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Life in ruins: DNA metabarcoding contributes to the history of Whalers Bay wooden structures at Deception Island, South Shetland Islands

Published online by Cambridge University Press:  17 December 2024

Paulo E.A.S. Câmara Open the ORCID record for Paulo E.A.S. Câmara [Opens in a new window] ,
Fabyano A. Lopes Open the ORCID record for Fabyano A. Lopes [Opens in a new window] ,
Fábio L.V. Bones ,
Micheline Carvalho-Silva Open the ORCID record for Micheline Carvalho-Silva [Opens in a new window] ,
Peter Convey Open the ORCID record for Peter Convey [Opens in a new window] ,
Láuren De Souza ,
Lívia Coelho  and
Luiz Rosa
Paulo E.A.S. Câmara*
Affiliation:
Botany Department, University of Brasília, Campus Darcy Ribeiro, Brasília, Brazil Federal University of Santa Catarina, Florianópolis, Brazil
Fabyano A. Lopes
Affiliation:
Federal University of Tocantins, Porto Nacional, Brazil
Fábio L.V. Bones
Affiliation:
Federal University of Santa Catarina, Florianópolis, Brazil
Micheline Carvalho-Silva
Affiliation:
Botany Department, University of Brasília, Campus Darcy Ribeiro, Brasília, Brazil
Peter Convey
Affiliation:
British Antarctic Survey, NERC, Cambridge, UK University of Johannesburg, Department of Zoology, Johannesburg, South Africa
Láuren De Souza
Affiliation:
Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
Lívia Coelho
Affiliation:
Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
Luiz Rosa
Affiliation:
Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
*
paducamara@gmail.com
Rights & Permissions [Opens in a new window]

Abstract

Deception Island is an Antarctic Specially Managed Area that houses historically important sites such as the remains of historical wooden buildings. The impacts of fungal communities on wood in polar historical sites have been investigated, but little is known of the impacts of other eukaryote groups. In the current study we used high-throughput sequencing to investigate the diversity of non-fungal eukaryotic organisms present in wood samples from Whalers Bay. Four sites were sampled, and DNA sequences representing three kingdoms (Chromista, Protozoa and Viridiplantae) and four phyla (Ciliophora, Perclozoa, Chlorophyta and Magnoliophyta) were identified, representing a total of 43 taxa. Biscoe House Annex hosted the richest diversity, with 20 taxa, followed by the whaling boat, Biscoe House and the Hunting Lodge, with 16, 15 and 12 taxa, respectively. The most frequently detected sequences were assigned to the ciliate group Sporadotrichida, some of which are known to play a role in cellulose degradation. Among the Chlorophyta, the sequences detected included common taxa previously recorded, but the flowering plant data represented only exotic taxa, probably associated with human activity or airborne transfer. The use of high-throughput sequencing provided valuable data on communities associated with anthropogenically sourced and now decaying wood in Antarctica.

Keywords

eDNAHSM 71HTSITSMaritime Antarctic

Information

Type
Biological Sciences
Information
Antarctic Science , Volume 36 , Issue 5 , October 2024 , pp. 281 - 289
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Copyright
Copyright © The Author(s), 2024. Published by Cambridge University Press on behalf of Antarctic Science Ltd

Introduction

Deception Island (62°57'S, 60°38'W), located in the South Shetland Islands archipelago, is one of few active volcanic locations in Antarctica today (Fig. 1). Due to its unique geothermally associated flora, exceptional aesthetic and scientific value and historical importance, compounded by exposure to multiple contemporary sources of human impact from both national research operations and the tourism industry, the entire island has been designated as Antarctic Specially Managed Area (ASMA) 4, and it also contains two Antarctic Specially Protected Areas (ASPAs 140 and 145). The area also includes two Historic Sites or Monuments (HSM 71 and 76), an important reminder that human activity in Antarctic marine exploitation dates back to the early 1820s (Held & Blanchette Reference Held and Blanchette2017).

Figure 1.

Location of Deception Island in the South Shetland Islands, Maritime Antarctica, where the samples were obtained.

The sealing industry was very active in the South Shetland Islands during the nineteenth century after the archipelago's discovery in the early 1820s, followed by the whaling industry in the early twentieth century. The first shore-based whaling station on the island was established in 1911 - the Aktieselskabet Hecktor Whaling Station at Whalers Bay - which operated until 1931 when it was no longer commercially viable. In 1944, as part of a military operation towards the end of the Second World War, the UK constructed its Base B. In the post-war years, now operated by the Falkland Islands Dependencies Survey, that base was expanded to include a small aerodrome and associated hangar. Base B included some buildings from the preceding whaling station but also expanded its footprint further with new buildings. Active aircraft operations took place from 1955 to 1957 and again from 1959 to 1969. Base B was decommissioned in 1969, at least in part because many of its structures were heavily damaged during volcanic eruptions in 1967 and 1969 (Smith Reference Smith1984, Morales et al. Reference Morales, Almendros and Carmona2017). The area was partially cleared by the UK in 1990–1992, but many structures dating from both the whaling and research eras remain, with many of these being constructed from or incorporating wood imported to the island (Fig. 2). The Whalers Bay site has been under the protection of the Antarctic Treaty since being designated as HSM 71 in 1995.

Figure 2.

Whalers Bay ruins where the wood samples were obtained. a. Whaling boat, b. Hunting Lodge, c. Biscoe House and d. Biscoe House Annex. Photographs: L.H. Rosa.

Whalers Bay is one of the most visited and popular sites in Antarctica by both national operator staff and the Antarctic tourism industry. Two national operators (Argentina and Spain) currently operate summer-only research stations on the island, with Chile and the UK previously operating year-round stations before the late 1960s' eruptions. Research and logistical support vessels from multiple national operators also routinely visit the island and land personnel in most summers. A total of ~160 000 tourists visited Whalers Bay between 2010 and 2019 (www.iaato.org; Carvalho-Silva et al. Reference Carvalho-Silva, Rosa, Pinto, Da Silva, Henriques, Convey and Câmara2021), the majority of whom visited and explored the ruins of HSM 71. Human impacts on Whalers Bay local terrestrial ecosystems, in the context of the presence of non-native species anthropogenically transferred to the island (Greenslade et al. Reference Greenslade, Potapov, Russell and Convey2012, Hughes et al. Reference Hughes, Pertierra, Molina-Montenegro and Convey2015) or of environmental DNA (eDNA) sequences assigned to exotic species (Rosa et al. Reference Rosa, da Silva, Ogaki, Pinto, Stech and Convey2020, Câmara et al. Reference Câmara, Carvalho-Silva, Pinto, Amorin, Henriques and da Silva2021b, Carvalho-Silva et al. Reference Carvalho-Silva, Rosa, Pinto, Da Silva, Henriques, Convey and Câmara2021), have received some research attention. Many of the wooden structures in Whalers Bay are > 100 years old and are increasingly deteriorating. The effects of decomposer fungal communities on the wood of many Antarctic and Arctic historical sites have been investigated, including on Deception Island (Held et al. Reference Held, Arenz, Blanchette, Barr and Chaplin2011, Held & Blanchette Reference Held and Blanchette2017, Blanchette et al. Reference Blanchette, Held, Jurgens, Stear and Dupont2021). However, little to nothing is known regarding the impacts of other organism groups that may have become established on these exotic wood habitats, such as microalgae and protozoans, as well as regarding the presence of pollen and spores.

Many organisms of these types are difficult to identify conclusively, requiring the development of appropriate culture methodologies, and some may be encysted. Recently developed molecular tools such as DNA metabarcoding using high-throughput sequencing (HTS; Taberlet et al. Reference Taberlet, Coissac, Pompanon, Brochmann and Willerslev2012) are increasingly being applied to infer the presence of active or dormant life forms, propagules, pollen and detritus of plants (Fahner et al. Reference Fahner, Shokralla, Baird and Hajibabaei2016). These methodologies use the total and even sometimes the degraded DNA extracted from environmental samples (e.g. water, soil or air). The methodology has the potential to increase by a factor of ~11 the number of taxa detected when compared with classical morphological approaches (Rippin et al. Reference Rippin, Borchhardt, Williams, Colesie, Jung and Büdel2018), and they can reveal the presence of DNA of taxa not detectable through traditional surveys. In the current study, we used HTS of eDNA to investigate the diversity of non-fungal eukaryotic organisms present in wood samples obtained from various sites in HSM 71 Whalers Bay on Deception Island.

Methods

Study sites and sampling

Four sites were selected for sampling: Biscoe House, an abandoned whaling boat, the Biscoe House Annex and the Hunting Lodge (Fig. 2), all located in close proximity to each other. Three small samples (~1 cm3) of wood from each site were obtained during the Antarctic summer (December 2016) and placed into individual sterilized Whirl-Pak bags (Sigma-Aldrich, USA), which were sealed and kept at -20°C for 3 weeks until being processed at the Microbiology Laboratory at the Federal University of Minas Gerais, Brazil. Data from each sample were obtained separately but are presented together in Table I.

Table I.

Taxa present in the four sampled sites based on the assignment of amplicon sequence variants. Numbers indicate the DNA reads present in each sample.

DNA extraction, amplification and sequencing

Total DNA was extracted using a modified sodium dodecyl sulphate (SDS) extraction method (Goldenberger et al. Reference Goldenberger, Perschil, Ritzler and Alwegg1995, Zhou et al. Reference Zhou, Bruns and Tiedje1996, Natarajan et al. Reference Natarajan, Zhang, Morono, Inagaki and Wang2016). Wood fragments of ~1 cm3 were added to plastic tubes each containing 2 ml of SDS extraction buffer (0.1 M ethylenediaminetetraacetic acid (EDTA) at pH 8 and 2% SDS) and ground with sterilized iron beads for 3 min before being incubated at 55°C for 16 h. Then, 330 μl of 5 M NaCl and 330 μl of pre-heated cetrimonium bromide (CTAB) 10% (55°C) were added; the solution was then vortexed, spun down and incubated at 55°C for 10 min. The solution was then transferred to a new tube, and 600 μl of chloroform was added and vortexed at maximum speed for 1 min. After that, the tubes were centrifuged at 13 000 rpm for 10 min and the supernatant transferred to a new tube.

The extracted DNA was cleaned using the Genomic DNA Purification Kit (QIAGEN, USA) following the manufacturer's instructions. Extractions were carried out under strict sterile conditions to avoid contamination (de Menezes et al. Reference de Menezes, Porto, Amorim, Zani, de Almeida Alves and Sales Junior2020). Samples were manipulated inside a sterile flow hood, and all equipment (forceps, spatula, etc.) was previously disinfected. ddH2O samples were used as blanks to ensure the absence of contamination.

DNA quality was analysed using agarose gel electrophoresis (1% agarose in 1 × Trisborate-EDTA) and then quantified using the Quanti- iT™ Pico Green dsDNA Assay (Invitrogen, USA). The internal transcribed spacer 2 region (ITS2) of the nuclear ribosomal DNA was used as a DNA barcode for molecular species identification (Chen et al. Reference Chen, Yao, Han, Liu, Song and Shi2010, Richardson et al. Reference Richardson, Lin, Sponsler, Quijia, Goodell and Johnson2015, Hadi et al. Reference Hadi, Santana, Brunale, Gomes, Oliveira and Matthiensen2016, Ruppert et al. Reference Ruppert, Kline and Rahman2019, Câmara et al. Reference Câmara, de Souza, Pinto, Convey, Amorim, Carvalho-Silva and Rosa2021a,Reference Câmara, Carvalho-Silva, Pinto, Amorin, Henriques and da Silvab, Reference Câmara, de Menezes, Oliveira, Souza, Amorim and Shaefer2022, Carvalho-Silva et al. Reference Carvalho-Silva, Rosa, Pinto, Da Silva, Henriques, Convey and Câmara2021) using the universal primers ITS3 and ITS4 (White et al. Reference White, Bruns, Lee, Taylor, Innis, Gelfand, Sninsky and White1990). Library construction and DNA amplification were performed using the Herculase II Fusion DNA Polymerase Nextera XT Index Kit V2, following the Illumina 16S Metagenomic Sequencing Library Preparation Part #15044223 Rev. B protocol. Paired-end sequencing (2 × 300 bp) was performed commercially on a MiSeq System (Illumina, USA) by Macrogen, Inc. (South Korea), including negative controls.

Data analyses and taxa identification

Quality analysis was carried out using BBDuk v. 38.87 in BBmap software (Bushnell Reference Bushnell2014) with the following parameters: Illumina adapters removing (Illumina artefacts and the PhiX Control v3 Library); ktrim = l; k = 23; mink = 11; hdist = 1; minlen = 50; tpe; tbo; qtrim = rl; trimq = 20; ftm = 5; maq = 20. The remaining sequences were imported into QIIME2 version 2021.4 (https://qiime2.org/) for bioinformatics analyses (Bolyen et al. Reference Bolyen, Rideout, Dillon, Bokulich, Abnet, Al-Ghalith and Alexander2019). The qiime2-dada2 plugin was used for filtering, dereplication, turning paired-end fastq files into merged files, removing chimeras and creating amplicon sequence variants (ASVs) with default parameters (Callahan et al. Reference Callahan, McMurdie, Rosen, Han, Johnson and Holmes2016). Taxonomic assignments of ASVs were determined using the qiime2-feature-classifier (Bokulich et al. Reference Bokulich, Kaehler, Rideout, Dillon, Bolyen and Knight2018) classify-sklearn against different databases; the sequence similarity threshold was set at 97%. Firstly, ASVs were classified against the PLANiTS2 database (Banchi et al. Reference Banchi, Ametrano, Greco, Stanković, Muggia and Pallavicini2020). After this step, ASVs that were not classified were filtered and classify-sklearn classified against the UNITE Eukaryotes ITS database version 8.3 (Abarenkov et al. Reference Abarenkov, Zirk, Piirmann, Pöhönen, Ivanov, Nilsson and Kõljalg2020). Finally, any remaining unclassified ASVs were filtered and aligned against the filtered National Center for Biotechnology Information (NCBI) non-redundant nucleotide sequences (nt) database (October 2021) using BLASTn (Camacho et al. Reference Camacho, Coulouris, Avagyan, Ma, Papadopoulos, Bealer and Madden2009) with default parameters; the nt database was filtered with the following keywords: ‘ITS1’, ‘ITS2’, ‘internal transcribed spacer’ and ‘internal transcribed spacer’. Taxonomic assignments were performed using MEGAN6 (Huson et al. Reference Huson, Beier, Flade, Górska, El-Hadidi and Mitra2016).

For comparative purposes, the number of reads can be used as a proxy for relative abundance (Giner et al. Reference Giner, Forn, Romac, Logares, de Vargas and Massana2016, Deiner et al. Reference Deiner, Bik, Mächler, Seymour, Lacoursière-Roussel and Altermatt2017, Câmara et al. Reference Câmara, de Souza, Pinto, Convey, Amorim, Carvalho-Silva and Rosa2021a,Reference Câmara, Carvalho-Silva, Pinto, Amorin, Henriques and da Silvab, Reference Câmara, de Menezes, Oliveira, Souza, Amorim and Shaefer2022). Classifications and systematic ranks for kingdoms and phyla followed Ruggiero et al. (Reference Ruggiero, Gordon, Orrell, Bailly, Bourgoin and Brusca2015). Venn diagrams were prepared as described by Bardou et al. (Reference Bardou, Mariette, Escudié, Djemiel and Klopp2014).

Results

A total of 2 327 468 reads were obtained, of which 2 218 794 remained after quality control (for detailed data, see Supplemental Table 1). A total of 19 820 reads were DNA sequences representing three kingdoms (Chromista, Protozoa and Viridiplantae) and four phyla (Ciliophora, Perclozoa, Chlorophyta and Magnoliophyta). The remaining reads corresponded to fungi (de Souza et al. Reference De Souza, Teixeira, Coelho, Lopes, Convey and Carvalho-Silva2022). All calculated rarefaction curves (Supplemental Fig. 1) reached a plateau, indicating that the sampling effort was sufficient to represent the taxa analysed in all sampled sites. Sequences representing a total of 43 taxa were detected (Table I). Biscoe House Annex hosted the greatest diversity, with 20 taxa, followed by the whaling boat, Biscoe House and the Hunting Lodge, with 16, 15 and 12 taxa, respectively. Representatives of the ciliate order Sporadotrichida were the most frequently detected sequences, this being the only ciliate taxa present at all sites, followed by the green algal genus Trebouxia, which was present in three of the four sites. The Venn diagram illustrates that only two taxa were detected at all sites (Sporadotrichida and Chlamydomonadales; Fig. 3).

Figure 3.

Venn diagram showing the taxa distribution and shared species among the different samples. Biscoe = Biscoe House; Biscoe HAnx = Biscoe House Annex; Hunting Lod = Hunting Lodge; Whal. Boat = Whaling boat.

Non-metric multidimensional scaling and cluster analysis did not identify any differences between sampled structures, which were in close proximity, of similar material and subject to the same environmental conditions. Data are available upon request.

Discussion

Among the Chromista detected, although giving the greatest taxonomic resolution of sequence assignments, none were assigned to species level. Fuscheria is a genus of approximately six species and is globally distributed, inhabiting terrestrial, fresh, brackish and marine environments (Petz et al. Reference Petz, Song and Wilbert1995). Two terrestrial species - Fuscheria lacustres and Fuscheria terricola - have been reported from the Antarctic continent near Casey Station (ATCM 2013, Thompson et al. Reference Thompson, Powell and Adams2019), and the Maritime Antarctic species Fuscheria marina has been reported from the Weddell Sea (Petz et al. Reference Petz, Song and Wilbert1995). The genus Homalogastra includes one species record (Homalogastra setosa) from Antarctica (Thompson et al. Reference Thompson, Powell and Adams2019). Trithigmostoma is a cosmopolitan genus with five species inhabiting fresh, marine and brackish water. It has been reported from Antarctica from soils in Wilkes Land (Petz & Foissner Reference Petz and Foissner1997). There are no previous records of these genera from Deception Island.

All other taxa were assigned to higher taxonomic levels. Some of these include taxa with wide geographical distributions, as also reported by Câmara et al. (Reference Câmara, de Souza, Pinto, Convey, Amorim, Carvalho-Silva and Rosa2021a). The very abundant order Sporadotrichida is a highly diverse group present in marine, freshwater and terrestrial habitats, containing four families and 83 genera, some of which are very common, such as Halteria, Oxytricha and Cyrtohymena (Parr et al. Reference Parr, Wilson, Leary, Schulz, Lans and Walley2014), which are all recorded from Antarctica (Thompson et al. Reference Thompson, Powell and Adams2019, Câmara et al. Reference Câmara, de Souza, Pinto, Convey, Amorim, Carvalho-Silva and Rosa2021a,Reference Câmara, Carvalho-Silva, Pinto, Amorin, Henriques and da Silvab,Reference Câmara, Convey, Rangel, Konrath, Barreto and Pintoc). As sequences were assigned only at the order level, and considering that this order contains many very common species, this may be suggestive of the presence of new and as yet undescribed species present on the wood sampled. Ciliates are known to feed on bacteria, which are likely to be present in decaying wood. Protists are also known to play an important role in cellulose degradation (Peterson et al. Reference Peterson, Stewart and Scharf2015). However, functional roles cannot be inferred directly in the current study. Ciliates in the class Spirotrichea and family Acropisthiidae are known to occur in both marine and terrestrial environments in Antarctica (De Broyer et al. Reference De Broyer, Clarke, Koubbi, Pakhomov, Scott, Vanden Berghe and Danis2020). The ciliate groups assigned here are widespread and have been previously recorded in Antarctica, and our data confirm their presence in decaying wood of anthropogenic origin.

Among the Protozoa, the genus Allovahlkampfia includes free-living amoebae that feed primarily on bacteria. It has previously been recorded from Deception and King George islands (Câmara et al. Reference Câmara, Carvalho-Silva, Pinto, Amorin, Henriques and da Silva2021b), and representatives are known to be capable of causing disease in humans (Mohamed et al. Reference Mohamed, Huseein, Farrag, Mostafa and Hassan2016, Tolba et al. Reference Tolba, Huseein, Farrag, Mohamed, Kobayashi and Suzuki2016). In contrast, Neovahlkampfia is a genus that includes only one described marine species that has not been previously recorded from Antarctica. The taxonomy of these genera remains poorly known (Jonckheere et al. Reference Jonckheere, Murase and Opperdoes2011). However, as with the ciliates, bacterivorous organisms are expected to be found on decaying wood.

The assigned Viridiplantae sequences include some very common taxa (genera Trebouxia, Chlamydomonas and Prasiola) previously recorded from multiple locations in Antarctica, including Deception Island (e.g. Câmara et al. Reference Câmara, de Souza, Pinto, Convey, Amorim, Carvalho-Silva and Rosa2021a,Reference Câmara, Carvalho-Silva, Pinto, Amorin, Henriques and da Silvab, Fonseca et al. Reference Fonseca, Câmara, Ogaki, Pinto, Lirio and Coria2022). The close proximity of the Whalers Bay sampling locations to the sea as well as to snow and ice could underlie the taxon composition found. Representatives of Trebouxia are very common and widespread in Antarctica (Câmara et al. Reference Câmara, de Souza, Pinto, Convey, Amorim, Carvalho-Silva and Rosa2021a,Reference Câmara, Carvalho-Silva, Pinto, Amorin, Henriques and da Silvab), and some members are also photobionts in lichens found growing on the wood surface as well as on other natural substrata (de Souza et al. Reference De Souza, Teixeira, Coelho, Lopes, Convey and Carvalho-Silva2022).

In contrast with the algae, the flowering plant (Magnoliophyta) sequence assignments all represented exotic taxa not native to Antarctica, and the presence of their DNA is probably indicative of either association with human activity or the airborne transfer of pollen. Petroselinum crispum (parsley) is a plant originally in the Mediterranean region but now widely cultivated around the planet and used for culinary purposes. Glycine soja (soybean), originally from Asia, is today one of the most important crop plants on the planet and is widely used as food (milk, tofu, oil, etc.). Eucalyptus fulgens (green scent bark) is a tree species endemic to Australia; however, this assignment could be an artefact arising from the quality or completeness of the database consulted, as the genus Eucalyptus includes > 700 species, many widely cultivated in the Americas, Europe, Asia and Africa for timber, cellulose or oil. The ruined wooden structures on Deception Island were primarily constructed of pine (Pinus sp.) and spruce (Picea sp.; Held et al. Reference Held, Arenz, Blanchette, Barr and Chaplin2011), genera that were not detected in the current study. However, even today many wooden materials are imported to Antarctica (Osyczka et al. Reference Osyczka, Mleczko, Karasiński and Chlebicki2012), and ~47% of the garbage found in Antarctica comprises or includes wood (Anfuso et al. Reference Anfuso, Bolívar-Anillo, Asensio-Montesinos, Portantiolo Manzolli, Portz and Villate Daza2020). Lityńska-Zając et al. (Reference Lityńska-Zając, Chwedorzewska, Olech, Korczak-Abshire and Augustyniuk-Kram2012) have also shown that many wood fragments arrive in Antarctica accidentally. Finally, the genus Prunus includes some of the most widely consumed food fruits, including cherries, almonds, plums, apricots and peaches, again suggestive of human influence.

Although we recognize that the possibility exists of pollen or plant propagules reaching Deception Island independently, taking into consideration the high number of visitors to the island (Roura Reference Roura2012, Carvalho-Silva et al. Reference Carvalho-Silva, Rosa, Pinto, Da Silva, Henriques, Convey and Câmara2021) and the ruderal nature of all of the flowering plant taxa assigned, we believe that there is a strong likelihood of the detection of flowering plant sequences here being a consequence of human activity. Carvalho-Silva et al. (Reference Carvalho-Silva, Rosa, Pinto, Da Silva, Henriques, Convey and Câmara2021), in a study of eDNA from Whalers Bay soil samples, similarly reported assignments of many taxa potentially linked with human activities, including foodstuffs.

It is always important to note that assignment of a DNA sequence from eDNA samples does not confirm the presence of the organism itself or viable parts of it. The identification of exotic eDNA highlights the need for protecting these ecosystems from inadvertent and irreversible genetic contamination. The method used here provided valuable and novel data on communities living on exotic decaying wood in Antarctica in addition to the better-studied Fungi and Bacteria.

Conclusions

Historical wooden ruins in Antarctica host a very diverse and largely unknown assembly of organisms, including some not previously reported from the region. DNA metabarcoding using HTS is a useful tool for detecting species that would be otherwise difficult or impossible to identify by morphology alone, including organisms that may be encysted or that cannot at present be grown in culture. The assignment of identities based on DNA sequences alone does not confirm the presence of living organisms or viable propagules, and the assignments themselves rely heavily on the quality of consulted databases, which has been increasing substantially in recent years. In addition, no single DNA marker is effective for all groups of organisms, and further studies using a wider range of markers, backed by traditional direct observation and culturing methods, will ultimately be required to provide a more thorough description of the diversity present. The data presented here will be useful in the development of conservation policies and in studies on colonization processes and human influence in Antarctica.

Author contributions

PEASC, MC-S, LdS and LR performed the fieldwork, PEASC, FAL and FLVB and performed the bioinformatic and data analysis, MC-S analysed the flowering plant data and PEASC analysed the non-flowering plant data. PEASC, PC and LR conceived the paper and its experimental design and provided funds. All of the authors participated in writing the paper.

Acknowledgements

We thank the Brazilian Navy and Air Force for logistical support and the Brazilian Antarctic Program (PROANTAR). We also thank the editor and the reviewers for handling this paper and working to make it better.

Competing interests

The authors declare no conflicts of interest.

Financial support

This study received financial support from the Brazilian Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Ministério da Ciência, Tecnologia e Inovação (MCTI) and Programa Antártico Brasileiro (PROANTAR). PC is supported by Natural Environment Research Council (NERC) core funding to the British Antarctic Survey (BAS) ‘Biodiversity, Evolution and Adaptation’ Team. Congresswoman Jô Moraes and the Instituto de Ciências Biológicas at Universidade de Brasília provided extra funds.

References

Abarenkov, K., Zirk, A., Piirmann, T., Pöhönen, R., Ivanov, F., Nilsson, H.R. & Kõljalg, U. 2020. UNITE QIIME Release for Eukaryotes 2. Version 4: 2020. Retrieved from https://doi.org/10.15156/BIO/786388CrossRefGoogle Scholar
Anfuso, G., Bolívar-Anillo, H.J., Asensio-Montesinos, F., Portantiolo Manzolli, R., Portz, L. & Villate Daza, D.A. 2020. Beach litter distribution in Admiralty Bay, King George Island, Antarctica. Marine Pollution Bulletin, 160, 10.1016/j.marpolbul.2020.111657.CrossRefGoogle Scholar
ATCM. 2013. Management Plan for Antarctic Specially Protected Area No 135. Retrieved from https://documents.ats.aq/recatt/att192_e.pdfGoogle Scholar
Banchi, E., Ametrano, C.G., Greco, S., Stanković, D., Muggia, L. & Pallavicini, A. 2020. PLANiTS: a curated sequence reference dataset for plant ITS DNA metabarcoding. Database: The Journal of Biological Databases and Curation, 2020, 10.1093/database/baz155.CrossRefGoogle ScholarPubMed
Bardou, P., Mariette, J., Escudié, F., Djemiel, C. & Klopp, C. 2014. Jvenn: an interactive Venn diagram viewer. BMC Bioinformatics, 15, 10.1186/1471-2105-15-293.CrossRefGoogle ScholarPubMed
Blanchette, R.A., Held, B.W., Jurgens, J., Stear, A. & Dupont, C. 2021. Fungi attacking historic wood of Fort Conger and the Peary Huts in the High Arctic. PLoS ONE, 16, 10.1371/journal.pone.0246049.CrossRefGoogle ScholarPubMed
Bokulich, N.A., Kaehler, B.D., Rideout, J.R., Dillon, M., Bolyen, E., Knight, R., et al. 2018. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin. Microbiome, 6, 10.1186/s40168-018-0470-z.CrossRefGoogle ScholarPubMed
Bolyen, E., Rideout, J.R., Dillon, M.R., Bokulich, N.A., Abnet, C.C., Al-Ghalith, G.A., Alexander, H., et al. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37, 10.1038/s41587-019-0209-9.Google ScholarPubMed
Bushnell, B. 2014. BBMap: a fast, accurate, splice-aware aligner. Berkeley, CA: Lawrence Berkeley National Lab (LBNL). Retrieved from sourceforge.net/projects/bbmapGoogle Scholar
Callahan, B.J., McMurdie, P.J., Rosen, M.J., Han, A.W., Johnson, A.J.A. & Holmes, S.P. 2016. DADA2: high-resolution sample inference from Illumina amplicon data. Nature Methods, 13, 10.1038/nmeth.3869.CrossRefGoogle ScholarPubMed
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K. & Madden, T.L. 2009. BLAST+: architecture and applications. BMC Bioinformatics, 10, 10.1186/1471-2105-10-421.CrossRefGoogle ScholarPubMed
Câmara, P.E.A.S., de Souza, L.M.D., Pinto, O., Convey, P., Amorim, E.T., Carvalho-Silva, M. & Rosa, L.H. 2021a. Periphyton diversity in two different Antarctic lakes assessed using metabarcoding. Antarctic Science, 33, 10.1017/S0954102021000316.CrossRefGoogle Scholar
Câmara, P.E.A.S., Carvalho-Silva, M., Pinto, O.H.B., Amorin, E.T., Henriques, D.K., da Silva, T.H., et al. 2021b. Diversity and ecology of Chlorophyta (Viridiplantae) assemblages in protected and non-protected sites in Deception Island (Antarctica, South Shetland Islands) assessed using an NGS approach. Microbial Ecology, 81, 10.1007/s00248-020-01584-9.CrossRefGoogle ScholarPubMed
Câmara, P.E.A.S., Convey, P., Rangel, S.B., Konrath, M., Barreto, C.C., Pinto, O.H.B., et al. 2021c. The largest moss carpet transplant in Antarctica and its bryosphere cryptic biodiversity. Extremophiles, 25, 10.1007/s00792-021-01235-y.CrossRefGoogle ScholarPubMed
Câmara, P.E.A.S., de Menezes, G.C.A., Oliveira, F.S., Souza, C.D., Amorim, E.T., Shaefer, C.E.G.R., et al. 2022. Diversity of Viridiplantae DNA present on rock surfaces in the Ellsworth Mountains, Continental Antarctica. Polar Biology, 45, 10.1007/s00300-022-03021-8.CrossRefGoogle Scholar
Carvalho-Silva, M., Rosa, L.H., Pinto, O., Da Silva, T., Henriques, D.K., Convey, P. & Câmara, P.E.A.S. 2021. Exploring the plant environmental DNA diversity in soil from two sites on Deception Island (Antarctica, South Shetland Islands) using metabarcoding. Antarctic Science, 33, 10.1017/S0954102021000274.CrossRefGoogle Scholar
Chen, S., Yao, H., Han, J., Liu, C., Song, J., Shi, L., et al. 2010. Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS One, 5, 10.1371/journal.pone.0008613.Google ScholarPubMed
De Broyer, C., Clarke, A., Koubbi, P., Pakhomov, E., Scott, F., Vanden Berghe, E. & Danis, B., eds. 2020. Register of Antarctic Marine Species. Spirotrichea. Retrieved from http://www.marinespecies.org/RAMS/aphia.php?p=taxdetails&id=1348Google Scholar
de Menezes, G.C.A., Porto, B.A., Amorim, S.S., Zani, C.L., de Almeida Alves, T.M., Sales Junior, P.A., et al. 2020. Fungi in glacial ice of Antarctica: diversity, distribution and bioprospecting of bioactive compounds. Extremophiles, 24, 10.1007/s00792-020-01161-5.CrossRefGoogle ScholarPubMed
De Souza, L.M.D., Teixeira, E.A.A., Coelho, L.C., Lopes, F.A.C., Convey, P., Carvalho-Silva, M., et al. 2022. Cryptic fungal diversity in historic wooden structures at Whalers Bay, Deception Island, Maritime Antarctic, revealed using DNA metabarcoding. Brazilian Journal of Microbiology, 54, 10.1007/s42770-022-00869-0.Google ScholarPubMed
Deiner, K., Bik, H.M., Mächler, E., Seymour, M., Lacoursière-Roussel, A., Altermatt, F., et al. 2017. Environmental DNA metabarcoding: transforming how we survey animal and plant communities. Molecular Ecology, 26, 10.1111/mec.14350.CrossRefGoogle ScholarPubMed
Fahner, N.A., Shokralla, S., Baird, D.J. & Hajibabaei, M. 2016. Large-scale monitoring of plants through environmental DNA metabarcoding of soil: recovery, resolution, and annotation of four DNA markers. PLoS One, 11, 10.1371/journal.pone.0157505.CrossRefGoogle ScholarPubMed
Fonseca, B.M., Câmara, P.E.A.S., Ogaki, M.B., Pinto, O.H.B., Lirio, J.M., Coria, S.H., et al. 2022. Green algae (Viridiplantae) in sediments from three lakes on Vega Island, Antarctica, assessed using DNA metabarcoding. Molecular Biology Reports, 49, 10.1007/s11033-021-06857-1.CrossRefGoogle ScholarPubMed
Giner, C.R., Forn, I., Romac, S., Logares, R., de Vargas, C. & Massana, R. 2016. Environmental sequencing provides reasonable estimates of the relative abundance of specific picoeukaryotes. Applied Environmental Microbiology, 82, 10.1128/AEM.00560-16.CrossRefGoogle ScholarPubMed
Goldenberger, D., Perschil, I., Ritzler, M. & Alwegg, M. 1995. A simple ‘universal’ DNA extraction procedure using SDS and Proteinase K is compatible with direct PCR amplification. PCR Methods and Applications, 4, 10.1101/gr.4.6.368.CrossRefGoogle ScholarPubMed
Greenslade, P., Potapov, M., Russell, D. & Convey, P. 2012. Global Collembola on Deception Island. Journal of Insect Science, 12, 10.1673/031.012.11101.CrossRefGoogle ScholarPubMed
Hadi, S.I.I.A., Santana, H., Brunale, P.P.M., Gomes, T.G., Oliveira, M.D., Matthiensen, A., et al. 2016. DNA barcoding green microalgae isolated from Neotropical inland waters. PLoS ONE, 11, 10.1371/journal.pone.0149284.CrossRefGoogle ScholarPubMed
Held, B.W. & Blanchette, R.A. 2017. Deception Island, Antarctica, harbors a diverse assemblage of wood decay fungi. Fungal Biology, 121, 10.1016/j.funbio.2016.11.009.CrossRefGoogle ScholarPubMed
Held, B.W., Arenz, B.E. & Blanchette, R.A. 2011 Factors influencing deterioration of historic structures at Deception Island, Antarctica. In Barr, S. & Chaplin, P., eds, Polar settlements – location, techniques and conservation. ICOMOS Monuments and Sites. Oslo, Norway: International Polar Heritage Committee, 35–43.Google Scholar
Hughes, K.A., Pertierra, L.R., Molina-Montenegro, M.A. & Convey, P. 2015. Biological invasions in terrestrial Antarctica: what is the current status and can we respond? Biodiversity and Conservation, 24, 10.1007/s10531-015-0896-6.CrossRefGoogle Scholar
Huson, D.H., Beier, S., Flade, I., Górska, A., El-Hadidi, M., Mitra, S., et al. 2016. MEGAN community edition - interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Computational Biology, 12, 10.1371/journal.pcbi.1004957.CrossRefGoogle ScholarPubMed
Jonckheere, J.F., Murase, J. & Opperdoes, F.R. 2011. A new thermophilic heterolobosean amoeba, Fumarolamoeba ceborucoi, gen. nov., sp. nov., isolated near a fumarole at a volcano in Mexico. Acta Protozoologica, 50, 10.4467/16890027AP.11.005.0005.Google Scholar
Lityńska-Zając, M., Chwedorzewska, K., Olech, M., Korczak-Abshire, M. & Augustyniuk-Kram, A. 2012. Diaspores and phyto-remains accidentally transported to the Antarctic station during three expeditions. Biodiversity and Conservation, 21, 10.1007/s10531-012-0371-6.CrossRefGoogle Scholar
Mohamed, M.E., Huseein, E.A., Farrag, H.M., Mostafa, F.A.A. & Hassan, A.T. 2016. Allovahlkampfia spelaea is a potential environmental host for pathogenic bacteria. Journal of Bacteriology and Parasitology, 7, 10.4172/2155-9597.1000255.CrossRefGoogle Scholar
Morales, J.V., Almendros, J. & Carmona, E. 2017. Detection of long-duration tremors at Deception Island volcano, Antarctica. Journal of Volcanology and Geothermal Research, 347, 10.1016/j.jvolgeores.2017.09.016.Google Scholar
Natarajan, V.P., Zhang, X., Morono, Y., Inagaki, F. & Wang, F. 2016. A modified SDS-Based DNA extraction method for high quality environmental DNA from seafloor environments. Frontiers in Microbiology, 7, 10.3389/fmicb.2016.00986.CrossRefGoogle ScholarPubMed
Osyczka, P., Mleczko, P., Karasiński, D. & Chlebicki, A. 2012. Timber transported to Antarctica: a potential and undesirable carrier for alien fungi and insects. Biological Invasions, 14, 10.1007/s10530-011-9991-0.CrossRefGoogle Scholar
Parr, C.S., Wilson, N., Leary, P., Schulz, K.S., Lans, K., Walley, L., et al. 2014. The Encyclopedia of Life v2: providing global access to knowledge about life on Earth. Biodiversity Data Journal, 2, 10.3897/BDJ.2.e1079.CrossRefGoogle Scholar
Peterson, B.F., Stewart, H.L. & Scharf, M.E. 2015. Quantification of symbiotic contributions to lower termite lignocellulose digestion using antimicrobial treatments. Insect Biochemical Molecular Biology, 59, 10.1016/j.ibmb.2015.02.009.CrossRefGoogle ScholarPubMed
Petz, W. & Foissner, W. 1997. Morphology and infraciliature of some soil ciliates (Protozoa, Ciliophora) from continental Antarctica, with notes on the morphogenesis of Sterkiella histriomuscorum. Polar Record, 33, 10.1017/S0032247400025407.CrossRefGoogle Scholar
Petz, W., Song, W. & Wilbert, N. 1995. Taxonomy and ecology of the ciliate fauna (Protozoa, Ciliophora) in the endopagial and pelagial of the Weddell Sea, Antarctica. Stapfia, 40, 1–223.Google Scholar
Richardson, R.T., Lin, C., Sponsler, D.B., Quijia, J.O., Goodell, K. & Johnson, R.M. 2015. Application of ITS2 metabarcoding to determine the provenance of pollen collected by honey bees in an agroecosystem. Applications in Plant Sciences, 3, 10.3732/apps.1400066.CrossRefGoogle Scholar
Rippin, M., Borchhardt, N., Williams, L., Colesie, C., Jung, P., Büdel, B., et al. 2018. Genus richness of microalgae and cyanobacteria in biological soil crusts from Svalbard and Livingston Island: morphological versus molecular approaches. Polar Biology, 41, 10.1007/s00300-018-2252-2.CrossRefGoogle Scholar
Rosa, L.H., da Silva, T.H., Ogaki, M.B., Pinto, O.H.B., Stech, M., Convey, P., et al. 2020. DNA metabarcoding uncovers fungal diversity in soils of protected and non-protected areas on Deception Island, Antarctica. Scientific Reports, 10, 10.1038/s41598-020-78934-7.CrossRefGoogle ScholarPubMed
Roura, M. 2012. Being there: examining the behavior of Antarctic tourists through their blogs. Polar Research, 201, 10.3402/polar.v31i0.10905.Google Scholar
Ruggiero, M.A., Gordon, D.P., Orrell, T.M., Bailly, N., Bourgoin, T., Brusca, R.C., et al. 2015. Correction: a higher level classification of all living organisms. PLoS ONE, 10, 10.1371/journal.pone.0130114.Google ScholarPubMed
Ruppert, K., Kline, R.J. & Rahman, M.S. 2019. Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: a systematic review in methods, monitoring, and applications of global eDNA. Global Ecology and Conservation, 17, 10.1016/j.gecco.2019.e00547.CrossRefGoogle Scholar
Smith, R.I.L 1984. Colonization and recovery by cryptogams following recent volcanic activity on Deception Island, South Shetland Islands. British Antarctic Survey Bulletin, 62, 25–51.Google Scholar
Taberlet, P., Coissac, E., Pompanon, F., Brochmann, C. & Willerslev, E. 2012. Towards next-generation biodiversity assessment using DNA metabarcoding. Molecular Ecology, 21, 10.1111/j.1365-294X.2012.05470.x.CrossRefGoogle ScholarPubMed
Thompson, A., Powell, G. & Adams, B. 2019. Provisional checklist of terrestrial heterotrophic protists from Antarctica. Antarctic Science, 31, 10.1017/S0954102019000361.CrossRefGoogle Scholar
Tolba, M.E.M., Huseein, E.A.M., Farrag, H.M.M., Mohamed, H.E.D., Kobayashi, S., Suzuki, J., et al. 2016. Allovahlkampfia spelaea causing keratitis in Humans. PLoS Neglected Tropical Diseases, 10, 10.1371/journal.pntd.0004841.CrossRefGoogle ScholarPubMed
White, T.J., Bruns, T., Lee, S. & Taylor, J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In Innis, M.A., Gelfand, D.H., Sninsky, J.J. & White, T.J., eds, PCR protocols: a guide to methods and applications. Molecular Biology Reports. London: Academic Press, 515–322.Google Scholar
Zhou, J., Bruns, M.A. & Tiedje, J.M. 1996. DNA recovery from soils of diverse composition. Applied and Environmental Microbiology, 62, 10.1128/aem.62.2.316-322.1996.CrossRefGoogle ScholarPubMed
Figure 0

Figure 1. Location of Deception Island in the South Shetland Islands, Maritime Antarctica, where the samples were obtained.

Figure 1

Figure 2. Whalers Bay ruins where the wood samples were obtained. a. Whaling boat, b. Hunting Lodge, c. Biscoe House and d. Biscoe House Annex. Photographs: L.H. Rosa.

Figure 2

Table I. Taxa present in the four sampled sites based on the assignment of amplicon sequence variants. Numbers indicate the DNA reads present in each sample.

Figure 3

Figure 3. Venn diagram showing the taxa distribution and shared species among the different samples. Biscoe = Biscoe House; Biscoe HAnx = Biscoe House Annex; Hunting Lod = Hunting Lodge; Whal. Boat = Whaling boat.