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M.E. Cevasco, S.M. Lechliter, A.E. Mosier, and J. Perez
22001155 SOUTHEASTERN NATURALIST 1V4o(2l.) :1346,1 N–3o7. 22
Initial Observations of Kleptoplasty in the Foraminifera of
Coastal South Carolina
Megan E. Cevasco1,*, Shawnee M. Lechliter1, Alexander E. Mosier1, and
Jasmine Perez1
Abstract - Kleptoplasty is a mixotrophic condition acquired by a heterotrophic grazer that
ingests photosynthetic eukaryotic cells, wherein the plastids are not digested but rather
are retained in the heterotrophic cell or organism in a photosynthetically active state. This
phenomenon has been described in select foraminiferal taxa inhabiting nearshore and
salt-marsh coastal habitats. We applied molecular and microscopic techniques to living
foraminifera collected from South Carolina salt marshes (Waties Island and North Inlet) to
determine if we could detect kleptoplasty. Sequence and confocal-imaging data recovered
from 2 foraminiferal genera (Elphidium and Haynesina) indicated the functional retention
of diatom plastids within these taxa.
Introduction
The term kleptoplasty is used to describe the ability of a heterotrophic organism
to retain the photosynthetic organelles (plastids) of its prey (Rumpho et al. 2011).
The sequestered plastids (kleptoplasts) remain functional within the herbivore for
extended periods of time, enabling it to engage in phototrophy, thus converting
a heterotroph into a mixotrophic chimera. Mixotrophy by kleptoplasty has been
shown to have important stabilizing effects on the trophic structuring in ecosystems
by increasing the total primary and secondary production in planktonic food webs,
facilitating carbon transfer from microbial to metazoan trophic levels, and enhancing
nutrient cycling (Hallock 2000, Handeler et al. 2009). Moreover, in addition to
providing energy and carbon fixation, kleptoplasty may also contribute to providing
oxygen in low-oxygen habitats (Bernhard and Bowser 1999).
The retention of microalgal plastids has been identified in taxonomically disparate
groups of invertebrates and marine protist hosts including dinoflagellates,
ciliates, and foraminifera (Stoecker et al. 2009). Concomitant with host diversity,
there is broad taxonomic diversity in the retained plastids ranging from haptophytes
to chlorophytes, as well as a broad range in duration (days to months) of plastid retention
within host taxa (Rumpho et al. 2011). This variability has led researchers to
disparate characterizations of the kleptoplastic condition ranging from an ecological
mechanism facilitating metabolic flexibility in the host taxa to an early evolutionary
stage in permanent plastid acquisition (Gast et al. 2006, Stoecker et al. 2009).
Foraminifera are protists characterized by a network of granuloreticulopods extending
from openings in an external calcite or agglutinated test (Pawlowski et al.
1Department of Biology, Coastal Carolina University, Conway, SC 29528. *Corresponding
author - mcevasco@coastal.edu.
Manuscript Editor: Pamela Hallock
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2013). Within the foraminifera, multiple genera are reported to harbor kleptoplasts:
Bulimina, Elphidium, Haynesina, Nonion, Nonionella, Reophax, and Stainforthia
(Pillet et al. 2011). The functional significance of these kleptoplasts to the foraminiferal
host cell, however, remains unresolved. Feeding experiments conducted
by Corriea and Lee (2002b) found that foraminifera preferentially retained diatom
plastids and then emitted auto-fluorescence after 8 weeks incubation in a 12-h
light/12-h dark cycle.
The purpose of this work was to document foraminiferal kleptoplasty using
confocal imaging as a tool to observe and characterize the condition in living
specimens. Our research tested the hypothesis that kleptoplasty is an observable
condition characteristic of select foraminiferal taxa resident in the salt marshes of
coastal South Carolina. Using field collections paired with morphological observations,
molecular identification, and confocal imaging, we explored the presence and
character of the kleptoplastic condition in living foraminferal specimens.
Methods
Specimen collection
We collected specimens for this study at Hog Inlet (33°50'38''N, 78°35'48''W)
of Waties Island within Anne Tilghman Boyce Coastal Reserve, and from the North
Inlet (33°19'28''N, 79.10'29.25''W) of Hobcaw Barony within Winyah Bay National
Estuarine Research Reserve. Both the Waties Island and North Inlet collection sites
are shallow, ocean-dominated, and subject to semi-diurnal tides resulting in fluctuating
water depths, temperatures, and salinities.
We collected specimens from both sites at low tide when the water level of the
creeks was <1 m such that the top 1 cm of creek-bed sediments were easily removed
by trowel. We took 10-cm3 sediment samples from the center of each creek bed and
from the base of the Spartina alterniflora (Loiseleur-Deslongchamps) (Smooth
Cordgrass)-dominated vegetation that lined the creek banks. We collected samples
of the fine-grained sand and silty loam creek sediments in triplicate and transferred
them into individual glass containers containing seawater for transport.
Specimen preparation
At the Coastal Carolina University, Conway, SC, we sieved samples and allowed
the 125-μm to 500-μm fractions to settle for 12 h in filter-sterilized seawater at 23
°C. We used sterile-transfer pipets to remove 0.2-ml increments from the top layer
of sediment slurry to a slide where, under magnification, we used sable brushes to
search for viable foraminifera, which we identified by the presence of extended granuloreticulopodia
in combination with distinctive pink to light brown cytoplasmic
coloring. We transferred living specimens to petri dishes containing sterile seawater.
Samples were subjected to additional cleaning with brushes and several transfers in
sterile seawater, placed on a 45-μm membrane filter, and rinsed by vacuum filtration
with 250 ml of sterile seawater. We selected potential kelptoplastic specimens
that met general morphological criteria characteristic of either the genus Elphidium
(de Montfort 1808) or the genus Haynesina (Banner and Culver 1978). We focused
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our collection efforts on these genera because they have been observed to engage in
plastid retention in locations along the coast of the northeastern US (Correia and Lee
2002 a, b) and the northwestern coast of Europe (Cedhagen 1991, Lopez 1979, Pillet
et al. 2011). Additionally, both genera had been previously reported as resident in
the salt marshes and nearshore habitats of North Inlet (Collins et al. 1995). Although
these potentially kelptoplastic genera are recognized by their planispiral involute
chamber arrangement, rounded to sub-acute peripheral angle, and a moderately depressed
umbilical area, species-level determinations are much more contentious due
to distinguishing characteristics that are not easily observed externally, as well as to a
high degree of phenotypic plasticity (Miller et al. 1982, Pillet et al. 2013, Schweizer
et al. 2008); thus, we identified our specimens to genus.
We kept potential kleptoplastic specimens in darkness for 5 days to allow for
the complete digestion of any microalgae or cyanobacteria within their cytoplasm.
We then divided remaining living specimens into subsets to be prepared for either
molecular analysis or confocal microscopy. To eliminate any residual surface contaminants,
we transferred both sets of specimens to 0.25-M EDTA solutions for
20 min to dissolve a majority of the calcite test encasing the foraminiferal cell via
chelation prior to either confocal imaging or DNA extraction.
Molecular techniques and analyses
DNA extraction and PCR. We extracted DNA from single foraminiferal specimens
including potential kleptoplastic genera Haynesina and Elphidium and the
non-kleptoplastic genus Quinqueloculina using the DNeasy® Plant Mini Kit (Qiagen
Inc., Valencia, CA). To efficiently extract nucleic acids, we used sterile blades
under 40x magnification to break specimens apart, and a micro-mortar and pestle to
pulverize the cellular contents within the DNeasy (Qiagen) lysis buffer. Following
extraction, we performed total DNA quantification using the Qubit® 2.0 Fluorometer
(Life Technologies, Grand Island, NY).
Using an approach modified from Pillet et al. (2011), we performed PCR amplification
on each specimen using 3 sets of primers: 18S foraminifera-ribosome
specific, 16S plastid specific, and 18S diatom-ribosome specific (Table 1). We
carried out the PCR reactions in a total volume of 25 μl using Ready-To-Go PCR
Table 1. Primers used to amplify foraminiferal and kleptoplastic sequences.
Target Primer name Oligonucleotide sequence Source
Diatom ribosome
DiatSSUF (for) 5'ACATCCAAGGAAGGCAGC A'3 Pillet et al. 2011
DiatSSUR (rev) 5'CTCTCAATCTGTCAATCCTCA'3 Pillet et al. 2011
Diatom plastid
PLA491F (for) 5'GAGGAATAAGCATCGGCTAA'3 Fuller et al. 2006
OXY1313R (rev) 5'CTTCACGTAGGCGAGTTGCAGC'3 West et al. 2001
Foraminifera ribosome
sA10 (for) 5'CTCAAAGATTAAGCCATGCAAGTGG'3 Schweizer et al. 2008
s17 (rev) 5'CGGTCACGTTCGTTGC'3 Schweizer et al. 2008
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beads (GE Biosciences, Pittsburgh, PA) with an amplification profile of 30 cycles
of 30 s denaturation at 94 °C, 30 s of annealing at 50 °C, and 45 s of extension at
72 °C, followed by a final 5-min extension at 72 °C. We used amplification products
from the foraminiferal-specific primers to determine the taxonomic identity
and phylogenetic affinities of the specimens. We used the differential amplification
patterns arising from algal-specific primers (plastid and ribosome) to indicate possible
plastid retention within a given foraminiferal host. Specifically, we selected
as likely kleptoplastic those specimens that generated amplification products from
only the plastid primers and not the ribosomal primers. Conversely, we removed
from further analyses the specimens generating PCR products from both sets of
algal primers (plastid and ribosomal) because the presence of algal-cell material
(other than plastid) within the host foraminifera obfuscated a determination of
kleptoplasty. We cleaned all amplification products selected for molecular analysis
using ExoSAP-IT ® (Affymetrics, Santa Clara, CA) and sent the samples to Selah
Genomics (University of South Carolina, Greenville, SC) for sequencing.
Phylogenetic analyses. We used the Geneious® 6.1.7 software package (Biomatters,
Aukland, NZ) to edit sequence data. We conducted BLASTn searches
(Altschul et al. 1990) to compare the sequences recovered in this study with
those in the NCBI database and included in phylogenetic reconstructions those
sequences from the NCBI database with high similarity to the query sequence.
We employed MAFFTv7.017 (Katoh et al. 2005) implementing a progressive fast
Fourier transform (FFT-NS-2) with a gap-opening penalty of 1.76 to perform alignments.
Aligned sequences were then phylogenetically analyzed under the maximum
likelihood optimality criterion implemented in PhyML 3.0 using a nearest neighbor
interchange-topology search (Guindon and Gascuel 2003). Statistical selection
of nucleotide-substitution models for phylogenetic likelihood analyses were determined
using jModelTest by employing multiple selection approaches such as
the likelihood ratio test and Akaike information criteria (Darriba et al. 2012). We
selected as optimal for both the (746-nucleotide, 20-terminal) plastid-data set (-lnL
= 2724.19) and the (2149-nucleotide, 19-terminal) foraminiferal-data set a simple
Jukes-Cantor model (JC69) in which both base frequencies and substitution rates
are equal-elected (Jukes and Cantor 1969). We determined branch support using
1000 bootstrap replicates implemented within the PhyML software.
Microscopic techniques and analyses
We used the confocal microscope (Zeiss 710) at the Hollings Cancer Center
(Medical University of South Carolina, Charleston, SC) to image the prepared
living foraminiferal cells. We produced composite images of the specimens using
the plastid auto-fluorescence overlaid with differential interference contrast (DIC)
microscopy and made optical sections of specimens at 1–2-μm intervals through
the specimen to determine the size and position of kleptoplasts within the foraminiferal
chambers. In addition, we performed spectral scans on a subset of plastids
to determine the wavelength-emission profile of the auto-fluorescence and used
Zeiss LSM image browser software (version 4.2) to analyze the confocal images.
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Specifically, we depth-coded images to determine the distribution of plastids within
the specimens, and used electronic calipers to determine plastid dimensions.
Results
Molecular data
We recovered 23 living potentially kleptoplastic foraminifera from the Waties
Island collection (October 2012). This number represented a total number of specimens
from 3 separate collection sites within the tidal creek. The collections from
North Inlet (May 2013) were similarly sparse and patchy—24 specimens. The estimated
population density of kleptoplastic specimens was 7.6 x 102/m2 for Waties
Island and 6.3 x 102/m2 for North Inlet collections. Of the Waties Island foraminifera
that we morphologically classified as potentially kleptoplastic, 15 belonged
to the genus Elphidium and 8 to Haynesina. From North Inlet, 16 belonged to the
genus Elphidium, while only 3 were identified as Haynesina. After specimen processing
(cleaning and incubation), a total of 13 and 14 viable specimens remained
from the Waties Island and North Inlet sites, respectively. Of these 27 foraminiferal
specimens that we subjected to DNA extraction and PCR, 19 specimens positively
amplified plastid sequences, though only 4 of those positive for plastid-sequence
amplification were also negative for algal ribosomal-sequence am plification.
Phylogenetic analysis of the foraminifera engaged in kleptoplasty confirmed that
they belonged to the genera Elphidium and Haynesina (Fig. 1). When compared to
other rotaliid foraminiferal sequences, the 3 kleptoplastic Elphidium specimens
collected from Waties Island and 2 Elphidium specimens from North Inlet form a
well bootstrap-supported (90) clade containing Elphidium exacavatum (Terquem)
sequences. A North Inlet specimen morphologically identified as belonging to the
genus Haynesina was placed within a clade, albeit with poor support values (59),
with the taxon Haynesina germanica (Ehrenberg) and 2 Elphidium species. We
used a non-kelptoplastic foraminiferal specimen (Quinqueloculina) collected at
Waties Island as an outgroup sequence along with a Quinqueloculina seminulum L.
ribosomal sequence from the NCBI database.
Only 4 of the 6 plastid amplicons from the set of amplification products showing
a kleptoplastic pattern generated sequence data sufficient for phylogenetic analysis
with 17 additional diatom and bacterial sequences from the NCBI database (Fig. 2).
Phylogenetic placement of these sequences indicates that they are diatom in origin.
All 4 of the sequences (Waties Island Elphidium and Haynesina and North Inlet
Elphidium amplifications) appear within a clade containing a marine raphid-diatom
sequence from the genus Amphora (Ehrenberg ex Kützing). This clade has moderate
(86) bootstrap support.
Microscopic data
Confocal imaging of the Waties Island and North Inlet foraminifera after a
5-d period of starvation in darkness identified autofluorescence originating from
distinct structures within the foraminiferal cell (Fig. 3). We processed the reconstruction
of z-stacked optical sections taken at 2-μm intervals into 3-dimensional
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representations of specimen fluorescence to provide a means of assessing the
number, position, and size of these active kleptoplastids within select depth strata
of living foraminifera. Spectral analysis of the individual structures consistently
showed emissions maxima at 672 nm, which corresponded to the spectral emissions
profile of chlorophyll a, and supported a photosynthetic plastid origin for
the fluorescence (Grabowski et al. 2001). Enumeration data compiled from 4
specimens identified an average of 9.6 ± 0.7 x 102 actively fluorescing plastids per
foraminiferal host. Although the enumeration data presented here provide only a
very coarse estimate of the number of plastids actively engaged in photosynthesis
within a single foraminiferal host because it was drawn from a small sample size,
the numbers correspond to previously reported estimates of plastid retention (Lopez
1979). Plastids appear to be distributed throughout the foraminiferal chambers as
is shown in the 3-D reconstructions of optical sections imaged between 20 μm and
80 μm (Fig. 3A) and between 20 μm and 120 μm (Fig. 3D). Data collected for 64
plastids measured from 4 chambers within Elphidium and Haynesina specimens
Figure 1. 18S rDNA phylogeny of foraminiferal specimens using a JC69 model as implemented
in PhyML. Sequences from field collections are indicated in bold. NCBI accession
numbers are given after the taxon name. Bootstrap values (>50) are indicated at the nodes.
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show a mean maximum length of 5.67 μm and width of 2.43 μm. We derived plastid
dimensions from the diameter of autofluorescent areas measur ed as a proxy for
plastid size (Fig. 3C, E; Table 2). We selected this method to exclude degraded
plastids from measurement. The measurements recorded are consistent with plastid
dimensions reported for raphid diatoms (Sato et al. 2013). We color-delineated
depth coding in which the strength of autofluorescence detected at selected depth
strata and used to determine the relative distribution of fluorescent signal within a
foraminiferal host was applied to depths between 10 and 120 μm (Fig. 3F, G, H).
Figure 2. 16S rDNA phylogeny of plastids retained within foraminiferal specimens using
a JC69 model as implemented in PhyML. Sequences from field collections are indicated in
bold. NCBI accession numbers are given after the taxon name. Bootstrap values (>50) are
indicated at the nodes.
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Figure 3. Confocal images of foraminiferal kleptoplasty. (A–C) Living Elphidium specimens
imaged with confocal microscopy. (A) 3-D reconstruction of 2-μm optical sections
imaged 20–80 μm below the cell surface. (B) DIC-image overlay to show position of
plastids within specimen chambers. (C) Diameter of autofluorescent areas as a proxy for
plastid size. (D) 3-D reconstruction of 2-μm optical sections of plastid autofluorescence
imaged 20–120 μm below the cell surface in a living Haynesina foraminfer. (E) Diameter
of autofluorescent areas within chambers as a proxy for plastid size. (F–H) Depth-coded
image showing the concentration of fluorescent signal within a living Haynesina specimen.
(F) Fluorescent signal 10–40 μm below surface of the specimen. (G) Fluorescent signal
from a depth range of 40–80 μm below the cell surface. (H) Fluorescent signal representing
depths of 10–120 μm. All scale bars are 100 μm unless otherwise indicated.
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Signal was detected throughout these sampled depth strata with the majority originating
from depths 40–80 μm below the cell surface (Fig. 3G).
Discussion
We anticipated the identification of kleptoplasty in foraminifera (Elphidium and
Haynesina) from both Waties Island and North Inlet based upon the broad distribution
profiles of these genera and from reports of these taxa inhabiting similar
habitats along the east coast of the US (Abbene et al. 2006, Culver and Horton
2005, Cushman 1936). Moreover, Collins et al. (1995) determined, based on the
observation of test (shell) characteristics, that a significant portion (22%) of the
total (non-living) foraminifera collected from a North Inlet marsh transect were
members of the genus Elphidium. In comparison to total (live and dead) population
estimates of kleptoplastic genera drawn from other locations (e.g., total Elphidium
density of 105/m2 by Lopez [1979] from Limfjorden, Denmark), the densities of living
kleptoplastic foraminifera from both collection sites were extremely low—7.6
x 102/m2 and 6.3 x 102/m2.
Molecular phylogenetic analysis supported the classification of the specimens
collected within the kleptoplastic genera Elphidium or Haynesina and revealed
phylogenetically structured sequence variability. Because we only sequenced 6
kleptoplastic specimens and based our identifications on the strict criteria imposed
in determining kleptoplasty, the taxonomic implications of the sequence variability
require further exploration in future analyses. It is notable that in Figure 1 all but
one of the foraminifera morphologically identified as Elphidium were found within
a strongly bootstrap-supported (90) clade that also contained 2 E. excavatum sequences.
The other Elphidium sequence belonged to a separate, poorly supported
(54) clade containing 3 different Elphidium sequences. Moreover, the placement
of the North Inlet Haynesina specimen within a poorly supported (59) clade containing
both Elphidium (family Elphidiidae) and Haynesina (family Nonionidae)
sequences is consistent with the complex paraphyletic relationships of these taxa
recovered by Pillet et al. (2013). In addition to improving taxon sampling, the
use of additional loci may help to resolve relationships among these taxa because
both of these kleptoplastic genera demonstrate rapid evolution relative to other
foraminifera (Schweizer et al. 2008). This characteristic is particularly relevant
to members of the Elphidiidae in which recent analyses contingent upon outgroup
designation recovered variable and complex paraphyletic relationships, including
the placement of Haynesina within the Elphidiidae (Pillet et al. 2013).
Table 2. Mean dimensions (μm) of plastids functionally retained within foraminiferal cells.
Foraminifera 1 2 3 4
Specimen Length Width Length Width Length Width Length Width
Chamber 1 4.75 3.00 5.25 2.75 4.50 3.00 5.50 2.00
Chamber 2 6.00 2.50 5.75 2.13 5.50 2.25 6.25 1.75
Chamber 3 5.13 3.25 6.50 3.25 6.25 1.75 5.75 1.50
Chamber 4 5.00 2.25 6.25 3.00 6.00 2.00 6.00 2.50
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The identity of retained plastid sequences as diatom in origin agrees with the
analyses presented in Pillet et al. (2011). As shown in Figure 2, the placement of
these sequences within a clade containing a broadly distributed benthic marine
diatom, Amphora coffeaeformis (Agardh) Kützing, indicates that plastid acquisition
is reflective of the hosts’ primary food source (diatoms). This result is also in
agreement with the results of the feeding experiments of Correia and Lee (2000)
that show Amphora coffeaeformis to be the preferred food choice of E. excavatum.
Although the plastid sequences are moderately supported sister taxa, the low number
of sequences recovered prevents us from drawing any robust conclusions about
the diversity of kleptoplastid donors and indicates the need for further sampling.
The loss of plastid sequences may indicate multiple diatom taxa contributing to the
kleptoplastic condition within a single host cell, as was evident in the foraminiferal
specimens investigated by Pillet et al. (2011). To overcome this issue, we are currently
cloning PCR amplifications of plastid sequences into bacterial vectors prior
to sequencing in our lab.
Data generated from confocal imaging supported molecular phylogenetic inferences
by providing evidence of functional diatom-derived plastids retained
within live foraminiferal hosts. In agreement with TEM data presented in Cedhagen
(1991), Correia and Lee (2002a), and Lopez (1979), confocal microscopy provided
the structural detail of retained plastids and provides images of the kleptoplastic
condition in live specimens. Correia and Lee (2002b) used autofluorescence data
from a random sampling of individual optical sections as a means of determining
plastid longevity after prolonged foraminiferal starvation. Using the 3-dimensional
reconstructions from live foraminiferal specimens optically sectioned at a set intervals,
confocal microscopy provides a means to create a functional snapshot, and
provides data on the spectral profile, number, size, and position of kleptoplasts
within the cell.
Such data can be used in combination with ultrastructural TEM imaging and
molecular sequence data to characterize foraminiferal kleptoplasty. For example,
results from this study indicate that after 5 d of starvation, living heterotrophic
foraminifers can actively emit chlorophyll a autofluorescence from >288 photosynthetic
plastids.
Despite the starvation period being 48 h longer, the numbers of plastids retained
per specimen observed in this study are lower than those reported in Lopez (1979)
for E. excavatum (1.2 ± 0.7 x 103), but may be reflective of confocal imaging detecting
only non-degraded plastids. This observation is worth further investigation
because it may indicate a period of stability after the kleptoplastic condition is
established rather than an immediate onset of plastid degeneration.
The emissions spectra, size, and distribution patterns of plastids observed in
the Waties Island and North Inlet specimens are consistent with previously reported
phylogenetic and ultrastructural data implicating diatom origins for plastids
retained in Elphidium and Haynesina specimens. When considered together, the
confocal data support a scenario in which the kleptoplastic condition within living
foraminifera is established when the plastids of diatoms being phagocytosed are
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vacuolated and transferred throughout the cell. Characterization of kleptoplasty in
foraminfera as a phenomenon of ecological convenience, a kind of opportunistic
photosynthetic farming, or alternatively, as a stage in ongoing symbiotic evolutionary
processes, remains an open question (Bernhard and Bowser 1999, Stoecker et
al. 2009). Using comparative data from multiple methodological approaches is
critical to understanding the many unknown parameters of this enigmatic phenomenon
as it relates to the complexity of microbial processes in salt-marsh habitats.
Acknowledgments
This project was supported by an NSF EAGER DEB grant (0935333), the Belle Baruch
Foundation Grant 35-2969, and the CCU PEG-grant (17-4802).
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