Fungal diversity in a sediment core from climate change impacted Boeckella Lake, Hope Bay, north-eastern Antarctic Peninsula assessed using metabarcoding.
Antarctica
Ecology
Extremophile
Fungi
Taxonomy
Journal
Extremophiles : life under extreme conditions
ISSN: 1433-4909
Titre abrégé: Extremophiles
Pays: Germany
ID NLM: 9706854
Informations de publication
Date de publication:
02 May 2022
02 May 2022
Historique:
received:
28
01
2022
accepted:
05
04
2022
entrez:
2
5
2022
pubmed:
3
5
2022
medline:
6
5
2022
Statut:
epublish
Résumé
We studied the fungal DNA present in a lake sediment core obtained from Trinity Peninsula, Hope Bay, north-eastern Antarctic Peninsula, using metabarcoding through high-throughput sequencing (HTS). Sequences obtained were assigned to 146 amplicon sequence variants (ASVs) primarily representing unknown fungi, followed by the phyla Ascomycota, Rozellomycota, Basidiomycota, Chytridiomycota and Mortierellomycota. The most abundant taxa were assigned to Fungal sp., Pseudeurotium hygrophilum, Rozellomycota sp. 1, Pseudeurotiaceae sp. 1 and Chytridiomycota sp. 1. The majority of the DNA reads, representing 40 ASVs, could only be assigned at higher taxonomic levels and may represent taxa not currently included in the sequence databases consulted and/or be previously undescribed fungi. Different sections of the core were characterized by high sequence diversity, richness and moderate ecological dominance indices. The assigned diversity was dominated by cosmopolitan cold-adapted fungi, including known saprotrophic, plant and animal pathogenic and symbiotic taxa. Despite the overall dominance of Ascomycota and Basidiomycota and psychrophilic Mortierellomycota, members of the cryptic phyla Rozellomycota and Chytridiomycota were also detected in abundance. As Boeckella Lake may cease to exist in approaching decades due the effects of local climatic changes, it also an important location for the study of the impacts of these changes on Antarctic microbial diversity.
Identifiants
pubmed: 35499659
doi: 10.1007/s00792-022-01264-1
pii: 10.1007/s00792-022-01264-1
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
16Informations de copyright
© 2022. The Author(s), under exclusive licence to Springer Japan KK, part of Springer Nature.
Références
Abarenkov K, Allan Z, Timo P et al (2020) UNITE QIIME release for eukaryotes. Version 04.02.2020. UNITE Community. https://doi.org/10.15156/BIO/786386
doi: 10.15156/BIO/786386
Arenz BE, Blanchette RA (2009) Investigations of fungal diversity in wooden structures and soils at historic sites on the Antarctic Peninsula. Can J Microbiol 55:46–56
pubmed: 19190700
doi: 10.1139/W08-120
Bardou P, Mariette J, Escudié F et al (2014) An interactive Venn diagram viewer. BMC Bioinform 15:293
doi: 10.1186/1471-2105-15-293
Bokulich NA, Kaehler BD, Rideout JR et al (2018) Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome 6:90
pubmed: 29773078
pmcid: 5956843
doi: 10.1186/s40168-018-0470-z
Bolyen E, Rideout JR, Dillon MR et al (2019) Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 37:852–857
pubmed: 31341288
pmcid: 7015180
doi: 10.1038/s41587-019-0209-9
Borruso L, Sannino C, Selbmann L et al (2018) A thin ice layer segregates two distinct fungal communities in Antarctic brines from Tarn Flat (Northern Victoria Land). Sci Rep 8:6582
pubmed: 29700429
pmcid: 5919928
doi: 10.1038/s41598-018-25079-3
Brunati M, Rojas JL, Sponga F et al (2009) Diversity and pharmaceutical screening of fungi from benthic mats of Antarctic lakes. Mar Genomics 2:43–50
pubmed: 21798171
doi: 10.1016/j.margen.2009.04.002
Callahan BJ, McMurdie PJ, Rosen MJ et al (2016) Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods 13:581–583
pubmed: 27214047
pmcid: 4927377
doi: 10.1038/nmeth.3869
Chaparro M, Chaparro M, Córdoba F et al (2017) Sedimentary analysis and magnetic properties of Lake Anónima, Vega Island. Antarct Sci 29:429–444
doi: 10.1017/S0954102017000116
Chen S, Yao H, Han J et al (2010) Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS ONE 5:e8613
pubmed: 20062805
pmcid: 2799520
doi: 10.1371/journal.pone.0008613
Connell L, Staudigel H (2013) Fungal diversity in a dark oligotrophic volcanic ecosystem (DOVE) on Mount Erebus, Antarctica. Biology 2:798–809
pubmed: 24832809
pmcid: 3960884
doi: 10.3390/biology2020798
de Menezes GCA, Câmara PEAS, Pinto OHB et al (2021) Fungal diversity present on rocks from a polar desert in continental Antarctica assessed using DNA metabarcoding. Extremophiles 25:193–202
pubmed: 33651232
doi: 10.1007/s00792-021-01221-4
de Souza LMD, Ogaki MB, Câmara PEAS et al (2021) Assessment of fungal diversity present in lakes of Maritime Antarctica using DNA metabarcoding: a temporal microcosm experiment. Extremophiles 25:77–84
pubmed: 33416982
doi: 10.1007/s00792-020-01212-x
Deiner K, Bik HM, Mächler E et al (2017) Environmental DNA metabarcoding: transforming how we survey animal and plant communities. Mol Ecol 26:5872–5895
pubmed: 28921802
doi: 10.1111/mec.14350
Ellis-Evans JC (1985) Fungi from maritime Antarctic freshwater environments. Brit Antartic Surv B 68:37–45
Ellis-Evans JC (1996) Microbial diversity and function in Antarctic freshwater ecosystems. Biodivers Conserv 5:1395–1431
doi: 10.1007/BF00051985
Emslie SD, McKenzie A, Marti LJ et al (2017) Recent occupation by Adelie Penguins (Pygoscelis adeliae) at Hope Bay and Seymour Island and the ‘northern enigma’ in the Antarctic Peninsula. Polar Biol 41:71–77
doi: 10.1007/s00300-017-2170-8
Ermolin E (2003) Primera experiência em diseño y construcción de undique en permafrost Antártico: Lago Boeckella, Bahía Esperanza. Contrib Inst Antar Argentino 537:1–41
Giner CR, Forn I, Romac S et al (2016) Environmental sequencing provides reasonable estimates of the relative abundance of specific picoeukaryotes. Appl Environ Microbiol 82:4757–4766
pubmed: 27235440
pmcid: 4984273
doi: 10.1128/AEM.00560-16
Gonçalves VN, Vaz AB, Rosa CA, Rosa LH (2012) Diversity and distribution of fungal communities in lakes of Antarctica. FEMS Microbiol Ecol 82:459–471
pubmed: 22671312
doi: 10.1111/j.1574-6941.2012.01424.x
Hammer Ø, Harper DAT, Ryan PD (2001) PAST: paleontological statistics software package for education and data analysis. Palaeontol Electron 4:9
Henríquez M, Vergara K, Norambuena J et al (2014) Diversity of cultivable fungi associated with Antarctic marine sponges and screening for their antimicrobial antitumoral and antioxidant potential. World J Microbiol Biotechnol 30:65–76
pubmed: 23824664
doi: 10.1007/s11274-013-1418-x
Hering D, Borja A, Jones JI et al (2018) Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive. Water Res 138:192–205
pubmed: 29602086
doi: 10.1016/j.watres.2018.03.003
Izaguirre I, Pizarro H, Allende L et al (2012) Responses of a Maritime Antarctic lake to a catastrophic draining event under a climate change scenario. Polar Biol 35:231–239
doi: 10.1007/s00300-011-1066-2
Joshi NA, Fass JN (2011) Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1.33) [Software]. https://github.com/najoshi/sickle
Kagami M, Miki T, Takimoto G (2014) Mycoloop: chytrids in aquatic food webs. Front Microbiol 5:166
pubmed: 24795703
pmcid: 4001071
doi: 10.3389/fmicb.2014.00166
Kirk PM, Cannon PF, Minter DW, Stalpers JA (2011) Dictionary of the fungi, 10th edn. CAB International, Wallingford, p 784
Kochkina GA, Ozerskaya SM, Ivanushkina NE et al (2014) Fungal diversity in the Antarctic active layer. Microbiology (moscow) 83:94–101
doi: 10.1134/S002626171402012X
Kochkina GA, Ivanushkina NE, Lupachev AV et al (2018) Diversity of mycelial fungi in natural and human-afected Antarctic soils. Polar Biol 42:47–64
doi: 10.1007/s00300-018-2398-y
Kujala K, Mikkonen A, Saravesi K, Ronkanen AK, Tiirola M (2018) Microbial diversity along a gradient in peatlandstreating miningafected Waters. FEMS Microbiol Ecol 94:1–15
doi: 10.1093/femsec/fiy145
Laybourn-Parry J, Pearce DA (2007) The biodiversity and ecology of Antarctic lakes: models for evolution. Philos Trans R Soc Lond B Biol Sci 362:2273–2289
pubmed: 17553775
pmcid: 2443172
doi: 10.1098/rstb.2006.1945
Letcher PM, Powell MJ (2018) A taxonomic summary and revision of Rozella (Cryptomycota). IMA Fungus 9:383–399
pubmed: 30622888
pmcid: 6317583
doi: 10.5598/imafungus.2018.09.02.09
Medinger R, Nolte V, Pandey RV, Jost S (2010) Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms. Mol Ecol 19:32–40
pubmed: 20331768
pmcid: 2953707
doi: 10.1111/j.1365-294X.2009.04478.x
Minnis AM, Lindner DL (2013) Phylogenetic evaluation of Geomyces and allies reveals no close relatives of Pseudogymnoascus destructans, comb. nov., in bat hibernacula of eastern North America. Fungal Biol 117:638–649
pubmed: 24012303
doi: 10.1016/j.funbio.2013.07.001
Nguyen NH, Song Z, Bates ST et al (2016) FUNGuild: an open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol 20:241–248
doi: 10.1016/j.funeco.2015.06.006
Nozal F, Montes M, Martín-Serrano A, Del Valle R (2014) Evolución glaciar en el entorno de Bahía Esperanza (Península Antártica) durate el Holoceno. XIX Congreso Geológico Argentino, Junio, Córdoba
Ogaki MB, Vieira R, Lírio JM et al (2019) Diversity and ecology of fungal assemblages present in lakes of Antarctica. In: Rosa LH (ed) Fungi of Antarctica: diversity, ecology and biotechnological applications. Springer Nature, Switzerland, pp 69–97
doi: 10.1007/978-3-030-18367-7_4
Ogaki MB, Teixeira DR, Vieira R et al (2020a) Diversity and bioprospecting of cultivable fungal assemblages in sediments of lakes in the Antarctic Peninsula. Fungal Biol 124:601–611
pubmed: 32448451
doi: 10.1016/j.funbio.2020.02.015
Ogaki MB, Vieira R, Muniz MC et al (2020b) Diversity, ecology, and bioprospecting of culturable fungi in lakes impacted by anthropogenic activities in Maritime Antarctica. Extremophiles 24:637–655
pubmed: 32533308
doi: 10.1007/s00792-020-01183-z
Ogaki MB, Câmara PEAS, Pinto OHB et al (2021) Diversity of fungal DNA in lake sediments on Vega Island, north-east Antarctic Peninsula assessed using DNA metabarcoding. Extremophiles 25:257–265
pubmed: 33837855
doi: 10.1007/s00792-021-01226-z
Oksanen J, Blanchet FG, Kindt R et al (2012) Community Ecology Package. R package version 2.0-5. Available: http://cran.r-project.org/web/packages/vegan/index.html
Píšková A, Roman M, Bulínová M et al (2019) Late-Holocene palaeoenvironmental changes at Lake Esmeralda (Vega Island, Antarctic Peninsula) based on a multi-proxy analysis of laminated lake sediment. Holocene 29:1155–1175
doi: 10.1177/0959683619838033
Pizarro H, Vinocur A, Tell G (2002) Periphyton on artificial substrata from three lakes of different trophic status at Hope Bay (Antarctica). Polar Biology 25(3):169–179. https://doi.org/10.1007/s003000100323
doi: 10.1007/s003000100323
Quesada A, Camacho A, Rochera C, Velázquez D (2009) Byers Peninsula: a reference site for coastal, terrestrial land limnetic ecosystem studies in maritime Antarctica. Polar Scie 3:181–187
doi: 10.1016/j.polar.2009.05.003
Richardson RT, Lin CH et al (2015) Application of ITS2 metabarcoding to determine the provenance of pollen collected by honey bees in an agroecosystem. Appl Plant Scie 3:1400066
doi: 10.3732/apps.1400066
Rojas-Jimenez K, Wurzbacher C, Bourne EC et al (2017) Early diverging lineages within Cryptomycota and Chytridiomycota dominate the fungal communities in ice-covered lakes of the McMurdo Dry Valleys, Antarctica. Sci Rep 7:15348
pubmed: 29127335
pmcid: 5681503
doi: 10.1038/s41598-017-15598-w
Rosa LH, Zani CL, Cantrell CL et al (2019) Fungi in Antarctica: diversity, ecology, effects of climate change, and bioprospection for bioactive compounds. In: Rosa LH (ed) Fungi of Antarctica: diversity, ecology and biotechnological applications. Springer, Switzerland, pp 1–18
doi: 10.1007/978-3-030-18367-7
Rosa LH, da Silva TH, Ogaki MB et al (2020a) DNA metabarcoding high-throughput sequencing uncovers cryptic fungal diversity in soils of protected and non-protected areas on Deception Island, Antarctica. Sci Rep 10:21986
pubmed: 33319803
pmcid: 7738542
doi: 10.1038/s41598-020-78934-7
Rosa LH, Pinto OHB, Convey P et al (2020b) DNA metabarcoding to assess the diversity of airborne fungi present in air over Keller Peninsula, King George Island, Antarctica. Microb Ecol 82:165–172
pubmed: 33161522
doi: 10.1007/s00248-020-01627-1
Rosa LH, Pinto OHB, Šantl-Temkiv T et al (2020c) DNA metabarcoding high-throughput sequencing of fungal diversity in air and snow of Livingston Island, South Shetland Islands, Antarctica. Sci Rep 10:21793
pubmed: 33311553
pmcid: 7733504
doi: 10.1038/s41598-020-78630-6
Seeber PA, von Hippel B, Kauserud H, Löber U, Stoof-Leichsenring KR, Herzschuh U, Epp LS (2021) Fungal biodiversity in Arctic paleoecosystems assessed by metabarcoding of lake sedimentary ancient DNA. bioRxiv 462738
Sogonov MV, Schroers HJ, Gams W, Dijksterhuis S (2005) The hyphomycete Teberdinia hygrophila gen. nov. sp. Nov. and related anamorphs of Pseudeurotium species. Mycologia 97:695709
doi: 10.1080/15572536.2006.11832799
Tedersoo L, Sánchez-Ramírez S, Kõljalg U et al (2018) High-level classification of the Fungi and a tool for evolutionary ecological analyses. Fungal Div 90:135–159
doi: 10.1007/s13225-018-0401-0
Vaz ABM, Rosa LH, Vieira MLA et al (2011) The diversity, extracellular enzymatic activities and photoprotective compounds of yeasts isolated in Antarctica. Braz J Microbiol 42:937–947
pubmed: 24031709
pmcid: 3768797
doi: 10.1590/S1517-83822011000300012
Vincent WF (2000) Evolutionary origins of Antarctic microbiota: invasion, selection and endemism. Antarc Sci 12:374–385
doi: 10.1017/S0954102000000420
Weber AA, Pawlowski J (2013) Can abundance of protists be inferred from sequence data: a case study of Foraminifera. PLoS ONE 8:e56739
pubmed: 23431390
pmcid: 3576339
doi: 10.1371/journal.pone.0056739
White TJ, Bruns T, Lee S et al (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR Protocols: a guide to methods and applications. Academic Press, pp 315–322
Zale R (1994a)
doi: 10.1017/S0033822200040480
Zale R (1994b) Changes in size of the Hope Bay Adelie penguin rookery as inferred from Lake Boeckella sediment. Ecography 17:297–304
doi: 10.1111/j.1600-0587.1994.tb00106.x
Zale R, Karlen W (1989) Lake sediment cores from the Antarctic Peninsula and surrounding islands. Geogr Ann 71(3–4):211–220
doi: 10.1080/04353676.1989.11880288