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Revista de Biología Tropical, ISSN: 2215-2075, Vol. 72: e57898, enero-diciembre 2024 (Publicado Set. 17, 2024)
Yeasts of Pichia (Pichiaceae) dominate the mycobiome of Hermetia illucens
(Diptera: Stratiomyidae) larvae during urban composting
Mónica Vallejo-Arróliga1; https://orcid.org/0000-0001-9651-891X
Keilor Rojas-Jimenez1*; https://orcid.org/0000-0003-4261-0010
1. Escuela de Biología, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica, monica.vallejo@ucr.ac.cr,
keilor.rojas@ucr.ac.cr
Received 07-XII-2023. Corrected 30-VII-2024. Accepted 07-IX-2024.
ABSTRACT
Introduction: Hermetia illucens is a fly found worldwide in tropical and temperate regions that feeds on decay-
ing organic matter in its larval stage, which makes them useful to accelerate composing processes. Bacterial
component on the larval guts that helps to degrade organic matter is well studied, however fungal communities
information is more scarse, specially in tropical regions.
Objective: To determine fungal communities in the gut of H. illucens larvae naturally occurring during urban
composting processes in a tropical region.
Methods: ITS sequencing was employed to characterize fungal communities present in H. illucens larval gut.
Results: The analysis of amplicon sequence variants (ASVs) unveiled a notable dominance of Saccharomycetales,
being yeasts of the genus Pichia the most abundant. Other relatively abundant yeasts were Candida and
Galactomyces and the genus Archaeospora from Archaeosporales. The last two groups not being reported in
H. illucens before.
Conclusions: Yeasts of the genus Pichia are the most abundant group, this result is in concordance with previous
studies which suggest a stable insect-yeast relation. The description of previously unreported fungal groups high-
lights the importance of continuing to explore the mycobiome dynamics of this larva. This study offers insight
into the mycobiome of naturally occurring H. illucens larvae in a tropical region.
Key words: fungi; mycobiome; yeasts; tropics; urban composting.
RESUMEN
Levaduras de Pichia (Pichiaceae) dominan el micobioma de las larvas de Hermetia illucens
(Diptera: Stratiomyidae) durante el compostaje urbano
Introducción: Hermetia illucens se distribuye mundialmente en regiones tropicales y templadas. En su estado
larval se alimenta de materia orgánica en descomposición, lo que las hace útiles para acelerar los procesos de
compostaje. Se han realizado diversos estudios sobre el componente bacteriano de los intestinos de las larvas que
ayuda a degradar la materia orgánica, sin embargo, información sobre las comunidades de microhongos es más
escasa, especialmente en regiones tropicales.
Objetivo: Determinar el micobioma presente en los intestinos de las larvas de H. illucens que se desarrollaron
naturalmente en compostajes urbanos en una región tropical.
Métodos: Se realizó secuenciación ITS para caracterizar las comunidades de microhongos presentes en el intes-
tino de las larvas.
Resultados: El análisis de variantes de secuencia de amplicones (ASV) reveló una notable dominancia de
Saccharomycetales, siendo las levaduras del género Pichia las más abundantes. Otras levaduras relativamente
https://doi.org/10.15517/rev.biol.trop..v71i1.57898
BOTANY AND MYCOLOGY
2Revista de Biología Tropical, ISSN: 2215-2075 Vol. 72: e57898, enero-diciembre 2024 (Publicado Set. 17, 2024)
INTRODUCTION
The black soldier fly (BSF), Hermetia illu-
cens (Linnaeus, 1758), is found worldwide in
tropical and temperate regions (Kaya et al.,
2021), mainly in manure and food waste dump
grounds (Kim et al., 2008). In its larval state,
it feeds on large amounts of decaying organic
matter, which makes it very useful for accelerat-
ing composting processes, and able to convert
low quality biomass into nutritional valuable
proteins (Czekała et al., 2020; Diener et al.,
2009). Furthermore, in its adult state, it is not
considered a pest or a disease vector, making
BFS larvae production safe and environmentally
friendly (Joosten et al., 2020). These character-
istics have increased BSF rearing and research
on its microbiota, which is fundamental for the
bioconversion process (Jiang et al., 2019).
The bacterial component of the BSF micro-
biome has been extensively studied, and a
core bacterial community has been described
(Cifuentes et al., 2022; IJdema et al., 2022;
Jiang et al., 2019). Information about how
diet source, insect developmental stage, and
location in the digestive tract influence bacte-
rial communities is also available (Bruno et
al., 2019; Querejeta et al., 2023; Wynants et al.,
2019). Fungal communities, on the other hand,
have been much less studied and there is not
enough data yet to elucidate if there is a core
fungal community. In the last few years, there
have been some studies about fungal composi-
tion using larvae reared under laboratory con-
ditions in different substrates (Boccazzi et al.,
2017; Klüber et al., 2022a; Klüber et al., 2022b;
Tanga et al., 2021; Tegtmeier et al., 2021).
However, information about the fungal com-
position of naturally occurring larvae is scarce,
and most of the studies have been developed
in subtropical or temperate regions, despite the
high abundance of BSF in tropical regions (da
Silva & Hesselberg, 2020).
Tropical regions, because of their intrinsic
abiotic characteristics such as heat and high
humidity, are recognized for concentrating the
greatest species diversity on the planet (Brown,
2014), and fungal diversity is not an exception
to this (Aime & Brearley, 2012; Boekhout et al.,
2021). Analyzing mycobiomes on BSF could
allow the identification of fungal species or
strains with unique and important character-
istics, such as the capacity to degrade complex
substrates that can be useful in industry and
bioremediation (Østergaard & Olsen, 2011). It
might also contribute to the global problem of
the identification of new antimicrobials (Gil-
Rodríguez & Garcia-Gutierrez, 2021).
Urban compost, on the other side, has an
increasing importance due to the rise in organic
waste production in the last few decades. Fungi
play a vital role in organic matter degradation
and are responsible for compost maturation
(Dehghani et al., 2012), thus characterizing
mycobiomes related to composting process
might help to make the process more efficient
and faster (El Hayany et al., 2022). It can also
help to discover thermotolerant microorgan-
isms, as temperatures during composting can
reach up to 70 °C due to the heat produced
by exergonic aerobic reactions derived from
microbial metabolism (Hemidat et al., 2018).
Thermotolerant fungi have a special interest in
industry because of the thermostability of their
abundantes fueron Candida y Galactomyces y el género Archaeospora de Archaeosporales. Los dos últimos grupos
no han sido reportados previamente en H. illucens.
Conclusión: Determinamos que las levaduras del género Pichia son el grupo más abundante. Este resultado
concuerda con estudios previos, lo que sugiere una relación estable entre estos dos organismos. La descripción
de grupos de hongos no reportados previamente resalta la importancia de continuar explorando la dinámica del
micobioma de esta larva. Este estudio proporciona información sobre el micobioma de las larvas de H. illucens
que se presentan naturalmente en una región tropical.
Palabras clave: hongos; microbioma; levaduras; trópico; compostaje urbano.
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enzymes, such as thermostable carbohydrate
active enzymes (CAZymes) (Di Piazza et al.,
2020; Gabriel et al., 2021), as they could be
used to improve industrial processes and have
biotechnological applications (Cruz-Ramírez
et al., 2012).
In this study, we characterize the fungal
communities present on BFS larva gut naturally
occurring during urban composting process-
es in a tropical region using Illumina high-
throughput sequencing of the ITS region. Our
aim is to identify the principal fungal groups
and to compare them with previous reports
under different conditions. This information
can contribute to a better understanding of the
ecology of this species, the composting micro-
bial dynamics, and it can set a precedent for
further research on the possible industrial and
biotechnological applications of the microor-
ganisms found.
MATERIALS AND METHODS
Sample collection and dissection: A total
of five H. illucens larvae (two to three weeks
old) (Fig. 1) were collected from household
compost produced in a tumbling composter
containing only common fruits and vegetables
typical of the Costa Rican diet (Furtado et
al., 2009), including both raw and cooked
materials. To collect the larvae, the composter
was rotated, and larvae were taken randomly.
Collections were made in Heredia, province
of Costa Rica (10°0’38.376’’ N & 84°7’47.964’’
W) in May 2023, where the mean temperature
is 27 °C and when H. illucens larvae are found
more frequently. After collection, larvae were
kept in Falcon tubes and starved for eight
hours to empty their ingested contents and
allow the transient mycobiome to pass through.
They were incubated at -80 °C for 10 min
for devitalization. Disinfection was made by
submerging larvae for 30 seconds in ethanol
90 %, 30 seconds in sterile distilled water, 30
seconds in sodium hypochlorite 2 %, and 30
seconds in distilled water. One millimeter of the
anterior part of the larvae were cut off and the
haemocoel was opened laterally using sterile
scissors. The guts were carefully removed using
sterile forceps and transferred individually into
Eppendorf tubes containing 250 μl of 1X PBS.
Samples were stored at -20 °C until their use.
Fig. 1. Life cycle of Hermetia illucens. The development stages and average duration for each stage are illustrated (modified
from De Smet et al., 2018). Only the larval stage, distinguishable by its whitish color, was used in this study.
4Revista de Biología Tropical, ISSN: 2215-2075 Vol. 72: e57898, enero-diciembre 2024 (Publicado Set. 17, 2024)
Molecular analyses: Guts were macer-
ated with sterile pistils, and DNA was extracted
individually using a DNA isolation kit (Pow-
erSoil, Qiagen, USA) following the manufac-
turers instructions. The eukaryotic amplicon
library was generated by amplifying the ITS2
region using primers ITS3-2024F (5’-GCATC-
GATGAAGAACGCAGC-3’) and ITS4-2409R
(5’-TCCTCCGCTTATTGATATGC-3’). Poly-
merase chain reaction (PCR) amplification of
targeted regions was performed using specific
primers connecting with barcodes. The PCR
program used the following conditions: 5 min
at 94 °C; 35 cycles of (30 s at 94 °C; 30 s at 50–67
°C; 30 s at 72 °C); 7 min at 72 °C. The PCR
products with the proper size were selected by
1 % agarose gel electrophoresis. Each samples
exact amount of PCR products was pooled,
end-repaired, A-tailed, and further ligated with
Illumina adapters. Libraries were sequenced
on a paired-end Illumina platform to generate
250 bp paired-end raw reads (Illumina Nova-
seq, Novogene Bioinformatics Technology Co.,
Ltd, CA, USA).
Bioinformatic analysis: We used the
DADA2 version 1.21 to process the Illumina
sequenced paired-end fasta files and to generate
a table of amplicon sequence variants (ASVs),
which are higher resolution analogs of the tra-
ditional OTUs (Callahan et al., 2016). Briefly,
we removed primers and adapters, inspected
the quality profiles of the reads, filtered and
trimmed sequences with a quality score < 30,
estimated error rates, modeled and corrected
amplicon errors, and inferred the sequence vari-
ants. Then, we merged the forward and reverse
reads to obtain the full denoised sequences,
removed chimeras, and constructed the ASV
table. We assigned taxonomy to the ASVs with
the function assignTaxonomy, of DADA2. For
the fungal taxonomic assignment, we used the
UNITE ITS database version 8.3, with default
parameters. We carried out a second taxonomic
assignment of the fungal ASVs using the tool
IDTAXA of DECIPHER with the same ver-
sion of UNITE as a reference and a confidence
threshold > 60 %, and additionally, a third
classification using the Classifier tool (Wang
et al., 2007) implemented in the Ribosomal
Database Project using as reference the Warcup
Fungal ITS trainset V2 database (Deshpande
et al., 2016). We verified and manually curated
the consistency between the taxonomic assign-
ments of the different programs. In cases of
discrepancies, a comparison with the BLAST
tool of NCBI was applied (Percent identity >
98 %). Sequence data were deposited at the
NCBI Sequence Read Archive under accession
number PRJNA1048874. Statistical analyses
and visualization of results were performed
with the R statistical program (R Core Team,
2023) and the Rstudio interface. Package Vegan
v2.6-4 (Oksanen et al., 2022) was used to calcu-
late alpha diversity estimators. The non-metric
multidimensional scaling analyses (NMDS)
weas generated using the ASV dataset, nor-
malized into relative abundances and then
converted into a Bray–Curtis similarity matrix.
RESULTS
After the removal of low-quality reads, a
total of 210 916 sequences were obtained from
the samples. The average number of sequences
per sample was 42 183 (ranging from 21 798
to 59 107). The fungal community was com-
posed of 329 ASVs, according to the analysis of
sequences of the ITS region. A total of 8 phyla,
21 classes, 40 orders, 67 families and 117 gen-
era were identified. Ascomycota was the most
abundant phylum with 192 561 of the sequenc-
es and 77 % of the ASVs while Glomeromycota
corresponded to 15 305 of the sequences and
3 % of the ASVs. Other less abundant phyla
were Rozellomycota, Basidiomycota, Kickxel-
lomycota, Monoblepharomycota, Mortierel-
lomycota, and Mucoromycota (Supplemental
Material Table 1).
The mycobiome in the guts of H. illucens
exhibited a relatively similar composition across
samples (Fig. 2). The order with the high-
est relative abundance was Saccharomycetales,
reaching 92.4 % in sample M1JL and 76.2 % in
sample M5JL. Archaeosporales was the second
most abundant order in four of the samples,
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with relative abundance ranging from 28.6 % to
10.5 %. In sample M5JL, however, Archaeospo-
rales was not prominent; instead, Rozellida was
the second most abundant order at 6.8 %. Nota-
bly, sample M5JL displayed higher diversity,
with 9.1 % of sequences corresponding to 38
orders with low abundance (SMT1). Addition-
ally, sample M5JL showed a higher presence
of Erysiphales and Capnodiales, with relative
abundances of 4 and 2.5 %, respectively. The
most abundant genera of Saccharomycetales
were Pichia, Galactomyces, and Candida, while
Archaeospora and Paramicrosporidium were the
most abundant genera of Archaeosporales and
Rozellida respectively.
The heat map (Fig. 3) illustrates variations
in the relative abundances of the most abun-
dant fungal genera in the sample. Pichia, the
dominant genus within the Saccharomycetales,
has a mean relative abundance of 65 %, rang-
ing from 75.3 % (M3LJ) to 47.8 % (M1JL). In
samples M1JL to M4JL, Galactomyces shows
relative abundances ranging from 18.2 to 7.0 %,
Candida from 8.4 to 8.8 %, and Archaeospora
from 14.8 to 4.7 %. These three genera have
low relative abundances in sample M5JL, where
other genera such as Paramicrospodium (6.8 %)
and Blumeria (4.0 %) are more predominant.
Regarding the alpha diversity indices, the
sample with the highest species richness pre-
sented 137 ASVs, while the sample with the
lowest species richness presented 70 ASVs. The
highest average value of the Shannon Index was
2.27 and the lowest was 1.85 (Fig. 4A). How-
ever, the composition of fungal communities
associated with all of the samples presented
values close to 0.0 in the NDMS analysis, indi-
cating they are relatively similar (Fig. 4B).
DISCUSSION
In this study, we found that yeasts, in par-
ticular the genus Pichia, dominate the mycobi-
ome of the intestinal tract of H. illucens larvae
during urban composting. Recently some stud-
ies have analyzed fungal communities on BSF,
most of them using colonies of larvae that
were reared under laboratory conditions with
different diets (Boccazzi et al., 2017; Klüber
et al. 2022a; Shokry et al., 2023; Tanga et al.
2021). To our knowledge, only one study has
analyzed the fungal composition of naturally
occurring BSF larvae from household composts
(Vitenberg & Opatovsky, 2022). All of these
studies were made in regions with subtropical
or temperate conditions, therefore, the present
study provides a first insight into the fungal
communities of naturally occurring BFS larvae
in a tropical region.
The dominance of Pichia found in this
investigation slightly differs with the previous
Fig. 2. Relative abundance of the fungal communities in
the guts of H. illucens larvae at order level during an urban
composting process.
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Fig. 3. Relative abundance of fungi associated with H. illucens larvae at genus level (more abundant genera are shown).
Fig. 4. A. Alpha diversity values of fungal communities of H. illucens larvae. The upper panel represents the richness of
Amplicon Sequence Variants (ASVs), while the panel below shows the values of the Shannon Index. B. NMDS of the fungal
community structure of the five H. illucens larvae samples.
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study of BFS larvae reared on household com-
post by Vitenberg & Opatovsky (2022), where
the most abundant genus was Candida (up to
70 % of the sequences), while Pichia was not
common (less than 10 % of the sequences).
However, Pichia has been reported as a com-
mon genus in other studies using different
substrates, suggesting a stable association with
BFS larval gut. Boccazzi et al. (2017), using
next-generation sequencing, reported Pichia
as the most abundant genus in larvae fed on
vegetable waste, comprising 53.2 to 93.7 % of
the sequences. Similarly, Tanga et al. (2021)
observed that Pichia was the only genus that
was not substrate specific, as it prevailed as an
abundant group on different substrates (brew-
ers’ spent grains, kitchen food waste, poultry
manure, and rabbit manure), and reaching up
to 70 % of the sequences when reared on brew-
ers’ substrate. Klüber et al. (2022a) isolated
Pichia from larvae reared on lignocellulose-rich
substrates, such as palm kernel meal. In addi-
tion, Shokry et al. (2023) isolated it from larvae
grown on substrates made of chicken feed,
waste from fish farms, chicken nonedible parts,
and kitchen waste.
Insect-yeast relations have been reported
in different insects of Hymenoptera, Coleop-
tera, and Diptera, where H. illucens belongs
to (Malassigné et al., 2021). The acquisition of
yeast could be from the environment (Morales-
Rodríguez et al., 2021; Rassati et al., 2019) but
it could also be vertically transmitted from
adults to larvae (Sacchi et al., 2008). This
was recently demonstrated on Drosophila flies
where yeasts acquired at the larval stage main-
tained through metamorphosis, and adult life,
and were transmitted to offspring (Guilhot
et al., 2023). The benefits obtained by insects
from these relations are varied. One of the most
important is nutritional, as yeast can provide
insects with digestive enzymes, essential amino
acids, vitamins, and sterols (Mendes et al., 2012;
Stefanini, 2018). It has also been suggested
that yeasts could play a role in the removal of
potentially toxic compounds present in the
insect’s diet (Mendes et al., 2012), as well as
protection against potential pathogens for the
host (Biedermann & Vega, 2020). The benefit
obtained by the yeasts is less understood, but
it has been related to transportation to new
habitats and a stable food source (Madden et
al., 2018).
Members of Saccharomycetales as Pichia
and Candida have been detected in other Dip-
tera larvae, like in some Drosophila species
(Chandler et al., 2012; Hamby et al., 2012) and
Aedes aegypti midguts and ovaries (Gusmão
et al., 2010). They could be playing a protec-
tion role against pathogens, as the yeast of
this genus is known to generate antimicrobial
compounds that can inhibit the growth of some
bacteria (Bajaj et al., 2013; Chelliah et al., 2016;
França et al., 2015). Several strains of Pichia
can produce mycocins that alter homeostasis in
other sensible yeast and disrupt cell membrane
function resulting in cell death (Golubev, 2006;
Santos et al., 2009). The presence of Pichia and
Candida in H. illucens gut might be also ben-
eficial for its growth and development as it has
been found that supplementation with Pichia
increases the survival rate and decreases devel-
opment time in Drosophila suzukii (Meshrif et
al., 2016). In H. illucens, supplementation with
Candida has proved to increase larval body
weight and significantly enhanced tyrosine,
purine, histidine, and vitamin B6 metabolism
(Kannan et al., 2023).
The high abundance of Pichia can also
have benefits boosting organic matter degrada-
tion. Inoculating compost with Pichia has been
shown to accelerate the composting process as
it degrades organic acids, this increases pH and
allows mesophilic and thermophilic bacteria
to proliferate faster, which in turn contrib-
utes to a vigorous organic matter degradation
(Nakasaki et al., 2013). The capacity to toler-
ate low pH levels might be also related to its
high dominance in this larvae gut. BSF gut
presents regions with different pH values, the
posterior midgut is alkaline, but the anterior
region has an acidic luminal content, and the
middle midgut presents pH levels around two
(Tettamanti et al., 2022). Survival and efficient
growth on these pH levels have been already
demonstrated in this yeast (Fletcher et al., 2015;
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Park et al., 2018). Further research needs to be
done to analyze how the location in the diges-
tive tract and its pH influences the dominance
of Pichia.
Isolation of yeasts from H. illucens larvae
could be of special interest due to the condi-
tions they could be exposed to during the
composting process, as temperatures during
the thermophilic phase can reach up to 70 °C
(Nozhevnikova et al., 2019). It is known that
thermotolerant yeasts can increase the produc-
tivity of industrial processes such as ethanol
production, by eliminating the energy used
to lower the temperature needed to maintain
microorganisms used in fermentation (Abdel-
Banat et al., 2010). Some strains of Pichia have
been already tested for this purpose. They
exhibited growth and ethanol production capa-
bility at temperatures up to 45 °C (Chamnipa et
al., 2018; Pongcharoen et al., 2018). Pichia and
Candida are useful in the production of other
industrially important compounds such as
malic acid, butyric acid, xylitol, biosurfactants,
lipids, and enzymes among others (Kieliszek
et al., 2017; Queiroz et al., 2023; Shrivastava et
al., 2023). The production of these compounds
can also be beneficial by utilizing thermotol-
erant microorganisms (Kumar et al., 2015;
Mehetre et al., 2019).
In the present study, we also identified two
groups that have not been reported as abundant
groups in BFS larvae before. Galactomyces,
another member of Saccharomycetales, have
been reported on Culex pipiens and Culex thei-
leri larvae, another insect that belongs to the
order Diptera (Steyn et al., 2016). The second
group is Archaespora of the order Archaeospo-
rales, which is an arbuscular mycorrhizal (AM)
fungus. Insects are known to have mutualistic
relations with AM, as they could be a good
source of nutrients for the insects and beneficial
for the fungus due to spores being vectored by
insects (Willis et al., 2013). There are no previ-
ous reports of this AM genus on insects’ guts to
our knowledge. If Galactomyces and Archaes-
pora are adapted to insects’ guts needs to be
elucidated. Alternately, these species of fungus
could have been common in the BFS growth
environment, and therefore, highly abundant
in the insect gut.
Galactomyces has biotechnological poten-
tial related to emerging pollutant removal.
Chaijak et al. (2018) reported ligninolytic
enzymes and phenol removal activity that can
be used to treat industrial wastewater. It can
also be effective in removing industrial dyes
such as Methylene Blue and Azo dyes that are
extensively used in textile, paper, food, and
pharmaceutical industries (Contreras et al.,
2019; Guo et al., 2019). Zhang et al. (2015)
demonstrated the effectivity of this yeast in
decomposing lincomycin, an antibiotic with a
very stable structure. Isolation of these yeasts
found in BFS larvae is needed for further
research on their temperature tolerance range,
enzymatic activities, and biotechnology appli-
cations. Additionally, while we focused on the
most abundant genera found, less abundant
genera could be cultivable and possess valuable
properties for biotechnological applications.
To conclude, this study offers insight into
the mycobiome of naturally occurring BSF
larvae in a tropical region. The abundance of
yeast like Pichia and Candida is consistent with
previous studies, and the high dominance of
Pichia in this and previous studies, suggests
a stable insect-yeast relation (Boccazzi et al.,
2017; Klüber et al., 2022a; Shokry et al., 2023;
Tanga et al., 2021). The description of previously
unreported fungal groups highlights the impor-
tance of continuing to explore the mycobiome
dynamics of this larva in different habitats. The
determination of dominant fungal groups can
contribute to better understand the efficiency
of H. illucens larva compost production, and
with further reseach it may improve its use in
urban composting and enhance organic waste
management in these environments. Lastly, we
emphasize the need for further investigation
of yeast strains and other fungi groups present
in this larva, as they could be adapted to more
extreme conditions characteristic of this larvaes
natural habitat.
Ethical statement: the authors declare that
they all agree with this publication and made
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Revista de Biología Tropical, ISSN: 2215-2075, Vol. 72: e57898, enero-diciembre 2024 (Publicado Set. 17, 2024)
significant contributions; that there is no con-
flict of interest of any kind; and that we fol-
lowed all pertinent ethical and legal procedures
and requirements. All financial sources are fully
and clearly stated in the acknowledgments sec-
tion. A signed document has been filed in the
journal archives.
ACKNOWLEDGMENTS
This work was developed as part of the
Environmental Biotechnology course (B0795/
SP8221), taught at the School of Biology, Uni-
versity of Costa Rica. We thank Ruth Mad-
rigal-Brenes and Vidal Salas-Lara for their
contribution during the dissection of the insects
and DNA extraction. We also thank Maria Fer-
nanda Cordero Pagoaga for the illustration
of Fig 1.
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