RESEARCH ARTICLE
Degradation of Root Community Traits as
Indicator for Transformation of Tropical
Lowland Rain Forests into Oil Palm and
Rubber Plantations
Josephine Sahner1☯, Sri Wilarso Budi2☯, Henry Barus3☯, Nur Edy1,3, Marike Meyer4, Marife
D. Corre5, Andrea Polle1*
1 Department for Forest Botany and Tree Physiology, Büsgen-Institute, Georg-August University Göttingen,
Göttingen, Germany, 2 Department of Sylviculture, Faculty of Forestry, Jalan Lingkar Akademik Campus,
IPB Darmaga, Bogor, Indonesia, 3 Department of Agrotechnology, Faculty of Agriculture, Tadulako
University, Palu, Indonesia, 4 Institute for Geography, Georg-August University Göttingen, Göttingen,
Germany, 5 Department for Soil Science of Tropical and Subtropical Ecosystems, Büsgen-Institute, Georg-
August University Göttingen, Göttingen, Germany
☯ These authors contributed equally to this work.
* apolle@gwdg.de
Abstract
Conversion of tropical forests into intensely managed plantations is a threat to ecosystem
functions. On Sumatra, Indonesia, oil palm (Elaeis guineensis) plantations are rapidly
expanding, displacing rain forests and extensively used rubber (Hevea brasiliensis) agro-
forests. Here, we tested the influence of land use systems on root traits including chemical
traits (carbon, nitrogen, mineral nutrients, potentially toxic elements [aluminium, iron] and
performance traits (root mass, vitality, mycorrhizal colonization). Traits were measured as
root community-weighed traits (RCWTs) in lowland rain forests, in rubber agro-forests
mixed with rain forest trees, in rubber and oil palm plantations in two landscapes (Bukit Dua-
belas and Harapan, Sumatra). We hypothesized that RCWTs vary with land use system
indicating increasing transformation intensity and loss of ecosystem functions. The main
factors found to be related to increasing transformation intensity were declining root vitality
and root sulfur, nitrogen, carbon, manganese concentrations and increasing root aluminium
and iron concentrations as well as increasing spore densities of arbuscular mycorrhizas.
Mycorrhizal abundance was high for arbuscular and low for ectomycorrhizas and unrelated
to changes in RCWTs. The decline in RCWTs showed significant correlations with soil nitro-
gen, soil pH and litter carbon. Thus, our study uncovered a relationship between deteriorat-
ing root community traits and loss of ecosystem functionality and showed that increasing
transformation intensity resulted in decreasing root nutrition and health. Based on these
results we suggest that land management that improves root vitality may enhance the eco-
logical functions of intense tropical production systems.
PLOS ONE | DOI:10.1371/journal.pone.0138077 September 14, 2015 1 / 19
OPEN ACCESS
Citation: Sahner J, Budi SW, Barus H, Edy N, Meyer
M, Corre MD, et al. (2015) Degradation of Root
Community Traits as Indicator for Transformation of
Tropical Lowland Rain Forests into Oil Palm and
Rubber Plantations. PLoS ONE 10(9): e0138077.
doi:10.1371/journal.pone.0138077
Editor: Robert Bradley, Institution and Department:
Université de Sherbrooke, CANADA
Received: February 7, 2015
Accepted: August 26, 2015
Published: September 14, 2015
Copyright: © 2015 Sahner et al. This is an open
access article distributed under the terms of the
Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any
medium, provided the original author and source are
credited.
Data Availability Statement: The raw data of this
study are deposited and available in the Dryad
repository under doi:10.5061/dryad.qf362/.
Funding: This work was supported by Deutsche
Forschungsgemeinschaft (http://www.dfg.de/),
CRC990: Ecological and Socioeconomic Functions of
Tropical Lowland Rainforest Transformation Systems
(Sumatra, Indonesia) project B07 (AP) and Project
A05 (MDC); Erasmus Mundus, EURASIA2 (http://
www.eurasia2.cz/page/erasmus-mundus) (NE);
Georg-August Universität Göttingen CRC990 internal
research grants awarded to counterparts and
Introduction
Globally, tropical rain forests are rapidly converted to plantation agriculture [1]. In Indonesia,
which is together with Malaysia the world´s largest producer of palm oil [2], 40% of the forest
(64 Mio ha) was lost since the countries´ independence in 1945 [3]. In the 1950s rubber (Hevea
brasiliensis) was introduced as a crop tree and is currently cultivated in two systems, in intense
monocultures often with high yielding clones (rubber plantation) or as jungle rubber. Jungle
rubber is a complex, extensive form of agro-forestry, usually established after swidden agricul-
ture, where rubber trees are grown together with naturally established secondary forest [4,5].
Tree species richness is lower but the forest structure of jungle rubber is similar to that of
unmanaged lowland rain forests [4–6]. Pristine lowland rain forests exist only in fragments
and most unmanaged forests, even in protected areas, are secondary forests. Since the 1990s
with the introduction of oil palms (Elaeis guineensis), expansion of plantation area at the
expense of primary and secondary forests has drastically increased [7], with particularly high
rates (> 2% per year) on Sumatra [8]. Because of the world´s increasing demand for biofuel,
chemical raw materials and edible oil, palm oil production is now a major driver for tropical
forest conversion [2]. The ecological consequences of this rapid transformation process are
severe, including for example massive loss in biodiversity, soil degradation, reduction in carbon
storage, decreased energy flux, increases in greenhouse gas emissions, etc. [9–12]. While the
alterations of above-ground ecosystem properties and processes have been intensively studied,
much less is known about the below-ground plant responses to these massive changes.
Roots together with their associated mycorrhizal fungi play a central role for nutrient uptake
and allocation to the above-ground parts; they further mediate carbon transfer to the soil,
thereby, eventually affecting biogeochemical cycles [13–16]. In tropical forests, most tree spe-
cies including the introduced rubber and oil palms form symbioses with arbuscular mycor-
rhizal (AM) fungi, but in lowland tropical forests also a number of native species occur, e.g.
dipterocarps that associate with ectomycorrhizal (EM) fungi [17].
The ability of tree roots to form mutualistic AM or EM associations is a typical species-
related trait that can mediate differences in plant nutrition, especially of phosphorus and nitro-
gen [18]. Root functional traits have often been studied in agroecological systems [19], but only
little information is available for forest trees, especially regarding the chemical root traits. In
tropical ecosystems with potentially 100s of species per hectare [5,6] in situ root traits are diffi-
cult to measure, because a trait is defined as a feature of a species [20]. Instead, information on
root traits can be gathered at the community level of the co-occurring species and can then be
defined as “root community-weighed traits” (RCWTs). Only few studies addressed the varia-
tion of RCWTs. Prieto et al. [21] found that root morphology, a trait related to resource acqui-
sition and root litter degradability, a trait indicating conservation of resources, co-varied for
root communities with land use across tropical, Mediterranean and montane climate. In grass-
land ecosystems RCWTs were correlated with plant productivity and ecosystem functions
[14,15]. We, therefore, anticipated that the traits of whole root communities would be useful
indicators of land transformation.
Here, we asked whether transformation of tropical rain forest into intensive rubber or oil
palm mono-plantations would affect functional traits of the root communities. An important
functional trait indicating resource conservation is the chemical composition of roots. In our
study we determined the concentrations of nutrients and other elements (C, N, P, N, K, S, Ca,
Mg, Mn, Fe, Al, Na) in roots from different land use systems. We further measured traits
related to plant performance and life style such as root mass, root vitality and colonization with
mycorrhizas (EM colonization, AM colonization including vesicles, arbuscules and spores). All
traits were determined in mixtures of roots collected in defined soil volumes and therefore
Root Traits and Tropical Forest Transformation
PLOS ONE | DOI:10.1371/journal.pone.0138077 September 14, 2015 2 / 19
stakeholders in the frame of Access and Benefit
Sharing (ABS) of the Convention of Biological
Diversity (CBD) (http://www.uni-goettingen.de/de/
310995.html) (SWB); and Deutsche
Forschungsgemeinschaft and Georg-August
Universität Göttingen open access publication fund
(http://www.sub.uni-goettingen.de/en/electronic-
publishing/open-access/open-access-publication-
funding/) (AP). The funders had no role in study
design, data collection and analysis, decision to
publish, or preparation of the manuscript.
Competing Interests: The authors have declared
that no competing interests exist.
represent RCWTs. Specifically, we hypothesized that chemical and performance parameters of
root communities vary with forest transformation and are related to transformation intensity.
Because land transformation results in degradation of ecosystem functions, we further tested
whether RCWTs were correlated with ecosystem properties such as soil carbon and nitrogen
concentrations. To test our hypotheses we selected four forest types (oil palm plantations, rub-
ber monoculture, rubber jungle and rain forest) in two landscapes on Sumatra and investigated
RCWTs and indicators for ecosystems functions (soil carbon and nitrogen concentrations, leaf
litter carbon and nitrogen concentrations, soil available phosphorus and base cations concen-
trations, soil pH).
Materials and Methods
Site description
The study sites were located on Sumatra, Province of Jambi (Indonesia) in two landscapes, i.e.,
the area of Harapan Rainforest and the area of the National Park Bukit 12 (Fig 1). In each land-
scape four land use systems were selected: secondary rain forest, jungle rubber, rubber planta-
tions and oil palm plantations. The study areas were in the lowlands (below 100m a.s.l.) on
deep, well drained, acid soil with low fertility [6]. The soils are classified as loam acrisol in
the Harapan and clay acrisol in the Bukit 12 landscape. The climate is tropical with annual
precipitation > 2000mm and only two months with less than 100 mm rain fall. In the Harapan
area the annual mean temperature is 26.9°C and the annual precipitation 2332mm (location:
Dusun Baru, http://en.climate-data.org/location/595657/); in the Bukit 12 area the mean
Fig 1. Maps of the province Jambi (A) with the landscapes Bukit 12 (B) and Harapan (C) on Sumatra
(Indonesia). The locations of the research plots are indicated.
doi:10.1371/journal.pone.0138077.g001
Root Traits and Tropical Forest Transformation
PLOS ONE | DOI:10.1371/journal.pone.0138077 September 14, 2015 3 / 19
annual temperature is 26.8°C and the precipitation sum is 2860mm (location: Lubuk
Kepayang, http://en.climate-data.org/location/587840/).
Sampling and export permission
Research permit (Kartu Izin Peneliti Asing, permission number: 333/SIP/FRP/SM/IX/2012)
was issued by the Ministry of Research and Technology RISTEK (Kementrian Ristek dan
Teknologi, Jakarta, Indonesia). The Research Center for Biology of the Indonesian Institute of
Science LIPI (Lembaga Ilmu Pengetahuan Indonesia, Jakarta, Indonesia) recommended issuing
a sample collection permit (Rekomendasi Ijin Pengambilan dan Angkut (SAT-DN) Sampel
Tanah dan Akar, number: 2696/IPH.1/KS:02/XI/2012). Collection permit (number: S.16/
KKH-2/2013) and export permit (reference number: 48/KKH-5/TRP/2014) were issued by the
Directorate General of Forest Protection and Nature Conservation PHKA (Perlindungan
Hutan dan Konservasi Alam, Jakarta, Indonesia) under the Ministry of Forestry of the Republic
of Indonesia. The Chamber of Agriculture of Lower Saxony (Plant Protection Office, Hanno-
ver, Germany) issued the import permits (Letter of Authority, numbers: DE-NI-12- 69 -2008-
61-EC, DE-NI-14- 08 -2008-61-EC).
Sampling design
In each of the two landscapes and in each forest type four plots (50 m x 50 m) were installed
resulting in 32 sampling sites (Table 1). Oil palm, rubber plantations and rubber jungle were
sampled in October and November 2012 and rain forest in November and December 2013. In
each plot, subplots of 5m x 5m were defined and soil samples were collected in three of these
subplots (designated as a, b, c). In each subplot five soil cores (0.04 m diameter and 0.20 m
depth) were extracted (four towards the corners and one in the centre of the subplot) at a dis-
tance of more than 1 m. Leaf litter was removed before soil sampling and kept separately. In
total 480 soil cores were taken in both landscapes (2 landscapes x 16 plots x 3 subplots x 5 soil
Table 1. Geographic location of the research plots in two landscapes and four forest types on Sumatra (Indonesia).
Bukit 12 Harapan
Plot latitude longitude altitude (m asl) plot latitude longitude altitude (m asl)
BF1 S 01°59'42.5'' E 102°45'08.1'' 83 HF1 S 02°09'09.9'' E 103°21'43.2'' 76
BF2 S 01° 58'55.1'' E 102°45'02.7'' 77 HF2 S 02°09'29.4'' E 103°20'01.5'' 75
BF3 S 01°56’33.9'' E 102°34’52.7'' 87 HF3 S 02°10'30.1'' E 103°19'57.8'' 58
BF4 S 01°56’31.0'' E 102°34’50.3'' 87 HF4 S 02°11'15.2'' E 103°20'33.4'' 77
BJ1 S 02°08'25.6'' E 102°51'04.3'' 74 HJ1 S 01°55'40.0'' E 103°15'33.8'' 51
BJ2 S 02°01'49.7'' E 102°46'16.7'' 76 HJ2 S 01°49'31.9'' E 103°17'39.2'' 84
BJ3 S 02°03'46.7'' E 102°48'03.5'' 89 HJ3 S 01°50'56.9'' E 103°17'59.9'' 95
BJ4 S 02°00'57.3'' E 102°45'12.3'' 60 HJ4 S 01°47'07.3'' E 103°16'36.9'' 57
BR1 S 02°05'30.7'' E 102°48'30.7'' 71 HR1 S 01°54'39.5'' E 103°16'00.1'' 77
BR2 S 02°05'06.8'' E 102°47'20.7'' 95 HR2 S 01°52'44.5'' E 103°16'28.4'' 59
BR3 S 02°05'43.0'' E 102°46'59.6'' 90 HR3 S 01°51'34.8'' E 103°18'02.1'' 90
BR4 S 02°04'36.1'' E 102°46'22.3'' 51 HR4 S 01°48'18.2'' E103°15'52.0'' 71
BO1 S 02°04'26.1'' E 102°48'55.1'' 75 HO1 S 01°54'35.6'' E 103°15'58.3'' 81
BO2 S 02°04'32.0'' E 102°47'30.7'' 84 HO2 S 01°53'00.7'' E 103°16'03.6'' 55
BO3 S 02°04'15.2'' E 102°47'30.6'' 71 HO3 S 01°51'28.4'' E 103°18'27.4'' 64
BO4 S 02°03'01.5'' E 102°45'12.1'' 34 HO4 S 01°47'12.7'' E 103°16'14.0'' 48
O = oil palm plantation, R = rubber plantation, J = jungle rubber, F = secondary rain forest.
doi:10.1371/journal.pone.0138077.t001
Root Traits and Tropical Forest Transformation
PLOS ONE | DOI:10.1371/journal.pone.0138077 September 14, 2015 4 / 19
cores). Soil cores and litter samples were stored individually in plastic bags in cool bags and
transported to the University of Jambi, where they were stored at 4°C until processing.
Sample preparation
Each soil core was weighed, sieved subsequently through two sieves with 10 and 5 mmmesh
size and separated into roots and bulk soil. The five samples from the same subplot were pooled
and well mixed yielding one root and one bulk soil sample per subplot. Litter samples of a sub-
plot were also pooled yielding a total number of 96 pooled samples per fraction.
Litter samples were dried in an oven at 80°C for 48h. Fresh bulk soil samples (about 20 g)
were initially air dried and then oven dried (105°C for 48 h) to determine the soil water content
according to the following equation:
Relative soil water content ðg g1 soilÞ ¼ weight of fresh soil ðgÞ  weight of oven dried soil ðgÞ
weight of fresh soil ðgÞ

 
Pooled root samples were washed and patted dry with tissue paper. The fresh root mass of
the sample was weighed. The roots were separated into coarse and fine roots according to the
root diameter. Fine roots (diameter 2 mm) were weighed, stored in wet tissue paper at 4°C,
used for root vitality and mycorrhizal analysis, and were subsequently oven-dried at 60°C for
48h. Fine root dry mass was calculated as:
Fine root mass ðg kg1soildwÞ ¼
dry weight of fine roots of subplot aþ subplot bþ subplot c ðgÞ
dry weight of soil of subplot aþ subplot bþ subplot c ðkgÞ

 
Dry aliquots of soil, roots and litter were stored in 50 ml reaction tubes (Falcon tube 50 ml,
115 x 28 mm, Sarstedt, Nümbrecht, Germany). Before closing the screw cap, a small reaction
tube (Eppendorf micro tube, 1.5 ml, Sarstedt, Nümbrecht, Germany) with perforated walls
containing silica gel (10 g (40 x 90 mm) desiccant bag silica gel orange, Carl Roth, Karlsruhe,
Germany) was added. The samples were shipped to the University of Göttingen (Göttingen,
Germany), IPB Bogor Agricultural University (Bogor, Indonesia) and Tadulako University
(Palu, Indonesia) for further analysis.
Analysis of root vitality and ectomycorrhizal (EM) colonization
The root tips of fresh fine roots were inspected using a dissecting microscope with an inte-
grated camera (Leica EZ4HD, Wetzlar, Germany) at 35-fold magnification. Aliquots of fine
roots were placed in a water-filled Petri dish (Petri dish 92 x 16 mm, Sarstedt, Nümbrecht, Ger-
many). In general, 250 roots tips were counted and scored as vital and dead root tips after col-
our of vascular tissue, strength and flexibility as described by Allen et al. (2000). On the vital
root tips the number of EM root tips was counted. EM root tips were recognized by presence
of a sheath or mantle of fungal tissue which enclosed the root and emanating hyphae [18].
Dead, non-EM, and vital EM root tips were documented by photos taken with the microscope
camera.
Arbuscular mycorrhizal (AM) colonization
Up to 25 fine root fragments per subplot with a length of 20 to 30 mmmeasured from the root
tip were stored in reaction tubes (Eppendorf micro tube 2ml, Sarstedt, Nümbrecht, Germany)
containing 70% ethanol (Rotisolv HPLC Gradient, Carl Roth, Karlsruhe, Germany). Roots
were stained following the method of Vierheilig et al. [22]. The root segments were washed sev-
eral times with ultra-purified water (ultra-pure water system, Arium 611, Sartorius, Göttingen,
Germany), briefly surfaced-dried on tissue paper and then bleached in 2 ml of 10% potassium
Root Traits and Tropical Forest Transformation
PLOS ONE | DOI:10.1371/journal.pone.0138077 September 14, 2015 5 / 19
hydroxide (KOH, Merck, Darmstadt, Germany) for 90 min at 90°C. Because not all roots were
bleached after one KOH treatment, this step was repeated with variation of the incubation time
and temperature until the objective was achieved. The bleached roots were carefully washed up
to three times with ultra-purified water to remove the KOH and then stained in 2 ml of a vine-
gar-ink-solution (10% acetic acid (Merck, Darmstadt, Germany), black ink (Sheaffer Skrip,
Shelton, USA) and ultra-purified water with a ratio of 1:1:8 for 45 min at room temperature.
The stained roots were washed with ultra-purified water to remove superfluous dye. Roots
were preserved up to eight weeks in lactoglycerol consisting of 86% glycerol (Carl Roth, Karls-
ruhe, Germany), 80% lactic acid (Carl Roth, Karlsruhe, Germany) and ultra-purified water
with a ratio of 1:1:1 before preparing microscope object slides.
For microscopic analysis, roots were cut into small segments (10 mm) and arranged with
forceps in a drop of lactoglycerol as the mountant on a microscope object slide. Cover slides
were gently pressed on root segments and flattened overnight using a lead weight (weight
between 40 and 50 g). Subsequently, the cover slides were sealed with colorless nail polish to
protect the specimen from drying. Three slides per sample were prepared and analyzed.
The gridline intersection method after McGonigle et al. [23] was used to determine AM col-
onization. The slides were placed under a compound microscope (Axio Observer Z.1, Zeiss,
Jena, Germany). With the computer program AxioVision LE (Zeiss, Jena, Germany) a gridline
was generated on the considered section (magnification 400x, distance between the intersects
100 μm) and the presence or absence of the following structures was recorded in 120 intersects
per sample: AM hyphae, arbuscules, and vesicles. For each recorded arbuscule and vesicle, a
hypha was also counted because these structures are always co-occurring. For each sample 120
intersects were counted. AM colonization was calculated as:
AM colonization ð%Þ ¼ number of hyphae
total number of intersects
 100
The relative abundance of arbuscules and vesicles was calculated correspondingly.
Determination of arbuscular mycorrhizal spore abundance
Air dried samples of bulk soil were stored in sealed plastic bags at 4°C. Spores from each soil
sample (n = 480) were isolated as described by Gerdemann and Nicolson [24]. Twenty gram of
soil of each sample was suspended in 500 ml of water, stirred manually for 10 min. The suspen-
sion was passed through sieves, which were arranged in a descending order from 250 μm,
125 μm and 63 μm and washed with tap water. The material retained on the sieves were layered
onto a a water-sucrose solution (50%) gradient and centrifuged at 900 x g for 2 min [25]. The
supernatant was washed with tap water for 3 min in a 63 μm sieve, filtrated onto a gridded filter
paper, then placed in a 90 mm diameter Petri dish. The spores obtained from all sieves were
counted under a binocular stereomicroscope with 100 to 400-fold magnification (Olympus
SZ61, Osaka, Japan). The number of spores were expressed as spores per 20 g soil sample.
Element analyses in plant and soil fractions
Dry samples of soil, roots and litter were ground to a fine powder in a ball mill (MM 2000,
Retsch, Haan, Germany). Aliquots of 0.7 to 0.9 mg per sample were weighed into tin capsules
(5 x 9mm, HEKAtech, Wegberg, Germany) and used for carbon and nitrogen analyses in an
Elemental Analyzer (EA 1108, Carlo Erba Instruments, Milan, Italy). Acetanilide (C: 71.09%,
N: 10.36%, HEKAtech, Wegberg, Germany) was used as the standard.
For analyses of the elements Al, Ca, Fe, K, Mg, Mn, Na, P and S (aluminum, calcium, iron,
potassium, magnesium, manganese, sodium, phosphorus and sulfur) a milled aliquot of 50 mg
Root Traits and Tropical Forest Transformation
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of dry soil or fine roots of each sample was digested in 2 ml of 65% nitric acid (HNO3, Merck,
Darmstadt, Germany) for 14h at 200°C. Afterwards each extract was completely transferred
into an Erlenmeyer flask. The polytetrafluoroethylene tubes (Loftfields Analytische Lösung,
Neu Eichenberg, Germany) used for the extraction were washed with HPLC grade water
(Chromanorm, VWR, Darmstadt, Germany), the washing solution was filtered through black
ribbon filter paper (filter papers MN 640w, O\ 90mm, ashless, Macherey-Nagel, Düren, Ger-
many) into the Erlenmeyer flask and the volume was adjusted to 25 ml with HPLC grade
water. Then elements in the extract were analysed by inductively coupled plasma optical emis-
sion spectrometry (ICP OES, iCAP 6300 Series, Thermo Fischer Scientific, Dreieich, Ger-
many).
Element concentration ðmg g1Þ ¼ element concentration ðmg l
1Þ x volume ðlÞ
mass of dry material ðgÞ
To calculate the sum of base cations, the concentrations of potassium, magnesium and cal-
cium were converted from mg g-1 into μmol g-1 and then added.
For the extraction of available phosphorus in soil the method of Bray and Kurtz [26] was
used. Air dried soil samples were sieved through a 2 mmmesh. Two grams of soil from each
sample were mixed with 15 ml of Bray solution containing 0.03 N NH4F and 0.025 N HCl and
were shaken (Finofors AG, Basel, Switzerland) for 5 min at 180 rpm at room temperature.
After shaking, the suspensions were filtered through a phosphorus-free folded filter (filter
papers MN 280 ¼ 125mm, Macherey-Nagel, Düren, Germany). Phosphorus concentrations of
the filtrates were analysed by ICP OES (iCAP 6300 Series, Thermo Fischer Scientific, Dreieich,
Germany).
Determination of soil pH
Soil pH was determined at a depth of 0.01 m. Soil was mixed with deionized water (1:4) and
used for pH measurements.
Maps of the sampling site
Maps of plot locations were generated the free software package GPS Visualizer (http://www.
gpsvisualizer.com/) [27].
Data analysis
The samples of each subplot (3 per plot) were analyzed individually. In rare cases (4 of 96 only
1 or 2 samples per subplot) were available. The subplot data were used to calculate plot means.
All further analyses were based on plot means. Plots means were used as input parameters to
construct the data matrices for principle component analysis (PCA). Significant principle com-
ponents (PCs) were determined by broken stick analysis. Non-metric multidimensional scaling
(NMDS) was conducted with Gover as similarity measure. Multivariate analyses were con-
ducted with the PAST free software package 2.17c (http://folk.uio.no/ohammer/past/, [28]).
The data were subjected to test the requirement of normal distribution by the Shapiro Wilks
test (P 0.05). When the P value of the Shapiro Wilks test was< 0.05, data were ln- or (-1/
square-root)-transformed to achieve normal distribution. In one case (ectomycorrhizal coloni-
zation), it was not possible to satisfy this criterion. The data were nevertheless included, but
their in- or exclusion did not affect the final result. Because the data had different units and
were subjected to different transformation procedures, the resulting matrix was z-score nor-
malized and then used for the analyses. Because of the use of normalized data, the relative
Root Traits and Tropical Forest Transformation
PLOS ONE | DOI:10.1371/journal.pone.0138077 September 14, 2015 7 / 19
importance of individual factors was not considered, but their correlation coefficient R2 with
the PCs. A linear mixed model with landscape a fixed factor and land use system as random
factor nested in landscape was used to test the contribution of the variables land use system
and landscape to the PCs (Statgraphics, Centurion XV, St Louis, Mo, USA). Variance compo-
nent analysis revealed no contribution of the factor landscape on PC1. Therefore, one-way
ANOVA with the only factor land use system was conducted for the PC1 data (post hoc test:
Tukey HSD) and the data were used to develop a general linear model with PC1 as the depen-
dent variable and soil and litter properties as independent variables. The categorical factors
land use system and landscape were not included in the model because they had been used to
develop PC1. Combinations of all eight predictors variables (soil N, soil C, soil pH, soil P, soil
cations, soil water content, litter C, litter N) were tested and the model with the lowest Akaike
information criterion (AIC = 0.569) containing three variables was chosen. When the data
were not-normal distributed the Kruskal Wallis test was conducted and medians and range of
the data were indicated.
Data deposition and availability
The raw data of this study are deposited and available in the Dryad repository under
doi:10.5061/dryad.qf362
Results
Root community-weighed traits are massively affected by the land use
system
Our measurements of the root nutrient elements represent RCWTs because the roots were col-
lected in defined soil volumes representing mixtures of tree species and understory weeds on
the plots. Root carbon, nitrogen, sulfur, manganese, and base cations concentrations showed a
decline in rubber and oil palm plantations compared with those from forest systems (Fig 2A,
2B, 2D, 2E and 2F). In both landscapes, Harapan and Bukit 12, the decline in the root nutrient
concentrations with land use type was similar. No clear influence of the land use system was
observed on the root phosphorus concentrations (Fig 2C). The concentrations iron and alu-
minium, both potentially toxic compounds at high concentrations, showed strong increases in
roots of oil palm and rubber plantations compared to jungle rubber and rain forest roots (Fig
2G and 2H).
We further determined RCWTs that are related to root vitality and mycorrhizal association
(fine root mass, colonization by ectomycorrhizal and AM fungi, AM vesicles, AM arbuscles,
AM spores in soil, dead root tips) (Fig 3). Fine root mass was higher in rain forest than in oil
palm plots, where also the highest fraction of distorted root tips was found (Fig 3A and 3B).
The fraction of mycorrhizal roots was stable (74.4 ± 1.7%) with the exception of the oil planta-
tions in Harapan (51.8 ± 7.5%, Fig 3C). EM colonization was detected in some plots in Hara-
pan rain forest with a maximum of 6% in one plot and in jungle rubber in both landscapes, but
their overall abundances were rare (Fig 3C). AM spore abundance was lowest in the rain forest
and highest in oil palm plantations (Fig 3D).
Root community-weighed traits indicate transformation intensity
PCA with all sixteen RCWTs shown in Fig 2 and Fig 3 revealed that the variables ectomycor-
rhizal colonization, abundance of AM arbuscules and Na resulted in insignificant loadings
with R< 0.5 and the parameters fine root mass and base cations showed collinearity with
other root properties and were therefore removed. The reduced PCA was based on eleven
Root Traits and Tropical Forest Transformation
PLOS ONE | DOI:10.1371/journal.pone.0138077 September 14, 2015 8 / 19
Fig 2. Chemical composition of roots in different land use systems. Carbon (A), nitrogen (B), phosphorus (C), sulfur (D), manganese (E), base cations
(F), iron (G) and aluminium (H) determined as root community-weight traits. Data indicate means (± SE). Different letters indicate significant differences at
P < 0.05. B = Bukit 12, H = Harapan, O = oil palm, R = rubber plantation, J = jungle rubber, F = forest.
doi:10.1371/journal.pone.0138077.g002
Root Traits and Tropical Forest Transformation
PLOS ONE | DOI:10.1371/journal.pone.0138077 September 14, 2015 9 / 19
RCTWs (Table 2) and resulted in two significant PCs that explained 42.4% (PC1) and 28.3%
(PC2) of the variation, respectively (Fig 4). PC1 separated the land use systems with the rain
Fig 3. Performance parameters of roots in different land use systems. (A) Fine root mass to a depth of 0.2 m, (B) Fraction of distorted root tips (100% is
the total number of inspected root tips), (C) Fraction of the inspected root lengths colonized with mycorrhizal hyphae (AMh), arbuscules (AMa), vesicles
(AMv) and fraction of vital root tips colonized with ectomycorrhizas (EM), (D) Number of arbuscular mycorrhizal spores. Data indicate means (± SE). Different
letters indicate significant differences at P < 0.05. B = Bukit 12, H = Harapan, O = oil palm, R = rubber plantation, J = jungle rubber, F = forest.
doi:10.1371/journal.pone.0138077.g003
Table 2. PCA loadings for correlations of root traits with PC1 and PC2.
Trait name Abbreviation PC1 PC2
Sulfur Sroot 0.838 0.180
Nitrogen Nroot 0.821 0.326
Carbon Croot 0.786 0.551
Manganese Mnroot 0.579 0.670
AM root colonization AMR 0.275 0.709
Phosphorus Proot 0.306 0.571
AM vesicles AMves -0.045 0.773
Iron Feroot -0.634 0.665
Dead root tips DeadR -0.592 -0.381
Aluminium Alroot -0.817 0.414
AM spores in soil AMspore -0.866 0.200
doi:10.1371/journal.pone.0138077.t002
Root Traits and Tropical Forest Transformation
PLOS ONE | DOI:10.1371/journal.pone.0138077 September 14, 2015 10 / 19
forests exhibiting the most positive and oil palm plantations the most negative scores (Fig 4).
Positive PC1 loadings with correlations of R 0.5 were C, N, S, and Mn (Table 2). Negative
PC1 loadings with R -0.5 were AM spores, dead root tips, Al and Fe (Table 2). RCWTs
related to mycorrhization (AM colonization, AM vesicles) and to phosphorus were not
strongly correlated with PC1 (Fig 4, Table 2), but were significant loadings on PC2.
To quantify the influence of the factors landscape and land use systems on the variation of
the PC1 and PC2 scores, the data were analyzed by general linear mixed models. Significant
models were obtained for both PCs with R2(adjusted for df) explaining 92.6% of the variation of
the PC1 scores and 32.9% of the PC2 scores (Table 3). However, the only significant factor was
land use system (Table 3). Analyses of the variance components (in the order of nesting)
showed that landscape contributed 0%, land use system 94.1% and the error term 5.9% to the
variation of PC1. For PC2 the contributions of the components to the total variation were error
term (58.4%), landscape (23.1%) and land use system (18.5%). Mean values of the PC1 scores
ordered the land use systems according to transformation intensity in the order:
forest> rubber jungle> rubber> oil palm (Table 4).
Transformation intensity is linked with ecosystem properties
In tropical ecosystems loss of forest cover and conversion into agricultural land use systems
has often been linked with loss in soil fertility and soil carbon contents [9,11]. We, therefore,
asked whether the RCWTs that ordered the land use systems according to transformation
Fig 4. Principle component analysis of root community-weighed traits. The traits used for PCA and their abbreviations are listed in Table 2. B = Bukit
12, H = Harapan, O = oil palm, R = rubber plantation, J = jungle rubber, F = forest.
doi:10.1371/journal.pone.0138077.g004
Root Traits and Tropical Forest Transformation
PLOS ONE | DOI:10.1371/journal.pone.0138077 September 14, 2015 11 / 19
intensity also corresponded to loss of ecosystem functions indicated by soil properties. Soil
(sum of base cations, available phosphorus, pH, water content, carbon, nitrogen) and litter
properties (carbon, nitrogen), which we measured as proxies for ecosystem functions showed
significant variations among different sites (Table 5). An NMDS conducted with the significant
loadings of RCWTs for PC1 (Table 2) and the environmental variables (Table 5) as explanatory
vectors indicated that soil pH and soil N were related to the negative scores of oil palm and rub-
ber plantations, while soil C and litter N and C were related to the positive scores of rain forest
and jungle rubber (Fig 5). However, it should be noted that the overall pH differences between
the plots were small (Table 5, mean pH of rain forest plots: 4.25 ± 0.03 and mean pH of the
other land use systems: 4.46 ± 0.13, P = 0.002).
To find out whether the PC1 scores which distinguish the land use systems independently
from landscape can be quantitatively related to ecosystem functions, we tested general linear
models. The PC1 scores were used as dependent and the environmental properties as indepen-
dent variables. The categorical factors land use system and landscape were not included in the
model, because they had been used to determine the PC1 components. The model with the
lowest AIC contained three significant components: soil nitrogen concentration, soil pH and
Table 4. Mean PC scores of the land use systems.
Site PC1 ± SE PC2 ± SE
BF 2.77 ± 0.31e 0.74 ± 0.62ab
HF 2.34 ± 0.17de -1.68 ± 0.32ab
BJ 0.86 ± 0.33c 0.30 ± 0.19ab
HJ 1.05 ± 0.26cd -0.66 ± 1.05ab
BR -1.25 ± 0.45b 1.60 ± 0.42b
HR 0.09 ± 0.37bc 1.22 ± 0.95ab
BO -3.06 ± 0.17a 0.35 ± 0.36ab
HO -2.84 ± 0.18a -1.87 ± 0.74a
Different letters in columns indicate significant differences at P < 0.05 determined with the HSD test.
B = Bukit 12, H = Harapan, O = oil palm, R = rubber plantation, J = jungle rubber, F = forest.
doi:10.1371/journal.pone.0138077.t004
Table 3. General linear mixedmodel for PC1 and PC2 as dependent variables and landscape and land use system (LUS) as categorical factors.
Source Sum of Squares Df Sum of Squares F-Ratio P-Value
Analysis of Variance for PC21
Model 136.46 7 19.49 56.31 <0.001
Residual 8.31 24 0.35
landscape 0.92 1 0.92 0.04 0.847
LUS(landscape) 135.54 6 22.59 65.25 <0.001
Residual 8.31 24 0.35
Total (corrected) 144.77 31
Analysis of Variance for PC2
Model 46.45 7 6.63 3.17 0.016
Residual 50.18 24 2.09
landscape 17.97 1 17.97 3.79 0.100
LUS(landscape) 28.47 6 4.74 2.27 0.071
Residual 50.18 24 2.09
Total (corrected) 96.63 31
Landscape was set as fixed and LUS as random factor nested in landscape.
doi:10.1371/journal.pone.0138077.t003
Root Traits and Tropical Forest Transformation
PLOS ONE | DOI:10.1371/journal.pone.0138077 September 14, 2015 12 / 19
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Root Traits and Tropical Forest Transformation
PLOS ONE | DOI:10.1371/journal.pone.0138077 September 14, 2015 13 / 19
litter carbon concentration (Table 6). The model explained 70% (R2 adjusted for d.f.) of the
variation. The P-value of the Durbin-Watson statistic was> 0.05 and therefore the model was
not significantly affected by serial autocorrelation in the residuals.
Discussion
Root community-weighed traits and soil properties vary with forest
transformation
Recent studies highlight the importance of functional structures of communities rather than
their biodiversity for ecosystem functioning [29–31]. Our study clearly demonstrates a decline
Fig 5. Nonmetric multidimensional scaling (NMDS) of root community-weighed traits.RCWTs with R>0.5 and R< 0.5 from Table 1 for PC1 were used
for NMDS. The following environmental parameters were plotted as explanatory variables: nitrogen and carbon concentrations in soil and litter (Nsoil, Csoil,
Clitter, Nlitter), available phosphorus in soil (Pavailsoil), sum of basic cations in soil (CatBsoil), soil water content (soilSWC) and soil pH (pH). B = Bukit 12,
H = Harapan, O = oil palm, R = rubber plantation, J = jungle rubber, F = forest. Stress: 0.106, R2 for coordinate 1: 0.785 and for coordinate 2: 0.0735.
doi:10.1371/journal.pone.0138077.g005
Table 6. Best general linear model for the relationship of PC1 with ecosystem properties.
Source Sum of Squares Df Mean Square F-Ratio P-Value
Model 106.2 3 35.4 25.71 <0.0001
Residual 38.55 28 1.37
Nsoil 6.37 1 52.15 37.88 0.0401
pH 26.14 1 26.14 18.99 0.0002
Clitter 52.16 1 52.16 37.88 <0.0001
Residual 38.55 28 1.37
Total (corrected) 144.76 31
doi:10.1371/journal.pone.0138077.t006
Root Traits and Tropical Forest Transformation
PLOS ONE | DOI:10.1371/journal.pone.0138077 September 14, 2015 14 / 19
of positive RCWTs such as high root mass and high nutrient concentrations in mono-culture
oil palm plantations compared with rain forest. Based on our design we cannot distinguish
whether the enhanced properties of the root communities in the rain forest were the result of
tree phylogenic diversity or of trait-enrichment due to the presence of forest tree species with
distinct features. We expected that the impact of dominant trees might have been traced by an
effect of the associated EM on RCWTs, because the root nutrient status of forest trees is
affected by symbioses with AM or EM fungi and fungal species identities [32–34]. However,
our data did not reveal an influence of the land use system on the mycorrhizal life traits. In con-
trast to the relatively stable AM colonization, AM spore abundance varied strongly with trans-
formation system. Fungi are propagated by spores, but spores are also resting structures, by
which the fungi survive unfavorable conditions [35]. In tropical systems increased spore abun-
dance correlated with decreased soil fertility [36]. The increased AM spore abundance in oil
palm and rubber monocultures, thus, points to links of these agricultural systems with ecolog-
ically important life traits.
A negative impact of monoculture oil palms was evident on soil carbon and nitrogen con-
tents. Conversion of tropical forests into agricultural production systems has often been shown
to result in decreased soil carbon and nitrogen pools [37–41]. The magnitude of this effect in
our study was similar to that in other tropical transformation system, e.g. in cash crops such as
maize on Central Sulawesi (Indonesia) [9]. In comparison with agricultural land use, agro-for-
estry systems recovered soil fertility [9]. A beneficial effect of jungle rubber, an extensive agro-
forest land use system, on soil properties was confirmed in our study because the carbon and
nitrogen concentrations in soil of this system were even higher or, at least, as high as in rain
forest soil. This finding is important because soil fertility has direct consequences for ecosystem
services such as biomass production, carbon cycling and carbon sequestration and has been
identified as the major regulator of forest carbon balance [42].
Soil properties and vegetation mutually influence each other because both compartments
are connected by matter flux. Alterations in plants traits are transmitted to the soil by the input
of degrading leaf and root litter as well as by root physiological activities (exudation of carbohy-
drates, organic acids, nutrient uptake) [43,44]. Therefore, RCWTs and soil properties are to
some extent inter-dependent. Our study provides some insights into the nature of these links
because the RCWTs that reflected transformation intensity were also linked with soil and litter
properties, i.e., soil pH, soil N and litter C concentrations. This finding is interesting because
litter carbon is the result of litter degradability, which in turn is driven by plant functional traits
[45]; soil nitrogen is important for soil fertility and forest productivity and therefore, eventually
has strong impact on forest carbon cycling [42]. Our findings, thus, link functional structures
of root communities with ecosystem functions, notably with those functions that are more
important for carbon sequestration than climate or the rising atmospheric CO2 concentration
[42,45]. This finding implies that RCWTs could be an important indicator for the functionality
of above- and below-ground ecosystem interactions.
Based on the present data, the cause-effect relationships remains unknown because mono-
culture species with unfavorable root traits could have affected soil properties or management
could have altered soil properties with negative consequences for root traits. Regardless the
ultimate reason, our results suggest that the loss in ecosystem functions in mono-cultures was
accompanied by complex alterations of root functional traits. Increased transformation inten-
sity was associated with diminished nutrient concentrations and low root mass on the hand
and increased concentrations of potentially phytotoxic metals (Al, Fe) and enhanced root tip
mortality on the other hand. The transformation intensity was thus indicated by contrasting
behavior of distinct RCWTs and not by the loss of traits abundance per se. Consequently, we
may expect that any management measure that improves root vitality may, eventually, enhance
Root Traits and Tropical Forest Transformation
PLOS ONE | DOI:10.1371/journal.pone.0138077 September 14, 2015 15 / 19
the ecological functions of tropical production systems. It will be important to investigate this
suggestion in future studies.
Degradation of root health is related to accumulation of plant toxic
elements
Chemical root traits that distinguished the monocultures, especially the oil palms, from ecosys-
tems with higher tree diversity were the enrichments in Fe and Al. Plant availability of Al is
modulated by soil acidity [46]. The soils in the Jambi lowland region are acrisols with pH val-
ues of 4.5 and below. In Bukit 12 higher concentrations of exchangeable Al were present than
in Harapan (0.54 ± 0.18 mg g-1 soildw versus 0.28 ± 0.04 mg g
-1 soildw), but without showing a
clear gradient among the land use systems as found here for the root communities [47]. In
each landscape the exchangeable Fe concentrations were highest in rain forest soil [47], where
root communities showed the lowest Fe enrichment. Therefore, the Al and Fe enrichments in
roots did not simply reflect soil conditions.
Excess Al accumulation is known to limit plant performance and affects root growth [48–
50]. Indeed, the morphological appearance of the oil palm roots on our plots resembled the
symptoms of Al toxicity with stubby root systems lacking fine root branches with many brown-
ish, distorted root tips [51]. Although oil palms are often cultivated in acid soils [52] injury due
to unfavorable soil conditions cannot be excluded. In field studies, a negative correlation
between exchangeable Al in soil and root density of oil palms was found [53]. Controlled stud-
ies confirmed the negative impact of Al on oil palm roots, especially on the length of the lateral
roots and number of root tips [54]. Cristancho et al. [54] further showed that Al-stressed oil
palms excreted significant concentrations of oxalic acids. Plant exudation of organic acids
influences the availability of other soil elements and mobilizes for example phosphorus and Fe
[55,56]. Here, we found high Fe concentrations in roots, whereas soil phosphorus availability
was low and root phosphorus concentrations remained unaffected by the land use system.
Excess Fe causes oxidative stress leading to cell destruction [56] and may have caused here,
together with Al, enhanced root tip mortality. It is important to note that the pH across all for-
est types was low, but not lower in plantations than in forest soil. Therefore, low pH may be a
pre-requisite, but was not the immediate reason for the observed decline in root health.
Currently, we can only speculate about the reasons for root distortion in oil palm planta-
tions. One possibility is that mono-cultures alter the soil microbial flora with negative effects
on Al or Fe solubilization and plant availability as found in other countries [57]. AM coloniza-
tion protects plant roots from Al stress [58], but here variation in AM abundance was unrelated
to Al concentrations. Phylogenetic analyses have shown high Al tolerance in tropical forest
trees [59–62]. Therefore, it is also possible that the introduced crop trees were less well-adapted
to the prevalent soil conditions than the native tree species and accumulated phytotoxic con-
centrations of Al and Fe over the years. As a consequence, root health may decline and root
soil exploration and root litter input into soil decrease, thereby, eventually leading to alterations
in soil properties. To disentangle the underlying mechanisms, experimental studies with mix-
tures of oil palm, rubber and native forest species are necessary. Thereby, feed-back effects
between ecosystem functions and functional traits of distinct tree species and their communi-
ties can be uncovered and used to develop improved management strategies.
Acknowledgments
We are grateful to M. Fastenrath, M. Franke-Klein and C. Kettner for excellent technical assis-
tance. We thank the following persons and organizations for granting us access to and use of
their properties: village leaders, local plot owners, PT Humusindo, PT REKI, PT Perkebunan
Root Traits and Tropical Forest Transformation
PLOS ONE | DOI:10.1371/journal.pone.0138077 September 14, 2015 16 / 19
Nusantara VI, and Bukit Dua Belas National Park. We acknowledge the help of Bambang Ira-
wan, Upik Yelianti and Efi Toding Tondok with administrative matters.
Author Contributions
Conceived and designed the experiments: AP. Performed the experiments: JS SWB HB NE
MMMDC. Analyzed the data: JS SWB HB NEMMMDC AP. Contributed reagents/materials/
analysis tools: JS SWB HB NE. Wrote the paper: JS SWB HB NEMDC AP.
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