UK) fitted with a
potassium bromide beam splitter and a deutroglycine
sulphate detector. A DATR accessory, with a single-
reflectance system, was used to produce transmission-like
spectra. The samples were dehydrated by freeze drying and
powdered by ball milling with zirconium balls. Samples
were placed directly on a DATR/KRS-5 crystal and a flat
tip powder press was used to achieve even distribution and
contact. Spectra were acquired by averaging 200 scans
at 4 cm1 resolution over the range 4000–350 cm1.
A correction was made to spectra for the ATR to allow
for differences in depth of beam penetration at different
wavelengths (Omnic software, version 7.2, Thermo Elec-
tron). All spectra were also corrected for attenuation by
water vapour and CO2. Minor differences in the amplitude
and baseline between runs were corrected by normalisation
of the data by subtraction of the sample minimum followed
by division by the average of all data points per sample.
First and second derivatives were calculated to determine
and test correlations of organic matter variables which
formed ‘shoulders’ rather than distinct peaks in the FTIR
profiles. Occasionally, spectral signals from silicate miner-
als were observed in a few samples from sites on, or close
to, nearly exhausted peatlands A notable example is shown
in Fig. 1A in the Scottish sample from an advanced stage of
regeneration at horizon 6 (22.5–27.5 cm depth), which
shows the diagnostic peaks at 3700 and 467 cm1 of
kaolinite. Mineral interference also manifests itself in the
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Table 1
Origin and general characteristics of peat samples

Country Site Regeneration Dominant vegetationb Years since

stagea abandonment
(estimate)

Finland (Aitoneva) A Early Eriophorum vaginatum 10

B Early Eriophorum vaginatum 10
C Early Carex rostrata 10
D* Early Sphagnum fallax 10
E Bare –
France (Baupte) A Bare – 5–10
B Early Eriophorum vaginatum 5–10
France (Le Russey) A Bare – 44
B* Early Sphagnum fallax, Eriophorum angustifolium 422
C* Advanced Sphagnum fallax, Eriophorum angustifolium, Calluna vulgaris 421 (o40)
D Reference Sphagnum fallax, Eriophorum angustifolium, Calluna vulgaris Intact

Switzerland (Chaux A* Early S. fallax (discontinuous), E. vaginatum, Polytrichum commune, P. 429

d’Abel) strictum
B Intermediate S. fallax, E. vaginatum, Polytrichum commune, P. strictum 442
C Advanced S. fallax (continuous), E. vaginatum, Polytrichum commune, P. 451
strictum, Vaccinium spp.
D* Reference S. fallax (continuous), E. vaginatum, Polytrichum commune, P. Intact
strictum, Vaccinium spp
Scotland A Bare – o5
(Middlemuir) B Early E. vaginatum, Agrostis canina, Calluna vulgaris, E. angustifolium, S. 5–10
auriculatum, S. cuspidatum
C Early E. angustifolium, S. auriculatum, E. vaginatum, S. cuspidatum 5–10
D Advanced S. palustre,C. vulgaris, E. vaginatum, Erica tetralix, Deschampsia 50
flexuosa, Molinia caerulea
a
Determined by assessment of vegetation diversity and depth of newly formed peat.
b
Based on % cover estimates. Only vegetation with 410% cover reported * Horizon 3 samples not analysed.

1030 cm1 polysaccharide band (Farmer, 1974) and could
potentially skew the accuracy of predictions of parameters
which differ in this spectral region (see ‘Statistical analyses’
below).
2.3. Micromorphological analysis
Micromorphological identification and quantification of
peat microremains were carried out using a DMR XP
Leica photonic microscope under transmitted light. Wet
bulk peat samples were mounted as smearslides and
analysed with  20 and  50 objectives. The surfaces of
the main categories were counted (in relative numeric
frequencies) through a grid reticule, used as surface unit,
and placed on the microscope ocular. Three thousand to
5000 items per sample were counted with an estimated
counting error of about 10%.
2.4. C and N determination
Carbon and nitrogen contents were determined by
combustion at 1100 1C with a CNS-2000 LECO apparatus,
on dried and crushed peat samples. Due to the total lack of
carbonates, total carbon (TC) was assumed to be total
organic carbon (TOC).
2.5. Characterisation of carbohydrate signatures
Carbohydrate analyses were performed on fine-grained
peat fractions (o200 mm, isolated by wet-sieving at 200 mm
under positive pressure using water circulation). Cellulosic
and hemicellulosic sugars were identified and quantified by
gas chromatography after appropriate hydrolysis. Total
sugars were determined by hydrolysis after treatment with
concentrated acid (see below) whereas labile (hemicellu-
losic) sugars were determined independently without this
treatment. Cellulosic sugar content was calculated by
difference between the total and hemicellulosic sugars.
A detailed procedure is given in Comont et al. (2006).
Briefly: for total sugar determination, 1 ml of 24 N H2SO4
was added to 100 mg sample dry weight. After 12 h at room
temperature, samples were diluted to 1.2 M H2SO4 and
heated at 100 1C for 4 h (hemicellulosic sugar analysis
begins directly at this hydrolysis stage). After cooling,
deoxy-6-glucose was added as an internal standard and
samples were neutralised with CaCO3. Any precipitate
formed during the neutralisation was discarded after
centrifugation and the supernatant transferred to a new
vial and subsequently evaporated to dryness. After
resuspension in methanol, the solution was purified
by centrifugation and the supernatant transferred and
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5
3340
1050

4
2920

relative abundance 3
2850

2
835

900
1 720

0
4000 3500 3000 2500 2000 1500 1000 500
0.8 wavenumber (cm-1) 0.8

0.6 0.6

0.4 0.4

0.2 0.2

0.0 0.0
4000 3900 3800 3700 3600 3500 1000 900 800 700 600 500 400
2.5

1600
1450 1265
2.0 1707
1650
1426
1371
relative abundance

1515
1720
1.5
1550

1.0

0.5

0.0
1800 1700 1600 1500 1400 1300 1200
wavenumber (cm-1)

Fig. 1. FTIR spectra of peat profile samples from the Scottish Site D (an advanced stage of regeneration), ranging from the surface moss layer at 0–5 cm
(solid line) through decomposing plant litter at 5–10 cm (dashed line) and highly humified peat at 22.5–27.5 cm (dash-dotted line) and at 42.5–47.5 cm
(dotted line). Relative abundances for each spectral signal were obtained by normalisation of data (see text). Characteristic FTIR bands of the major
biochemical descriptors have been marked on the whole spectrum (A) and in the region containing the lignin, carboxylate and peptide markers (B). The
left and right insets represent magnified sections of the spectrum of the 22.5–27.5 cm horizon. Spectral markers indicative of mineral interference in this
sample have been marked with arrows (see text).

evaporated under vacuum. The resulting carbohydrates maintained for 10 min. The injector split was off at the start
were dissolved in trimethylsilylated pyridine (Sylon BFT, time and turned on after 2 min. The injector and detector
Supelco) and immediately analysed by GC-FID using a were maintained at 240 and 300 1C, respectively. A mixture
25 m  0.25 mm CPSil5CB (0.25 mm film thickness) column. of eight monosaccharides (ribose, arabinose, xylose,
Oven settings were as follows: an initial oven temperature rhamnose, fucose, glucose, mannose and galactose) was
(60 1C) was ramped at 30 1C min1 to 120 1C where it was used as an external standard for compound identification
maintained for 1 min, then ramped to 240 1C at 3 1C min1 through peak retention times and for individual response
and finally at 20 1C min1 up to 310 1C where it was coefficient determination.
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2.6. Statistical analyses inclusion of samples with obvious traces of mineral

All statistical analyses were performed using Genstat for
Windows (8th edition, VSN International). FTIR spectral
data in the diamond interference region (2200–1900 cm1)
were excluded from analyses. Relationships between FTIR
spectra (‘x’ variate, as zero, first and second order
derivatives) and the corresponding organic matter (micro-
morphological and carbohydrate) datasets as well as
carbon and nitrogen contents and their ratios (‘y’ variates)
were assessed using PLS analyses. PLS models were
built for each horizon separately (i.e. four models for
each ‘y’ variate), to avoid overfitting due to autocorrelation
of horizons taken from within the same core. The datasets
for each horizon were randomly split (50:50) into
sets of sites used for calibration of the four PLS model,
and sites used for validation (except for horizon 3,
where the ratio was 54:46, respectively). We investigated
each ‘y’ variate (e.g. C, N, C:N ratio, percentage mannose,
etc.) separately in individual PLS models, using leave-
one-set-out cross validation. The Genstat procedure
returned the number of latent roots (dimensions), the
predicted residual error sum of squares (PRESS), percen-
tage of variance explained and PLS loadings. The number
of roots used for each PLS analysis was set at the
number that returned minimum PRESS and therefore
minimised the root mean square error of cross-validation
(RMSECV, calculated from PRESS using the square root
of (PRESS/n)). Significance levels were estimated using
Osten’s F-test. All models were built with and without
interferences.
2.7. Assessment of the fit of PLS models and reconstruction
of carbohydrate and micromorphological signatures
To assess the fit of the PLS models, we reassembled the
entire dataset of 67 samples by combining data from the
four individual horizon models and by analysing the slopes
and the r2 of observed versus predicted values of the
combined validation datasets in linear regression. The
multivariate datasets for carbohydrate and micromorpho-
logical remains were reduced in dimensions by principal
component analysis (PCA) performed on the reassembled
datasets of both the observed and predicted values (here-
after referred to as ‘carbohydrate’ and ‘micromorphologi-
cal’ signatures). We then assessed the fit of these models
using linear regression of the first principal component
scores for the reassembled observed versus fitted validation
datasets.
3. Results
3.1. Patterns of FTIR carbon chemistry signatures
Sample characterisation using FTIR spectroscopy con-
cerned the correct assignment of the observed spectral
characteristics to the most likely origin of the absorption
bands. A summary of the most characteristic bands
observed in peat and their assignment is presented in

Table 2
Assignment of the principal descriptive IR absorption bands in peat samples

Wavenumber Assignment Characterisation Reference

(cm1)

3340 g (O–H) stretching Cellulose, in samples with defined Cocozza et al. (2003)
3340 peak
2920 Antisymmetric CH2 Fats, wax, lipids Niemeyer et al. (1992), Cocozza et al. (2003)
2850 Symmetric CH2 Fats, wax, lipids Niemeyer et al. (1992), Cocozza et al. (2003)
1720 CQO stretch of COOH or COOR Carboxylic acids, aromatic esters Niemeyer et al. (1992), Haberhauer et al. (1998),
Cocozza et al. (2003), Gondar et al. (2005)
1710–1707 CQO stretch of COOH Free organic acids Gondar et al. (2005)
1653 CQO of amide I Proteinaceous origin Ibarra et al. (1996), Zaccheo et al. (2002)
1650–1600 Aromatic CQC stretching and/or Lignin and other aromatics, or Niemeyer et al. (1992), Cocozza et al. (2003)
asymmetric C–O stretch in COO– aromatic or aliphatic carboxylates
1550 N–H in plane (amide-II) Proteinaceous origin Ibarra et al. (1996), Zaccheo et al. (2002)
1515–1513 Aromatic CQC stretching Lignin/phenolic backbone Cocozza et al. (2003)
1426 Symmetric C–O stretch from COO– or Carboxylate/carboxylic structures Parker (1971)
stretch and OH deformation (COOH) (humic acids)
1450, 1371 C–H deformations Phenolic (lignin) and aliphatic Parker (1971)
structures
1265 C–O stretching of phenolic OH and/or Indicative of lignin backbone Niemeyer et al. (1992), Ibarra et al. (1996)
(approximately) arylmethylethers
1080–1030 Combination of C–O stretching and O–H Polysaccharides Grube et al. (2006)
deformation
900 Out of phase ring stretching (ring Cellulose, corresponding band to Zaccheo et al. (2002)
‘breathing’) sharpened 3340 peak
720 CH2 wag Long chain (4C4) alkanes Ibarra et al. (1996)
835 Aromatic CH out of plane Lignin Zaccheo et al. (2002)
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Table 2. Generally, FTIR analysis on the peat horizon
samples showed a decline of the main polysaccharide
markers (absorption bands around 3400 and 1040 cm1)
and relative increase of the main bands assigned to lignin-
like (1513, 1450, 1371, 1265 and 835 cm1) and aliphatic
structures (2920 and 2850 cm1) with depth, as expected
with increasing humification. Fig. 1 shows an example
from a Scottish peat core at an advanced stage of
regeneration. Spectral bands indicative of ‘carboxylates’,
which include contributions from vibrations of aromatic
and aliphatic carboxylates (R-COO–), and/or aromatic
CQC structures also increased in relative terms with depth
(1650–1600 and 1426 cm1). Other notable results were the
low relative absorption values in the 1707 cm1 region in
the samples from the Baupte peatland (data not shown).
Peat samples from Baupte had consistently higher pH
values and we therefore attributed this lack of absorption
in the 1707 cm1 region to the majority of acids being
present in the carboxylate form. A reduction in intensity of
the 1720 cm1 absorption band with increasing pH values
was previously shown in FTIR analyses on peat samples
where the sample pH was moderated (Gondar et al., 2005).
In low pH environments however, for example as observed
in the profile of the Scottish peat samples (e.g. Fig. 1), this
variation is related to peat decomposition rather than pH
changes and increases in intensity of this band illustrate
progressive free acid release with increasing humification.
3.2. PLS calibrations with chemical and organic matter
parameters
The FTIR data were assessed against the data obtained
from organic matter analyses (variation of the original data
shown in Table 3) using individual PLS analyses. In the
cases of the elemental analyses, the percentage variance
explained in linear regression was above 60% for the
majority of the analytes and all were significant in PLS of
the zero order FTIR data (Table 4). The fit in linear
regression for individual micromorphological remains was
generally poor with only a few cases where individual
plant-specific remains were adequately predicted, for
example preserved Cyperaceae and Polytrichum tissue in
horizon 3 samples and structureless Cyperaceae tissue in
horizon 8 samples. These predictions, however, were not
mirrored across all four horizons (Table 4). For individual
carbohydrates, the fit was generally better, where half or

Table 3
Organic matter parameters measured with average, standard deviation and range observed within each horizon.

Parameter 0–5 cm 5–10 cm 22.5–27.5 cm 42.5–47.5 cm

Average SD Range Average SD Range Average SD Range Average SD Range

Elemental
Total C (%) 49.3 3.8 42.9–54.5 51.3 3.4 45.3–57.0 53.8 3.0 48.1–59.3 54.7 3.8 45.9–60.6
Total N (%) 1.7 0.5 1.0–2.5 1.9 0.4 1.3–2.6 2.1 0.7 1.2–3.2 1.8 0.6 1.0–2.9
C/N ratio 31.8 8.8 19.8–49.1 28.6 6.6 19.7–43.4 29.2 10.6 15.1–49.2 33.2 12.4 15.6–59.7
Micromorphology
Amorphous organic matter (%) 29.2 21.1 0.9–71.8 24.2 16.1 1.0–63.6 19.0 9.4 6.5–40.2 12.6 11.7 2.0–38.2
Preserved Cyperaceae (%) 22.4 30.7 0–79.9 15.3 18.4 0–47.6 1.3 4.0 0–16.8 3.0 10.0 0–40.9
Preserved Sphagnum (%) 3.6 7.2 0–23.1 7.0 7.8 0–22.4 6.4 7.8 0–27.3 1.2 2.1 0–7.1
Preserved Polytrichum (%) 2.5 6.1 0–22.1 1.8 5.2 0–20.8 0.1 0.1 0–0.4 0.6 1.3 0–4.7
Undetermined preserved tissue (%) 2.7 5.1 0–14.7 1.9 3.2 0–11.4 4.1 5.9 0–19.1 1.9 3.7 0–12.3
Structureless Cyperaceae (%) 0.1 0.3 0–0.9 5.6 9.2 0–31.9 5.7 10.3 0–31.4 5.5 11.4 0–41.8
Structureless Sphagnum (%) 0.1 0.2 0–0.7 0.2 0.7 0–2.9 0.9 1.7 0–5.1 0.8 1.7 0–5.2
Structureless Polytrichum (%) 0 0 0 0.4 1.9 0–8.1 0 0 0 0 0 0
Undetermined structureless (%) 10.7 11.8 0.4–40.1 9.6 8.7 0.3–28.1 12.1 11.8 0.4–43.7 11.1 7.9 1.1–31.0
Mucilage (%) 24.7 20.1 0–58.1 27.2 16.2 2.7–54.6 47.3 20.5 10.9–89.0 59.7 21.9 16.3–94.4
Microorganisms (%) 3.1 1.9 0.8–7.6 3.8 3.2 0.1–12.9 2.3 1.7 0.3–6.3 3.1 2.3 0.1–9.8
Cuticles/spores/pollen (%) 0.6 0.8 0–2.8 2.5 6.7 0–28.4 0.7 0.9 0–2.7 0.3 0.5 0–1.4
Gelified or oxidised debris (%) 0.1 0.1 0–0.3 0.2 0.5 0–1.9 0.1 0.2 0–0.6 0.2 0.7 0–2.8

Carbohydrates
Total sugars (mg g1) 177.0 81.1 54–346 151.1 51.7 41–255 116.8 41.3 48–190 104.8 45.8 41–195
Hemicellulosic sugars (mg g1) 112.3 51.0 33–180 100.1 34.2 30.0–151.9 74.0 29.6 30.8–119.3 67.5 33.2 27.2–123.1
Cellulosic sugars (mg g1) 64.8 38.7 17–173 51.0 25.0 11.0–102.8 42.9 21.4 13.5–99.6 37.3 23.6 10.8–86.1
Xylose (%) 20.3 3.8 16.2–28.2 19.5 4.7 10.5–27.6 19.3 4.6 12.2–31.0 18.9 3.3 13.3–26.5
Arabinose (%) 8.2 5.6 2.3–19.6 7.9 5.0 2.1–18.8 5.6 4.6 2.1–17.3 5.0 4.2 1.7–16.0
Hemicellulosic glucose (%) 32.2 11.3 19.2–49.4 36.0 10.5 18.4–50.1 40.8 10.9 16.4–55.9 42.5 10.9 21.6–58.5
Mannose (%) 10.3 2.0 6.3–12.8 10.9 1.8 8.7–16.4 10.3 1.8 7.5–14.2 10.1 1.9 7.6–13.8
Rhamnose (%) 8.3 2.2 4.4–12.6 7.2 1.3 4.8–9.6 7.4 1.5 4.1–10.7 7.4 2.2 2.7–11.1
Galactose (%) 9.0 8.7 0.5–26.9 6.6 6.6 0.3–17.7 5.7 5.7 0.5–14.1 4.9 5.0 0.2–12.4
Ribose (%) 1.9 1.5 0.3–4.1 1.6 1.6 0–5.1 2.3 2.0 0.2–6.3 2.3 1.9 0.2–5.7
Fucose (%) 9.8 7.3 2.5–23.2 10.3 6.7 2.4–19.6 8.8 5.8 2.0–16.3 9.0 5.5 1.8–16.0
Table 4
Partial least squares analysis results of zero-order FTIR spectra versus peat micromorphological and chemical properties

Parameter 0–5 cm (n ¼ 13) 5–10 cm (n ¼ 18) 22.5–27.5 cm (n ¼ 18) 42.5–47.5 cm (n ¼ 18a)

Number of latent Variance accounted Significanceb RMSECVc Latent Variance Significance RMSECV Latent Variance Significance RMSECV Latent Variance Significance RMSECV
roots for (r2) roots roots roots

Elemental
Total C (%) 4 0.92 *** 3.6 2 0.73 *** 2.2 2 0.68 *** 2.4 4 0.75 *** 3.2
Total N (%) 2 0.78 *** 0.4 2 0.57 *** 0.4 6 0.90 *** 0.5 4 0.78 *** 0.4
C/N ratio 1 0.65 *** 7.5 3 0.69 *** 7.8 4 0.79 *** 7.9 3 0.75 *** 8.6

Micromorphology

R.R.E. Artz et al. / Soil Biology & Biochemistry 40 (2008) 515–527

Amorphous organic 1 0.42 *** 18.0 1 0.39 *** 14.5 1 0.18 ** 10.9 2 0.49 *** 10.1
matter (%)
Preserved Cyperaceae (%) 3 0.83 *** 21.0 1 0.35 *** 15.4 4 0.63 *** 5.1 1 0.34 ns 10.0
Preserved Sphagnum (%) 1 0.17 *** 7.6 2 0.26 *** 8.4 1 0.16 ** 11.1 1 0.06 ns 4.0
Preserved Polytrichum (%) 3 0.85 *** 6.2 1 0.23 ** 5.9 1 0.22 ** 0.1 1 0.32 *** 1.3
Undetermined preserved 1 0.41 *** 4.0 1 0.03 ns 4.3 1 0.15 ** 6.5 1 0.06 ns 4.8
tissue (%)

ARTICLE IN PRESS
Structureless Cyperaceae 1 0.10 * 0.2 2 0.34 *** 11.2 1 0.46 *** 7.5 3 0.88 *** 6.2
(%)
Structureless Sphagnum 1 0.13 *** 0.2 1 0.03 ns 0.7 1 0.30 ns 1.8 2 0.18 *** 1.6
(%)
Structureless Polytrichum n/a n/a n/a n/a 1 0.12 ** 2.1 n/a n/a n/a n/a n/a n/a n/a n/a
(%)
Undetermined 1 0.27 *** 11.4 1 0.19 ** 8.6 1 0.22 ** 15.7 1 0.32 ** 10.7
structureless (%)
Mucilage (%) 1 0.20 ** 26.4 1 0.27 *** 15.6 1 0.31 ** 22.5 1 0.45 *** 18.1
Microorganisms (%) 1 0.15 ns 1.8 1 0.21 *** 2.9 1 0.29 *** 1.5 1 0.24 ns 2.3
Cuticles/spores/pollen (%) 1 0.29 *** 0.9 1 0.52 ** 8.4 1 0.20 ** 1.1 1 0.34 * 0.5
Gelified or oxidised debris 1 0.44 ** 0.1 1 0.20 ** 0.6 1 0.12 ** 0.2 1 0.34 * 0.9
(%)

Carbohydrates
Total sugars (mg g1) 2 0.85 *** 34.9 1 0.56 *** 34.0 2 0.51 ** 27.0 1 0.50 *** 33.2
Hemicellulosic sugars 2 0.90 *** 20.1 3 0.78 *** 28.8 2 0.34 ** 21.9 2 0.86 *** 12.7
(mg g1)
Cellulosic sugars (mg g1) 3 0.90 *** 28.8 1 0.32 *** 21.7 1 0.10 *** 17.5 1 0.23 * 22.9
Xylose (%) 3 0.59 *** 4.6 1 0.23 ** 6.7 3 0.24 *** 3.4 3 0.43 *** 3.4
Arabinose (%) 3 0.67 *** 6.9 3 0.64 *** 3.3 2 0.15 *** 3.1 3 0.78 *** 2.9
Hemicellulosic glucose 3 0.58 *** 10.0 3 0.66 *** 8.9 2 0.29 ** 8.0 2 0.58 *** 9.2
(%)
Mannose (%) 1 0.11 ns 2.6 1 0.09 * 2.2 1 0.02 ns 2.2 2 0.36 *** 2.0
Rhamnose (%) 1 0.31 *** 1.9 1 0.25 ns 1.3 2 0.07 ns 1.8 2 0.51 *** 2.2
Galactose (%) 3 0.86 *** 4.3 2 0.61 *** 5.7 2 0.00 ns 2.9 2 0.89 *** 2.1
Ribose (%) 3 0.87 *** 0.8 1 0.17 ** 1.8 2 0.02 ns 1.1 4 0.90 *** 1.2
Fucose (%) 2 0.90 *** 2.2 3 0.88 *** 4.0 2 0.00 ns 2.7 4 0.93 *** 2.3

PLS analyses were performed on the datasets for each horizon separately.
a
Except carbohydrates, where n ¼ 17. n/a-not applicable (where this micromorphological type was not present in the examined horizon).
b
significance at po0.05 (*), po0.01 (**), po0.001 (***), not significant (ns).
c
Root mean square error of cross-validation in PLS.

521
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522 R.R.E. Artz et al. / Soil Biology & Biochemistry 40 (2008) 515–527

more of the individual carbohydrates were predicted with

reasonable accuracy (r240.6, Table 4) in horizons 3, 4 and

loadings (arbitrary units)

8. The notable exception were the horizon 6 samples where
none of the individual PLS models were able to predict
carbohydrate constituents adequately. The RMSECV
values for the C:N and carbohydrate PLS models
(Table 4) were generally lower than the standard deviation
of the original datasets (Table 3). PLS using the first or
second derivative did increase the percentage variance
explained, but only marginally (data not shown). Analysis
without samples that were characterised by spectral
interference by silicate minerals, or those with elevated
4000 3600 3200 2800 2400 2000 1600 1200 800 400
pH values, did not increase the amount of variability
explained by PLS (data not shown). wavenumber (cm-1)
Total C content was associated with positive loadings in
the main polysaccharide envelopes at 3300 and 1030 cm1

loadings (arbitrary units)

and negative loadings of the wax markers at 2920 and
2850 cm1 (Fig. 2A), although the influence of the
polysaccharide regions became less pronounced with
depth. Total N content was associated with positive
loadings in the bands representing the amide I and II
regions (Table 2) as previously reported by Chapman et al.
(2001) and there was an additional negative correlation
with the wax markers at 2920 and 2850 cm1 (Fig. 2B). The
influence of the amide bands became more pronounced
with depth, whereas the loadings of the polysaccharide
regions became less influential for the prediction of total N. 4000 3600 3200 2800 2400 2000 1600 1200 800 400
In some cases, the differences in loadings were more wavenumber (cm-1)
subtle. For example, the PLS loadings for mucilage were
visually very similar to those of total C content (not
relative loading differences

shown). We therefore also examined the relative differences

in PLS loadings between organic matter parameters using
subtraction. An example of relative differences in PLS
loadings is shown for the difference in loadings between
fucose and xylose, where the main discriminatory region
was within the main 1200–800 cm1 polysaccharide envel-
ope (e.g. Fig. 2C). Within this polysaccharide envelope,
there were subtle differences in the bands which contrib-
uted more or less to the discrimination between different
neutral sugars. In the example shown, there were two
discriminatory regions between prediction of fucose versus 1200 1150 1100 1050 1000 950 900 850 800
xylose at around 1060 and 1016 cm1. wavenumber (cm-1)

3.3. Predictive PLS of FTIR spectra as a tool in organic
matter studies of regenerating peatlands
To assess the potential of predictive PLS of FTIR
spectra for organic matter parameters, we reconstructed
the composition of the organic matter datasets (i.e.
micromorphological and carbohydrate signatures) using
the PLS outputs. Examples of the changes of the
carbohydrate composition and correlation with the pre-
dicted values with depth are shown for the four contrasting
regenerating sites of the peatland at Middlemuir, Scotland
(Fig. 3). The fitted and observed values were in reasonable
agreement for the monomeric carbohydrate composition.
For example, the fitted carbohydrate composition was able
Fig. 2. Loadings generated by partial least squares analysis of zero-order
FTIR-ATR absorbances against (A) Total C and (B) total N content.
Relative differences in PLS loadings between different organic matter
parameters as assessed by subtraction of loadings can show predictive
properties of FTIR data in the assignment of single-neutral sugars (C).
Differences in loadings of fucose versus xylose within the polysaccharide
envelope are shown as an example. Data shown are loadings generated in
models built separately for each of the following horizons: surface
vegetation layer or the cut peat surface at 0–5 cm (solid line) through
decomposing plant litter at 5–10 cm (dashed line) and highly humified peat
at 22.5–27.5 cm (dash-dotted line) and at 42.5–47.5 cm (dotted line). The
loadings for each horizons are offset on the y-axis for visual clarity.
to reconstruct the relative increase in galactose concentra-
tion (caused by an increase in Sphagnum cover) and the
relative decrease in hemicellulosic glucose in horizon 3 for
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R.R.E. Artz et al. / Soil Biology & Biochemistry 40 (2008) 515–527 523

Odserved Fitted
0% 20% 40% 60% 80% 100% 0% 20% 40% 60% 80% 100%

3 3
horizon

4 4

6 6

8 8

0% 20% 40% 60% 80% 100% 0% 20% 40% 60% 80% 100%

3 3
horizon

4 4

6 6

8 8

0% 20% 40% 60% 80% 100% 0% 20% 40% 60% 80% 100%

3 3
horizon

4 4

6 6

8 8

0% 20% 40% 60% 80% 100% 0% 20% 40% 60% 80% 100%

3 3
horizon

4 4

6 6

8 8

Fig. 3. Relative quantities (%) of each of the neutral sugars in the observed (left graphs) or reconstructed (fitted, right graphs) datasets following predictive
PLS from FTIR spectroscopic data. The example shown here illustrates the carbohydrate composition at each of the four regeneration stages (A–D, refer
to Table 1 for explanation of the site codes) of the Middlemuir peatland. Changes with depth (horizons 3–8) are depicted. Relative quantities of neutral
sugars are indicated by different fills, from left to right: xylose (no fill), arabinose (dark grey), hemicellulosic glucose (large hatched), mannose (light grey),
rhamnose (medium grey), galactose (diagonally hatched), ribose (black) and fucose (small hatched).

Site B and for horizons 3 and 4 in Site D (Fig. 3). Minor
changes in the profile were, however, less accurately
predicted. We combined the observed and predicted values
from individual PLS analyses for each subset of multi-
variate organic matter analyses (i.e. micromorphological
and carbohydrates), respectively, and analysed these
reconstructed organic matter datasets using PCA. In
PCA of the carbohydrate signatures, the first principal
component (which explained the majority of the variance
in the dataset) differentiated by site as well as horizon
depth (Fig. 4) and likely represented the level of decom-
position of each sample. For example, the four horizon
samples from the core from Site A (early regeneration, bare
peat) were not very differentiated along the first principal
component, whereas the horizon 3 samples from Site B
(early regeneration with cover of Eriophorum vaginatum,
etc., Table 1) showed strong differentiation along Axis 1
compared to the lower horizons. This was not as
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524 R.R.E. Artz et al. / Soil Biology & Biochemistry 40 (2008) 515–527

Principal component 1 (88.2 %)

-300 -250 -200 -150 -100 -50 0 50 100 150

4
horizon

Principal component 1 (90.6 %)

-300 -250 -200 -150 -100 -50 0 50 100 150

4
horizon

Fig. 4. Loading of the first principal component scores in observed (A) and reconstructed (B) carbohydrate signatures with depth (horizons 3–8) and site
(A—no fill; B—light grey, C—diagonally hatched, and D—black) in the samples from the Middlemuir peatland. Please refer to Table 1 for explanation of
the site codes.

pronounced for Site C, where the vegetation cover was
different from Site B (Table 1). The core from the most
advanced stage of regeneration showed strong differentia-
tion of all four horizons along Axis 1.
Over the entire dataset of 67 samples from all 19 sites in
Europe, values for the observed versus predicted C:N
ratio’s were highly correlated and linear regression
explained 74% of the variance with a slope of 0.803
(Fig. 5A). Linear regression of the first principal compo-
nents of the observed versus fitted carbohydrate signatures
(Fig. 5B) explained 70% of the variance with a slope of
only 0.730. The first principal components of the carbohy-
drate datasets explained the majority of the variance in
both the observed and fitted datasets and the values were
similar (88.2 and 90.6%, respectively). In contrast, for the
micromorphological signatures, linear regression explained
only 52% of the variance and the slope was only 0.588 in
comparisons of the first principal components of the
observed and fitted composite datasets (Fig. 5C). In
addition, the amount of variance explained by the first
principal components of the micromorphological signature
was both lower (52.4, and 61.4%, respectively) and more
dissimilar between the observed and fitted datasets than for
carbohydrate signatures.
4. Discussion
4.1. Predictive potential of peat FTIR-based PLS models
Infrared spectroscopic data from peat samples, both in
the mid and near IR ranges, have been used previously to
predict various organic matter parameters. Good correla-
tions by PLS between various parameters such as total C
and N, pH, ash content, total organic matter, and IR
analyses of organic soils have been shown on numerous
occasions (Palmborg and Nordgren, 1993; Chapman et al.,
2001; Tremblay and Gagne, 2002; Couteaux et al., 2003;
Zimmermann et al., 2007; Rinnan and Rinnan, 2007). The
r2 of linear regression of observed versus fitted parameters
is often used as a first criterion of the predictive qualities of
a model. If r2 is 40.8, the model allows for quantitative
prediction, while values between 0.5 and 0.7 indicate that
 ARTICLE IN PRESS
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the model may be useful for rough screening (Couteaux
et al., 2003). Our analysis of the linear regression of PLS
models for each horizon (Table 4) and an analysis of the
four horizon-specific models together (Fig. 5) indicated
that, for prediction of the C:N ratio and carbohydrate
composition, the models would be adequate to allow for
rough screening as the slope and/or r2 were around 0.7.
70
60
50
C:N fitted
Other studies have shown reasonable prediction of a small
range of functional chemical signatures of soils and
sediments, such as relative concentrations of amino acids
and amino sugars (Holmgren and Norden, 1988) or humic
and fulvic acids (Tremblay and Gagne, 2002). The PLS
models for micromorphological remains (both for each
individual variable in horizon-specific models and in the
composite model analysis) were generally poor. A possible
reason for this may be the size of sample used in direct
microscopic analysis compared to the use of a homo-
genised sample as for FTIR spectroscopy. Another possible
factor is the three-dimensionality of the chemical analyses
(as these are based on mass), compared to micromorpho-
logical analyses which essentially extrapolate the mass of
microremains based on the area they occupy within

40
smearslides. Other reports have, however, shown the ability
30 to separate major vegetational differences using near
infrared spectroscopy, where the authors were able to
20 build good PLS models with high levels of explained
r2 = 0.74 variance for the content of leaf material from Ericales and
10 slope = 0.803 Sphagnum spp. in a single-peat core sectioned to 1 cm
0 samples (McTiernan et al., 1998). In the near infra-red, the
0 10 20 30 40 50 60 70 vibrational characteristics of the N–H and O–H stretch
C:N observed regions are more separated, while the mid-IR is dominated
by the O–H stretch regions. Use of data from near infrared
200 analyses may therefore improve the prediction of organic
matter parameters.
We also observed a number of cases where the variance
PC1 fitted values (90.6 %)

100
explained for the individual carbohydrate parameters was
rather low (Table 4). That we were still able to reassemble
0 reasonably matching neutral sugar profiles (Figs. 3 and 5,
overall r2=0.70 with slope 0.730) of a large variety of
-100
peatland samples from five European locations with large
differences in plant cover and degree of decomposition
despite observing relatively low correlation of each princi-
-200 pal monomer with FTIR spectra may at first seem puzzling.
r2 = 0.70
slope = 0.730
Kačuráková et al. (2000) investigated individual plant cell
-300 wall compounds (pectic polysaccharides, hemicelluloses and
-300 -200 -100 0 100 200
PC1 observed values (88.2 %)
Fig. 5. Predictive properties of individual PLS models based on FTIR
60 data to describe the following organic matter properties of peat. The data
from the four individual horizon-based models were combined to assess
the overall fit of each predictor set. (A) Predicted (x) versus observed (y)
40
values of C/N ratios. (B) Regression plot of the first principal component
PC1 fitted values (61.4 %)

scores of PCA performed on the PLS predicted (x) versus observed (y)
20
values of the micromorphological remains. Each micromorphological
parameter was used in individual PLS analyses and the predicted data
0 were used for PCA-based reconstruction. Variance explained by the first
principal component for each PCA are shown in brackets on each axis. (C)
-20 Regression plot of the principal component scores of PCA performed on
the PLS predicted (x) versus observed (y) values of the carbohydrate
-40 monomer analyses. Each carbohydrate parameter was used in individual
PLS analyses and the predicted data were used for PCA-based
-60 r2 = 0.52 reconstruction. Variance explained by the first principal component for
slope = 0.586 each PCA are shown in brackets on each axis. Symbols indicate the
-80 samples used for calibration (filled symbols) and validation (empty
-80 -60 -40 -20 0 20 40 60 symbols) of the PLS models. The solid lines indicate the mean regression
PC1 observed values (52.4 %) for the validation datasets and the slope and r2 of the mean regression are
indicated in the lower right corner.
 ARTICLE IN PRESS
526 R.R.E. Artz et al. / Soil Biology & Biochemistry 40 (2008) 515–527
monosaccharides) by FTIR spectrocopy and were able to
determine spectral marker regions for a large number of
compounds within the 1200–800 cm1 region. They attrib-
uted the main differences between individual cell wall
constituents to both C-OH relative steric positions within
the monomer side chains as well as the vibrational
characteristics of the pyranose backbones. Carbohydrate
analysis reports on the individual components of each
(hemi)cellulose type present in the more biologically
decomposed size fractions, whereas the FTIR spectra
report on the spectral properties of both the side-chain
monomers and the pyranose backbones. In agreement with
Kačuráková et al. (2000), we showed that the spectral
markers within the 1200–800 cm1 region were discrimina-
tory for the relative differences in PLS prediction between
neutral sugars (e.g. Fig. 2C). The correlation of the
carbohydrate datasets is therefore most likely explained
by both methodologies essentially reporting on the original
composition of the parent vegetational material. In much
simpler matrices, neutral sugar concentrations have pre-
viously been successfully predicted with IR spectra.
Examples are prediction of mannose content (from
mannans and mannoproteins) in wines (Coimbra et al.,
2005) and xylose content from olive pulp polysaccharides
(Coimbra et al., 1999). In general, however, our datasets
were rather small (range of n was 13–18) when compared to
other studies employing IR data in predictive PLS models
(Couteaux et al., 2003, Zimmermann et al., 2007) and
higher sample numbers might improve the predictive
properties of FTIR-based models for peat soils in future.
4.2. Applications for PLS prediction of organic matter
parameters in restoration monitoring
The main strength of this study is the ability to roughly
reconstruct (Fig. 5) the relative differences between peat
samples from different stages of regeneration and from
widely differing locations with their associated differences
in vegetation structures, and hence micromorphological
and chemical composition. In peatland restoration pro-
jects, it is often difficult to ascertain the regeneration
boundary, i.e. the interphase between the cut horizon of
remaining catotelm and the accumulated organic matter
during regeneration. The C:N ratio and micromorpholo-
gical composition of peat have been previously used as an
indicator of this regeneration boundary by Comont et al.
(2006). A simple ratio of the polysaccharide to carboxylate
FTIR band intensity has previously been shown to explain
68.7% of the community catabolic response to a suite of
simple carbon sources (Artz et al., 2006) and other studies
have shown good predictive properties of PLS analyses on
FTIR and NIR data with microbial biomass (Chapman
et al., 2001; Couteaux et al., 2003; Rinnan and Rinnan,
2007). There are other reports where IR data have been
used in prediction of various organic matter parameters
such as cellulose content and cellulose decomposition rates
(Hartmann and Appel, 2006) or the relative quantities of
phenolic compounds and leaf litter decomposition rates
(Stolter et al., 2006). The composition of carbohydrate
monomers is also indicative of the origin of the OM (i.e.
vegetation-type specific, Moers et al., 1989; Wicks et al.,
1991; Popper and Fry, 2003). The botanical composition of
peat, i.e. the composition of litter entering the organic
matter pool, has been implicated in the degree of
decomposition on numerous occasions (Verhoeven and
Toth, 1995; Belyea, 1996; Frolking et al., 1998) and
therefore the composition of the organic matter in restored
peatlands may be critical to their long-term carbon
sequestration potential. Indeed, Andersen et al. (2006)
showed that the substrate quality (in terms of availability
of N, P and soluble organic carbon) of the organic matter
in vegetational successions on cutover peatlands was
related to the evolution of the total microbial biomass
and their respiration activity. Therefore, monitoring of
restoration projects should include evaluations whether
organic matter parameters return to values more closely
resembling intact peatland systems. FTIR spectroscopy
coupled with predictive PLS analysis may be a useful, low-
cost, first screening tool in the assessment and monitoring
of restoration success in peatland ecosystems.
Acknowledgements
This work was part of the RECIPE initiative, funded
through a grant by the EU Framework 5. SJC is funded by
the Scottish Executive Environment and Rural Affairs
Department. The authors gratefully acknowledge analyti-
cal assistance provided by M. Hatton and N. Lottier.
We would like to thank Prof. David Elston (BioSS),
Dr. Charlie Shand (Macaulay Institute) and two anon-
ymous reviewers for constructive comments on earlier
versions of this manuscript.
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