A Bright Idea—Metabarcoding Arthropods from Light Fixtures
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A bright idea—metabarcoding arthropods from light fixtures Vasco Elbrecht1,2, Angie Lindner3, Laura Manerus2 and Dirk Steinke2,4 1 Department of Environmental Systems Science Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zurich, Zurich, Switzerland 2 Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada 3 Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany 4 Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada ABSTRACT Arthropod communities in buildings have not been extensively studied, although humans have always shared their homes with them. In this study we explored if arthropod DNA can be retrieved and metabarcoded from indoor environments through the collection of dead specimens in light fixtures to better understand what shapes arthropod diversity in our homes. Insects were collected from 45 light fixtures at the Centre for Biodiversity Genomics (CBG, Guelph, Canada), and by community scientists at 12 different residential homes in Southern Ontario. The CBG ground floor of the CBG showed the greatest arthropod diversity, especially in light fixtures that were continuously illuminated. The community scientist samples varied strongly by light fixture type, lightbulb used, time passed since lamp was last cleaned, and specimen size. In all cases, the majority of OTUs was not shared between samples even within the same building. This study demonstrates that light fixtures might be a useful resource to determine arthropod diversity in our homes, but individual samples are likely not representative of the full diversity. Subjects Biodiversity, Ecology, Entomology, Molecular Biology, Zoology Keywords Community science, Citizen science, Insects, DNA barcoding Submitted 25 May 2021 INTRODUCTION Accepted 1 July 2021 Published 26 July 2021 Humans have always been sharing their living spaces with a large variety of organisms Corresponding author ranging from microbes to vertebrates. Arthropods, as the most diverse group of animals Dirk Steinke, [email protected] (Mora et al., 2011), are a key component of this biodiversity at our homes (Sattler Academic editor et al., 2011), and even in seemingly unhospitable environments such as modern urban Marcio Pie settlements some of them thrive and even continue to provide a number of ecosystem Additional Information and services (Prather et al., 2013). It is however, poorly understood how arthropod diversity is Declarations can be found on fl page 10 in uenced by increased urbanization (Mata et al., 2017) or by the drastic alterations DOI 10.7717/peerj.11841 of ecosystems that are currently fragmenting populations and putting natural habitats at risk (Steffen et al., 2015). What we do know is that biodiversity in our homes is richer than Copyright 2021 Elbrecht et al. it was once thought (Bertone et al., 2016) and while most of our small cohabitants are Distributed under harmless, others can be vectors for allergies or diseases. Some can damage food, clothing, Creative Commons CC-BY 4.0 or building structure, thereby indirectly affecting human well-being (Bertone et al., 2016). In order to mitigate any potential detrimental effects and to better manage risks posed How to cite this article Elbrecht V, Lindner A, Manerus L, Steinke D. 2021. A bright idea—metabarcoding arthropods from light fixtures. PeerJ 9:e11841 DOI 10.7717/peerj.11841 by some arthropod species, it is critical to understand which species have found their way into our homes (Schoelitsz, Meerburg & Takken, 2019). Only very few studies have investigated the diversity of arthropods in homes. One of the most extensive of them surveyed 50 homes in North Carolina, USA by collecting insects from all visible surfaces in all rooms of free-standing homes (Bertone et al., 2016). Results showed that insect assemblages in homes are influenced by several factors, such as the fauna living around the house and the form and availability of access points to homes. Other studies related community composition to the presence of carpets (Leong et al., 2017) as well as to socio-economic factors (Leong et al., 2016). Interestingly, factors such as the level of tidiness or the use of pesticides, as well as pet ownership seemed to have no significant influence on community composition (Leong et al., 2017). However, authors often note that one potential shortcoming of their studies could have been insufficient taxonomic identification, which was often restricted to family level (Bertone et al., 2016). Identification of many arthropod groups is often challenging, due to lack of identification keys, availability of taxonomic experts, damaged specimens or life stages which do not allow for a reliable species level identification. Especially when sample sizes are thousands of specimens, identification higher than family or even order level becomes a substantial time constraint. DNA-based methods of species delimitation such as DNA barcoding (Hebert et al., 2003) can substantially speed up the identification process and reliably provide species level identities. Especially when using DNA barcoding for bulk samples (DNA metabarcoding), the species composition of entire communities can be rapidly determined (Ritter et al., 2019; Steinke et al., 2021a, 2021b). Studies used metabarcoding of house dust to detect arthropods (Madden et al., 2016) and pollen (Craine et al., 2017) in hundreds of samples collected across the USA. With high sample size and increased taxonomic resolution they were able to show that location of the home, presence of pets and the presence of a basement had significant effects on arthropod community diversity (Madden et al., 2016). Capturing such information from house dust using DNA-based methods has the advantage that no taxonomic expertise is needed for collecting or identifying contents of the samples. Consequently, sample collection can be done by community scientists. For this study we explored if arthropod DNA can be retrieved from indoor environments through the collection of dead specimens in light fixtures. As many arthropods are attracted to light sources (Shimoda & Honda, 2013) they often accumulate in light fixtures for many years. Such samples might be ideal for metabarcoding, as specimens are dry, which means the DNA is likely fairly well preserved. We tested the feasibility of a metabarcoding approach to explore arthropod communities collected in light fixtures of 12 residential homes in Ontario and did some more standardized sampling within the Centre for Biodiversity Genomics (CBG, Guelph, Canada) where we were able to collect samples from the same lamp type across the entire building to test for reproducibility and representativeness of samples. Elbrecht et al. (2021), PeerJ, DOI 10.7717/peerj.11841 2/13 Figure 1 Location of the 12 insect samples collected by community scientists. Map (A) shows the samples collected in Ontario, Canada, with section (B) providing a detailed overview of samples collected in the City of Guelph. The Centre for Biodiversity Genomics (CBG) where additional samples were collected is marked with a yellow star. The area of each green circle corresponds to the number of arthropod OTUs detected in the respective sample. Full-size DOI: 10.7717/peerj.11841/fig-1 MATERIALS AND METHODS Sample collection Arthropods were collected by community scientists in early 2019 at 12 locations in Southern Ontario, Canada. They used gloves to remove the remains from individual lamps and to transfer them into a 50 ml falcon tube. All participants were asked to fill out a survey to provide details about sampling location, room type, personal habits as well as an estimate as to when the light fixture was last cleaned (see Table S1 for details). In addition, in April 2019, we collected samples from 45 light fixtures within the Centre for Biodiversity Genomics (CBG) building (Fig. 1B). Light fixtures in basement, ground floor and first floor are identical and equipped with the same type of incandescent light bulbs, thereby ensuring comparable sampling conditions across floors. The light fixtures measure 58 × 58 cm with an area of 20 × 58 cm in which specimens can accumulate (see Fig. S2). Eighteen of the 45 lights are automatically turned off every night for 10 h, as part of the building’s energy saving system (highlighted in Fig. S1). All light fixtures were last cleaned in August 2015. Samples were collected directly into 2 ml reaction tubes or 20 ml IKA Ultraturax tubes, with two or ten steel beads (Ø 4 mm) added for sample grinding, depending on the amount of specimens (Fig. S3). Community science samples were handled identically. DNA extraction and metabarcoding We followed a scalable metabarcoding laboratory workflow that uses 96 well microplates (Elbrecht & Steinke, 2019). The plate included additional 22 freshwater macroinvertebrate samples of a different project, 12 negative controls and nine extraction blanks. Eight of the latter were filled with extracted DNA of another project (see Table S2 for plate map). Samples with higher biomass were ground in IKA Ultraturax tubes for 30 min at 4,000 Elbrecht et al. (2021), PeerJ, DOI 10.7717/peerj.11841 3/13 rpm, while samples in 2 ml tubes were ground for 90 s at 28 Hz. Approximately 20 mg of ground tissue was used for DNA extraction using a DNeasy 96 Blood and Tissue Kit (Qiagen, Hilden, Germany). To reduce the risk of cross contamination tissue was aliquoted and lysed in individual 1.5 ml tubes. During incubation at 56 C for 3 h, tubes were gently inverted 5 times every hour to ensure mixing of tissue and lysis buffer. After cooling and subsequent brief centrifugation, 410 µL of AL buffer was added to the lysate and the tube immediately shaken. Subsequently, the lysate was centrifuged at 16,000g for 1 min to precipitate cuticula fragments. The supernatant was transferred to the column extraction plate. The remainder of the DNA extraction process was carried out following manufacturer’s protocols. Extraction success was visualized on a 1% agarose gel (Fig. S4A). Metabarcoding was carried out using a two-step fusion primer PCR protocol (Steinke et al., 2021a).