Fungal communities in groundwater springs along the volcanic zone of Iceland

References

• Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389–3402. doi: 10.1093/nar/25.17.3389
   PubMed Web of Science ®Google Scholar
• Babič MN, Zalar P, Ženko B, Džeroski S, Gunde-Cimerman N. 2016. Yeasts and yeast-like fungi in tap water and groundwater, and their transmission to household appliances. Fungal Ecol. 20:30–39. doi: 10.1016/j.funeco.2015.10.001
   Web of Science ®Google Scholar
• Bengtsson-Palme J, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, De Wit P, Sánchez-García M, Ebersberger I, de Sousa F, et al. 2013. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods Ecol Evol. 4:914–919.
   Web of Science ®Google Scholar
• Bochdansky AB, Clouse MA, Herndl GJ. 2017. Eukaryotic microbes, principally fungi and labyrinthulomycetes, dominate biomass on bathypelagic marine snow. ISME J. 11:362–373. doi: 10.1038/ismej.2016.113
   Web of Science ®Google Scholar
• Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30:2114–2120. doi: 10.1093/bioinformatics/btu170
   PubMed Web of Science ®Google Scholar
• Brad T, Braster M, van Breukelen BM, van Straalen NM, Röling WF. 2008. Eukaryotic diversity in an anaerobic aquifer polluted with landfill leachate. Appl Environ Microbiol. 74:3959–3968. doi: 10.1128/AEM.02820-07
   PubMed Web of Science ®Google Scholar
• Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. 2016. Genbank. Nucleic Acids Res. 44:D67–D72. doi: 10.1093/nar/gkv1276
   PubMed Web of Science ®Google Scholar
• Comeau AM, Vincent WF, Bernier L, Lovejoy C. 2016. Novel chytrid lineages dominate fungal sequences in diverse marine and freshwater habitats. Sci Rep. 6:30120. doi: 10.1038/srep30120
   PubMed Web of Science ®Google Scholar
• de Garcia V, Zalar P, Brizzio S, Gunde-Cimerman N, van Broock M. 2012. Cryptococcus species (Tremellales) from glacial biomes in the Southern (Patagonia) and Northern (Svalbard) hemispheres. FEMS Microbiol Ecol. 82:523–539. doi: 10.1111/j.1574-6941.2012.01465.x
   Web of Science ®Google Scholar
• Ekendahl S, O’Neill AH, Thomsson E, Pedersen K. 2003. Characterisation of yeasts isolated from deep igneous rock aquifers of the Fennoscandian Shield. Microb Ecol. 46:416–428. doi: 10.1007/s00248-003-2008-5
   PubMed Web of Science ®Google Scholar
• Frenken T, Alacid E, Berger SA, Bourne EC, Gerphagnon M, Grossart HP, Gsell AS, Ibelings BW, Kagami M, Küpper FC, et al. 2017. Integrating chytrid fungal parasites into plankton ecology: research gaps and needs. Environ Microbiol. 19:3802–3822. doi: 10.1111/1462-2920.13827
   Web of Science ®Google Scholar
• Gleick PH. 1996. Water resources. In: Schneider SH, editor. Encyclopedia of climate and weather. Oxford (UK): Oxford University Press; p. 817–823.
   Google Scholar
• Geirsdóttir Á, Miller GH, Axford Y, Ólafsdóttir S. 2009. Holocene and latest Pleistocene climate and glacier fluctuations in Iceland. Quat Sci Rev. 28:2107–2118. doi: 10.1016/j.quascirev.2009.03.013
   Web of Science ®Google Scholar
• Graça MA, Hyde K, Chauvet E. 2016. Aquatic hyphomycetes and litter decomposition in tropical–subtropical low order streams. Fungal Ecol. 19:182–189. doi: 10.1016/j.funeco.2015.08.001
   Web of Science ®Google Scholar
• Griebler C, Lueders T. 2009. Microbial biodiversity in groundwater ecosystems. Freshw Biol. 54:649–677. doi: 10.1111/j.1365-2427.2008.02013.x
   Web of Science ®Google Scholar
• Grossart HP, Van den Wyngaert S, Kagami M, Wurzbacher C, Cunliffe M, Rojas-Jimenez K. 2019. Fungi in aquatic ecosystems. Nat Rev Microbiol. 17:339–354. doi: 10.1038/s41579-019-0175-8
   PubMed Web of Science ®Google Scholar
• Grossart HP, Wurzbacher C, James TY, Kagami M. 2016. Discovery of dark matter fungi in aquatic ecosystems demands a reappraisal of the phylogeny and ecology of zoosporic fungi. Fungal Ecol. 19:28–38. doi: 10.1016/j.funeco.2015.06.004
   Web of Science ®Google Scholar
• Gudmundsdóttir R, Kornobis E, Kristjánsson BK, Pálsson S. 2018. Genetic analysis of ciliates living on the groundwater amphipod Crangonyx islandicus (Amphipoda: Crangonyctidae). Acta Zool. 99:188–198. doi: 10.1111/azo.12204
   Web of Science ®Google Scholar
• Hawksworth D, Lücking R. 2017. Fungal diversity revisited: 2.2 to 3.8 million species. In: Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N, editors. The fungal kingdom. Washington (DC): ASM Press; p. 79–95.
   Google Scholar
• Heeger F, Bourne EC, Baschien C, Yurkov A, Bunk B, Spröer C, Overmann J, Mazzoni CJ, Monaghan MT. 2018. Long-read DNA metabarcoding of ribosomal RNA in the analysis of fungi from aquatic environments. Mol Ecol Resour. 18:1500–1514. doi: 10.1111/1755-0998.12937
   Web of Science ®Google Scholar
• Heeger F, Wurzbacher C, Bourne EC, Mazzoni CJ, Monaghan MT. 2019. Combining the 5.8S and ITS2 to improve classification of fungi. Methods Ecol Evol. 10:1702–1711. doi: 10.1111/2041-210X.13266
   Web of Science ®Google Scholar
• Hyde KD, Udayanga D, Manamgoda DS, Tedersoo L, Larsson E, Abarenkov K, Bertrand YJK, Oxelman B, Hartmann M, Kauserud H, et al. 2013. Incorporating molecular data in fungal systematics: a guide for aspiring researchers. Curr Res Environ Appl Mycol J Fungal Biol. 3:1–32. doi: 10.5943/cream/3/1/1
   Google Scholar
• Jones MDM, Forn I, Gadelha C, Egan MJ, Bass D, Massana R, Richards TA. 2011. Discovery of novel intermediate forms redefines the fungal tree of life. Nature. 474:200–203. doi: 10.1038/nature09984
   PubMed Web of Science ®Google Scholar
• Kagami M, Miki T, Takimoto G. 2014. Mycoloop: chytrids in aquatic food webs. Front Microbiol. 5:166. doi: 10.3389/fmicb.2014.00166
   PubMed Web of Science ®Google Scholar
• Khomich M, Cox F, Andrew CJ, Andersen T, Kauserud H, Davey ML. 2018. Coming up short: identifying substrate and geographic biases in fungal sequence databases. Fungal Ecol. 36:75–80. doi: 10.1016/j.funeco.2018.08.002
   Web of Science ®Google Scholar
• Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AF, Bahram M, Bates ST, Bengtsson-Palme J, Callaghan TM, Douglas B, et al. 2013. Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol. 22:5271–5277. doi: 10.1111/mec.12481
   PubMed Web of Science ®Google Scholar
• Kornobis E, Pálsson S, Kristjansson BK, Svavarsson J. 2010. Molecular evidence of the survival of subterranean amphipods (Arthropoda) during Ice Age underneath glaciers in Iceland. Mol Ecol. 19:2516–2530.
   Web of Science ®Google Scholar
• Kristjánsson BK, Svavarsson J. 2004. Crymostygidae, a new family of subterranean freshwater gammaridean amphipods (Crustacea) recorded from subarctic Europe. J Nat Hist. 38:1881–1894. doi: 10.1080/00222930310001597295
   Web of Science ®Google Scholar
• Lara E, Moreira D, López-García P. 2010. The environmental clade LKM11 and Rozella form the deepest branching clade of fungi. Protist. 161:116–121. doi: 10.1016/j.protis.2009.06.005
   Web of Science ®Google Scholar
• Le Calvez T, Burgaud G, Mahé S, Barbier G, Vandenkoornhuyse P. 2009. Fungal diversity in deep-sea hydrothermal ecosystems. Appl Environ Microbiol. 75:6415–6421. doi: 10.1128/AEM.00653-09
   PubMed Web of Science ®Google Scholar
• Livermore JA, Mattes TE. 2013. Phylogenetic detection of novel Cryptomycota in an Iowa (United States) aquifer and from previously collected marine and freshwater targeted high-throughput sequencing sets. Environ Microbiol. 15:2333–2341. doi: 10.1111/1462-2920.12106
   Web of Science ®Google Scholar
• Mahé F, Rognes T, Quince C, De Vargas C, Dunthorn M. 2015. Swarm v2: highly-scalable and high-resolution amplicon clustering. PeerJ. 3:e1420. doi: 10.7717/peerj.1420
   PubMed Web of Science ®Google Scholar
• Monchy S, Sanciu G, Jobard M, Rasconi S, Gerphagnon M, Chabé M, Cian A, Meloni D, Niquil N, Christaki U, et al. 2011. Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing. Environ Microbiol. 13:1433–1453. doi: 10.1111/j.1462-2920.2011.02444.x
   PubMed Web of Science ®Google Scholar
• Nawaz A, Purahong W, Lehmann R, Herrmann M, Küsel K, Totsche KU, Buscot F, Wubet T. 2016. Superimposed pristine limestone aquifers with marked hydrochemical differences exhibit distinct fungal communities. Front Microbiol. 7:666. doi: 10.3389/fmicb.2016.00666
   Web of Science ®Google Scholar
• Nawaz A, Purahong W, Lehmann R, Herrmann M, Totsche KU, Küsel K, Wubet T, Buscot F. 2018. First insights into the living groundwater mycobiome of the terrestrial biogeosphere. Water Res. 145:50–61. doi: 10.1016/j.watres.2018.07.067
   PubMed Web of Science ®Google Scholar
• Neufeld JD, Schafer H, Cox MJ, Boden R, McDonald IR, Murrell JC. 2007. Stable-isotope probing implicates Methylophaga spp. and novel Gammaproteobacteria in marine methanol and methylamine metabolism. ISME J. 1:480–491. doi: 10.1038/ismej.2007.65
   PubMed Web of Science ®Google Scholar
• Nilsson RH, Tedersoo L, Abarenkov K, Ryberg M, Kristiansson E, Hartmann M, Schoch CL, Nylander JA, Bergsten J, Porter TM, et al. 2012. Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences. MycoKeys. 4:37–63. doi: 10.3897/mycokeys.4.3606
   Google Scholar
• Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR, O’Hara RB, Simpson GL. 2017. Solymos P. vegan: community ecology package. R Package Version. 2:4–4.
   Google Scholar
• Pereira VJ, Fernandes D, Carvalho G, Benoliel MJ, San Romão MV, Crespo MB. 2010. Assessment of the presence and dynamics of fungi in drinking water sources using cultural and molecular methods. Water Res. 44:4850–4859. doi: 10.1016/j.watres.2010.07.018
   Web of Science ®Google Scholar
• Perkins A, Ganzert L, Rojas-Jimenez K, Fonvielle J, Hose G, Grossart HP. 2019. Highly diverse fungal communities in carbon-rich aquifers of two contrasting lakes in Northeast Germany. Fungal Ecol. 41:116–125. doi: 10.1016/j.funeco.2019.04.004
   Web of Science ®Google Scholar
• Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Fungal Barcoding Consortium. 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proc Natl Acad Sci USA. 109:6241–6246. doi: 10.1073/pnas.1117018109
   PubMed Web of Science ®Google Scholar
• Sohlberg E, Bomberg M, Miettinen H, Nyyssönen M, Salavirta H, Vikman M, Itävaara M. 2015. Revealing the unexplored fungal communities in deep groundwater of crystalline bedrock fracture zones in Olkiluoto, Finland. Front Microbiol. 6:573. doi: 10.3389/fmicb.2015.00573
   PubMed Web of Science ®Google Scholar
• Svavarsson J, Kristjansson BK. 2006. Crangonyx islandicus sp. nov., a subterranean freshwater amphipod (Crustacea, Amphipoda, Crangonyctidae) from springs in lava fields in Iceland. Zootaxa. 1365:1–7. doi: 10.11646/zootaxa.1365.1.1
   Google Scholar
• Sveinbjörnsdóttir ÁE, Johnsen SJ. 1992. Stable isotope study of the Thingvallavatn area. Groundwater origin, age and evaporation models. Oikos. 64:136–150. doi: 10.2307/3545049
   Web of Science ®Google Scholar
• Tedersoo L, Anslan S, Bahram M, Põlme S, Riit T, Liiv I, Kõljalg U, Kisand V, Nilsson RH, Hildebrand F, et al. 2015. Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. MycoKeys. 10:1–43. doi: 10.3897/mycokeys.10.4852
   Web of Science ®Google Scholar
• Tedersoo L, Bahram M, Puusepp R, Nilsson RH, James TY. 2017. Novel soil-inhabiting clades fill gaps in the fungal tree of life. Microbiome. 5:42. doi: 10.1186/s40168-017-0259-5
   Web of Science ®Google Scholar
• Tsui CK, Baschien C, Goh TK. 2016. Biology and ecology of freshwater fungi. In: Li DW, editor. Biology of microfungi: fungal biology. Cham (Switzerland): Springer; p. 285–313.
   Google Scholar
• Wurzbacher C, Nilsson RH, Rautio M, Peura S. 2017. Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds. ISME J. 11:1938–1941. doi: 10.1038/ismej.2017.54
   Web of Science ®Google Scholar
• Wurzbacher C, Warthmann N, Bourne EC, Attermeyer K, Allgaier M, Powell JR, Detering H, Mbedi S, Grossart HP, Monaghan MT. 2016. High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany). MycoKeys. 16:17–44. doi: 10.3897/mycokeys.16.9646
   Google Scholar
• Zhang J, Kobert K, Flouri T, Stamatakis A. 2014. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics. 30:614–620. doi: 10.1093/bioinformatics/btt593
   PubMed Web of Science ®Google Scholar