Journal of Arid Environments 113 (2015) 121e125

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Journal of Arid Environments

journal homepage: www.elsevier.com/locate/jaridenv

Sourceesink dynamics shapes the spatial distribution of soil protists

in an arid shrubland of northern Chile

ndez a, b, c, *
Leonardo D. Ferna
a
Laboratory of Soil Biology, Institute of Biology, University of Neucha^tel, Rue Emile Argand 11, 2000 Neucha
^tel, Switzerland
b
Laboratorio de Ecología Evolutiva y Filoinforma
tica, Departamento de Zoología, Facultad de Ciencias Naturales y Oceanogra
ficas,
Universidad de Concepcio
n, Barrio Universitario s/n, Casilla 160-C, Concepcio
n, Chile
c
Centro de Estudios en Biodiversidad (CEBCH), Magallanes, 1979 Osorno, Chile

a r t i c l e i n f o a b s t r a c t

Article history: Arid shrublands are spatially heterogeneous environments composed of shrubs patches surrounded by a
Received 13 May 2014 matrix of bare soil. In this biome, bare soils harbor fewer protist species than soils covered by shrubs
Received in revised form because they represent low quality habitats for most of them. Furthermore, protist species composition
6 October 2014
in bare soils often represents a subset of that found in soils covered by shrubs. This pattern suggests that
Accepted 9 October 2014
Available online 16 October 2014
the variability in protist species composition is the result of a non-random mechanism. I performed a
nested analysis to test the hypothesis that the sourceesink dynamics is shaping the spatial distribution of
soil testate amoebae (a polyphyletic group of protists) in an arid shrubland of northern Chile. I found that
Keywords:
Arcellinida
assemblages of soil testate amoebae are significantly nested in this biome. The species-poor assemblages
Cercozoa inhabiting bare soils are thus, only a subset of species-rich assemblages located in vegetated soils. This
Colonizationeextinction dynamics nested pattern may be the result of a colonizationeextinction tradeoff characterized by species-poor bare
Morphological traits soils acting as ‘sinks’ maintained by the permanent colonization of individuals coming from species-rich
Nested subset pattern of species vegetated soils acting as ‘sources’. Thus, the sourceesink dynamics represents a valid conceptual
composition framework to explain the spatial patterns of soil protists distribution in arid shrublands.
Testate amoebae © 2014 Elsevier Ltd. All rights reserved.

1. Introduction composition of bare soils only represents a subset of that found in

Arid shrublands are fragmented landscapes composed of large
areas of bare soil and widely separated shrub patches. In this
biome, bare soils harbor fewer protist species than soils covered
by shrubs because they represent low quality habitats for most of
them, e.g. low water and nutrient content, high desiccation risk
(Bamforth, 2008; Robinson et al., 2002). Instead, soils located
under shrubs comprise higher quality habitats for protists, since
plants provide shading, create heterogeneity in soils, intercept and
retain water, and concentrate nutrients under their canopy (del-
Val et al., 2006; Schlesinger et al., 1996). In addition, studies of
protist species composition in arid shrublands often found no
species replacement (i.e. species turnover) between bare soils and
those covered by shrubs (Bamforth, 2008; Robinson et al., 2002).
Variation in species composition between both habitats is thus
only due to differences in species richness and protist species
* Corresponding author. Laboratory of Soil Biology, Institute of Biology, University
^tel, Rue Emile Argand 11, 2000 Neuch^
of Neucha atel, Switzerland.
E-mail addresses: limnoleo@gmail.com, leonardo.fernandez@unine.ch.
soils beneath shrubs. This suggests that the variability in protist
species composition is the result of a non-random mechanism
such as sourceesink dynamics. This model predicts that species-
poor assemblages inhabiting sink (low quality) habitats are
constituted by non-viable populations maintained by a constant
colonization of individuals coming from species-rich assemblages
located in source (high quality) habitats (Pulliam, 1988). As a result
a nested subset pattern of species composition occurs, in which
impoverished sites tend to be proper subsets of the richer sites
(Atmar and Patterson, 1993; Wright et al., 1998). The empirical
study of the sourceesink dynamics is a difficult task because it
requires long-term studies that often are impracticable. However,
the ecological concept of nestedness provides an alternative and
robust framework to indirectly infer the relative importance of the
sourceesink dynamics in shaping the spatial distribution of spe-
cies. Nestedness predicts that when depauperate sites tend to be
simple subsets of richer ones, a nested subset pattern of species
composition emerges, suggesting a highly ordered system in
which both colonization and extinction may be actively shaping
species occurrence across sites (Atmar and Patterson, 1993; Wright
et al., 1998). In arid shrublands, nested assemblages of soil protists

http://dx.doi.org/10.1016/j.jaridenv.2014.10.007
0140-1963/© 2014 Elsevier Ltd. All rights reserved.
122
ndez / Journal of Arid Environments 113 (2015) 121e125
L.D. Ferna

may imply that the spatial variation in species composition is
determined by sourceesink dynamics, where sink (bare soils)
habitats would be characterized by high extinction rates, so spe-
cies richness in those zones should be maintained mainly by the
permanent colonization of individuals coming from source
(vegetated soils) habitats, where populations would be actively
growing and reproducing.
In this study, I tested the hypothesis that the sourceesink
dynamics is shaping the spatial patterns of soil protists distri-
bution in arid shrublands. For this task I searched for the occur-
rence of a nested subset pattern of species composition among
assemblages of testate amoebae inhabiting an arid shrubland of
northern Chile. Testate amoebae are a polyphyletic group of
protists (composed mainly by Cercozoa and Arcellinida) in which
the amoeboid body is protected by a shell. The shells show a wide
range of morphological adaptations related to the availability of
soil water. Overall, dry and bare surface soils favor species with
cryptostome or plagiostome shell types (i.e. shells with a well-
protected or hidden aperture). Meanwhile, stable soils with
mediumehigh moisture availability allow the occurrence of
species with axial and acrostome shell types (i.e. terminal or well
visible aperture). Testate amoebae inhabiting arid soils of
northern Chile have not been documented before, so this study
also aimed to expand our knowledge on eukaryotic microor-
ganisms that inhabit this region.
2.3. Statistical analyses
ManneWhitney U-tests were performed in PAST v1.5 (Hammer
et al., 2001) to test whether bare and vegetated soils differ in: (1)
testate amoeba species richness; and (2) the number of occurrences
of different shell types (cryptostomeeplagiostome versus
axialeacrostome). Statistical inference was based on a random
permutation test (10,000 iterations) to calculate the 95% confidence
intervals.
To rule out possible bias in the sampling effort, a spe-
cieseaccumulation curve based on the Chao2 estimator was
calculated in EstimateS v9.1 (Colwell, 2006). This method estimates
what proportion of the total diversity of a site has been detected by
plotting the observed number of species as a function of the
accumulated number of samples. Statistical inference was based on
a random permutation test (50,000 iterations) to calculate the 95%
confidence intervals.
The NODF index was used to explore the occurrence of a nested
subset pattern of species composition in the matrix. This index
was also calculated independently for columns and rows of the
matrix. Nestedness among columns represents differences in
species richness and nestedness among rows represent differ-
ences in species incidence. Decomposing nestedness into its
among-column and among-row components allow calculating to
which extent gradients in the characteristics of sites (habitat

2. Materials and methods

Table 1
Testate amoeba species recorded in a 10-km2 area of an arid shrubland of northern
2.1. Study site Chile.

In March 2007, I studied a 10-km2 area of an arid shrubland in Species Number of occurrences

the Coquimbo Region of northern Chile. The study site was located Study Under Bare Shell Note
on the southern edge of the Atacama Desert about 40 km from the site plants soil type
Pacific Coast (29
590 S; 70
470 W). The regional climate is charac- Arcella arenaria Greeff, 1866 37 25 12 AX a
terized as mediterranean-arid with hot dry summers and cool Arcella vulgaris Ehrenberg, 1830 24 18 6 AX c
winters (del-Val et al., 2006). Mean annual temperature is 13.6
C Argynnia sp. 6 3 3 AC a
Centropyxis aculeata (Ehrenberg, 1838) 35 17 18 PL c
and mean annual precipitation is 147 mm, nearly 95% of which falls Centropyxis aerophila Deflandre, 1929 28 17 11 PL a
during the winter (del-Val et al., 2006). The vegetation of the study Centropyxis constricta (Ehrenberg, 1841) 19 11 8 PL a
site is shrubesteppe type and consists of vegetation patches sur- Centropyxis discoides (Penard, 1890) 21 12 9 PL a
rounded by a matrix of bare soil (Gajardo, 1994). Centropyxis plagiostoma Bonnet and 42 25 17 PL a
Thomas, 1955
Cryptodifflugia oviformis Penard, 1890 13 9 4 AC a
2.2. Sampling and sample treatment Cyclopyxis eurystoma Deflandre, 1929 31 16 15 AX a
Cyclopyxis humilis Bonnet, 1962 13 6 7 AX a
Cyclopyxis kahli (Deflandre, 1929) 15 8 7 AX a
I randomly located ten 100-m long transects in the study site
Cyclopyxis sp. 9 5 4 AX a
and extracted 10-cm3 of soil at each 20-m interval. For each sample Difflugia distenda (Penard, 1989) 8 6 2 AC a
I noted whether it was taken from beneath vegetation or from bare Difflugia oblonga Ehrenberg, 1838 15 10 5 AC a
soil. Within 1e2 days, samples were washed through 500 and Euglypha cristata acicularis Wailes, 1912 14 7 7 AC a, b, d
300 mm mesh sieves to remove the coarse material. Each sample Euglypha strigosa (Ehrenberg, 1871) 11 6 5 AC a
Euglypha tuberculata Dujardin, 1841 7 4 3 AC a
was explored by using direct observation and by culture methods
Netzelia wailesi (Ogden, 1980) 11 9 2 AC a
for documenting species occurrence. The use of cultures allowed Phryganella acropodia (Hertwig and 17 12 5 AX a
for the detection of species that were encysted1 at the time of Lesser, 1874)
sampling. Cultures were prepared following the procedures Phryganella sp. 5 3 2 AX a
described by Wilkinson and Smith (2006) and examined for the Plagiopyxis cf. declivis Bonnet and 32 22 10 CR a
Thomas, 1955
presence of organisms after 2, 4, 6, 8, 10, 20, 40 and 60 days of Scutiglypha cabrolae De Smet and 21 12 9 AC c
incubation at 20
C. The identification and further sorting of taxa in Gibson, 2009
different shell types were based on traditional references (Bonnet, Scutiglypha crenulata (Wailes, 1912) 21 11 10 AC a, b
1975; Ferna
ndez et al., 2012 and taxonomic references cited Scutiglypha scutigera (Penard, 1911) 7 7 0 AC a, b, d
Tracheleuglypha dentata (Penard, 1890) 14 9 5 AC a
therein). Species occurrence data were used to construct a binary
Trinema complanatum Penard, 1890 9 6 3 PL a
matrix (i.e. columns as samples and rows as taxa) on which all Trinema enchelys (Ehrenberg, 1838) 24 15 9 PL a, d
subsequent statistical analyses were based. Trinema lineare Penard, 1890 29 18 11 PL a

AC ¼ acrostome shell type; AX ¼ axial shell type; CR ¼ cryptostome shell type;

1
A cyst is a dormant stage that allows the organism to survive under adverse
environmental conditions, e.g. during droughts. The encysted organisms may be
overlooked by direct observation methods.
PL ¼ plagiostome shell type; a ¼ first record for northern Chile; b ¼ first record for
southwestern South America; c ¼ species previously recorded in northern Chile;
d ¼ species only found in cultures. Maximum possible number of occurrences per
species ¼ 50.

ndez / Journal of Arid Environments 113 (2015) 121e125
L.D. Ferna 123

Fig. 1. Scanning Electron Microscope pictures of some testate amoebae exhibiting the morphological shell types observed in the study site. AC ¼ acrostome shell type; AX ¼ axial
shell type; CR ¼ cryptostome shell type; PL ¼ plagiostome shell type. (a) Arcella arenaria Greeff, 1866 (AX); (b) Centropyxis aculeata (Ehrenberg, 1838) (PL); (c) Centropyxis constricta
(Ehrenberg, 1841) (PL); (d) Cyclopyxis eurystoma Deflandre, 1929 (AX); (e) Plagiopyxis cf. declivis Bonnet and Thomas, 1955 (CR); (f) Difflugia distenda (Penard, 1899) (AC); (g) Netzelia
wailesi (Ogden, 1980) (AC); (h) Tracheleuglypha dentata (Penard, 1890) (AC); (i) Scutiglypha cabrolae De Smet and Gibson, 2009 (AC); (j) Difflugia oblonga Ehrenberg, 1838 (AC); (k)
Trinema complanatum Penard, 1890 (PL); (l) Trinema lineare Penard, 1890 (PL). For scanning electron microscopy, the individuals were cleaned by several transfers through distilled
water, mounted on coverslips and finally air-dried. The individuals on coverslips were coated with gold and examined with a JEOL JSM-6380 operating at 15 kV.

quality) and traits of species (shell type) contribute to the whole-
matrix nestedness (Almeida-Neto and Ulrich, 2011). The NODF
index ranges from 0 to 100, where high values are consistent with
higher degrees of nestedness. The statistical significance of these
analyses was evaluated with a rowecolumn null-model (50,000
permutations, p < 0.05), a conservative algorithm that minimizes
Type I errors (Ulrich and Gotelli, 2010). Nestedness and null-model
calculations were done using NODF v2.0 (Almeida-Neto and
Ulrich, 2011).
3. Results
I observed 29 testate amoeba taxa in the 50 analyzed samples,
including three taxa that could not be identified to species level. All
but three species are reported here for the first time in northern
Chile. Four of these species also represented first records for
southwestern South America. Nine species exhibited a cryptostome
or plagiostome shell type, while the remaining 20 species showed
an axial or acrostome shell type. A detailed species list, including
their shell types and occurrences in the habitats are given in Table 1.
Fig. 1 shows some testate amoeba species and shell types observed
in the study site.
In most cases testate amoeba taxa were found by using a direct
observation method, suggesting that they were ecologically active
in the study site. Only two additional taxa were found after using a
culture method (Table 1). The exploration of the cultures after 20,
40 and 60 days revealed no new taxa on plates, indicating that all
the diversity present in the samples was found (Fig. 2A). Further-
more, the specieseaccumulation curve showed that all data points
fell within the 95% confidence intervals estimated with Chao2
(Fig. 2B) and thus that sampling was sufficiently exhaustive to
obtain a reasonable estimate of the total diversity in the studied
habitats.
Soil samples collected from beneath vegetation exhibited a
higher number of testate amoeba species than bare soils (Fig. 3A).
Cryptostome and plagiostome shell types were widely distributed,
as they exhibited a greater number of occurrences than the species
with an axial and acrostome shell types in both vegetated soils and
bare soils (Fig. 3B and C).
The NODF index value obtained for the whole matrix revealed
that testate amoeba assemblages are significantly nested at the
study site (Table 2). The NODF index value for columns and rows
confirmed that this nested pattern is due to a simultaneous species
overlap from species-poor sites to species-rich sites and co-
occurrence from limited to widely distributed species (Table 2).

Fig. 2. Number of testate amoeba species: (A) recorded as a function of the cumulative number of culture days. The plot does not consider fluctuations in species abundance, but
only the species occurrence in cultures after 60 days of incubation at 20
C (broken line); and (B) predicted by Chao2 estimator (specieseaccumulation curve) as a function of the
sampling effort (solid line) and the lower and upper 95% confidence intervals of the null distribution of 50,000 random permutations (broken lines) sampled without replacement
from the observed dataset (number seed ¼ 123456789).
124
ndez / Journal of Arid Environments 113 (2015) 121e125
L.D. Ferna

Fig. 3. ManneWhitney U-tests (U) performed to test whether soils under vegetation (UV) and bare soils (BS) differ in: (A) testate amoeba species richness; and (B, C) the number of
occurrences of different shell types (cryptostomeeplagiostome type [cp] and axialeacrostome type [aa]). Statistical inference was based on a Monte Carlo permutation test (10,000
iterations) to calculate the 95% confidence intervals. Error bars represent standard deviation.

4. Discussion conceptual framework to explain the spatial patterns of soil protists

This study provided strong support for the hypothesis that the
sourceesink dynamics is shaping the spatial patterns of soil protist
distribution in arid shrublands. Here, testate amoeba species rich-
ness was higher in vegetated soils than in bare soils and only those
species with cryptostome and plagiostome morphological traits
were widely distributed in harsh soils. In line with these results,
testate amoeba assemblages were significantly nested at the study
site, and nestedness components showed that this pattern was
simultaneously caused by connected gradients in the characteris-
tics of sites and traits of species. Nestedness among-columns
confirmed that species composition of bare soils was a proper
subset of that found in soils covered by shrubs, pointing out that all
the variation in species composition was due to differences in
species richness between both habitats; i.e. there was no species
turnover. Meanwhile, nestedness among-rows demonstrated that
less distributed species (axialeacrostome shell types) were found
in a subset of the sites in which those species with higher incidence
occurred (cryptostomeeplagiostome shell types). The observed
nested pattern was robust to possible methodological artefacts,
since these pitfalls were avoided and controlled by using two in-
dependent and complementary methods: cultures and spe-
cieseaccumulation curve. Cultures allowed the detection of all
species that were present in the samples, including those that were
encysted. The specieseaccumulation curve confirmed that very few
additional species would be recorded with a higher sampling effort.
This comprehensive picture strongly suggests that the spatial pat-
terns of soil testate amoebae distribution is the result of a colo-
nizationeextinction tradeoff characterized by species-poor bare
soils acting as ‘sinks’ maintained by the permanent colonization of
individuals coming from species-rich vegetated soils acting as
‘sources’. Thus, the sourceesink dynamics represents a valid
Table 2
Degree to which species-poor assemblages inhabiting bare soils are subsets of
species-rich assemblages located in vegetated soils in a 10-km2 area of an arid
shrubland of northern Chile. Nestedness was based on a presenceeabsence data
matrix ordered according to the marginal row/column sums. Below are shown the
observed (NODFobs) and expected (NODFexp) values of NODF index for the whole
matrix (NODFmatrix), columns (NODFcolumns) and rows (NODFrows). Statistical infer-
ence was based on the lower and upper confidence limits (L95%CL, U95%CL,
respectively) of the null distribution of 50,000 randomized matrices.
NODFobs NODFexp L95%CL U95%CL
NODFmatrix 45.71 32.49 30.26 34.70
NODFcolumns 46.12 32.52 30.14 34.85
NODFrows 44.48 32.41 30.30 34.48
distribution in arid shrublands.
A core question to sourceesink theory is why individuals would
leave a high quality habitat for another of lower quality, where high
mortality could result in a population decline toward extinction.
Soil protists disperse passively, relying mainly on wind to colonize
other sites (Foissner, 1987). As a result, sourceesink dynamics can
arise simply because external agents dispersed propagules, forcing
individuals to grow in a poor habitat (Remes, 2000). However, this
does not imply that all soil protists are equally likely to disperse and
colonize low quality habitats in arid shrublands. In soil, the distri-
bution (both horizontal and vertical) of protists is mainly deter-
mined by the extent to which the species exhibit traits that allow
them to avoid dehydration (Bonnet, 1975). Consequently, only a
selected subset of taxa occurring in vegetated soils can colonize
bare soils (Bamforth, 2008), leading to the observed nested pattern
of species composition. In this study, the selected subset of taxa was
represented by species with cryptostome and plagiostome
morphological traits. These taxa are more abundant in the less
stable upper soil horizons (Foissner, 1987) and can establish pop-
ulations in bare soils because they tolerate better stressful condi-
tions (Bamforth, 2008; Robinson et al., 2002). Accordingly, they are
more likely to be passively dispersed than those taxa with
axialeacrostome morphological traits and/or living below-ground
(Ferna
ndez and Zapata, 2011; Mitchell and Meisterfeld, 2005).
Thus, while the sourceesink dynamics may arise primarily from the
passive dispersal of soil protists, the impoverished assemblages of
protists inhabiting bare soils may primarily be due to the contin-
uous and differential immigration of species that exhibit both traits
to withstand stressful abiotic conditions and a shallow vertical
distribution in soil. Finally, these results suggest that the sour-
ceesink dynamics also could be shaping the spatial patterns of soil
protists distribution in other fragmented landscapes as well as in
those exhibiting gradients in habitat quality.
Acknowledgments
I appreciate the financial support of CONICYT-Chile (doctoral
scholarships N
21110037 and 78130011), the Wildlife Conservation
Society (Karukinka grant Nº 2012), the Direccio
n de Postgrado of
the Universidad de Concepcio
n, and the IDPOB of the University of
Neucha^tel. I thank (in alphabetic order) Edward Mitchell, Jaime
P-value
Zapata, Ralf Meisterfeld and Stuart Bamforth as well as Andrey
0.002 Tsyganov, Yuri Mazei and another (anonymous) reviewer for their
0.002 valuable suggestions. I'm very grateful to Fabiola Barrientos-Loebel,
0.002
who performed the digital artwork of Fig. 1.

ndez / Journal of Arid Environments 113 (2015) 121e125
L.D. Ferna 125

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