Bacterial diversity in Icelandic cold spring sources and in relation to the groundwater amphipod Crangonyx islandicus

Autoři: Ragnhildur Guðmundsdóttir aff001;  Agnes-Katharina Kreiling aff001;  Bjarni Kristófer Kristjánsson aff002;  Viggó Þór Marteinsson aff003;  Snæbjörn Pálsson aff001
Působiště autorů: Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland aff001;  Department of Aquaculture and Fish Biology, Hólar University, Sauðárkrókur, Iceland aff002;  Matis ohf./Icelandic Food and Biotech R&D, Reykjavík, Iceland aff003;  Faculty of Food Science and Nutrition, University of Iceland, Reykjavík, Iceland aff004
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article


Crangonyx islandicus is a groundwater amphipod endemic to Iceland, considered to have survived the Ice Ages in subglacial refugia. Currently the species is found in spring sources in lava fields along the tectonic plate boundary of the country. The discovery of a groundwater species in this inaccessible habitat indicates a hidden ecosystem possibly based on chemoautotrophic microorganisms as primary producers. To explore this spring ecosystem, we assessed its microbial diversity and analysed whether and how the diversity varied between the amphipods and the spring water, and if was dependent on environmental factors and geological settings. Isolated DNA from spring water and from amphipods was analysed using metabarcoding methods, targeting the 16S rRNA gene. Two genera of bacteria, Halomonas and Shewanella were dominating in the amphipod samples in terms of relative abundance, but not in the groundwater samples where Flavobacterium, Pseudomonas and Alkanindiges among others were dominating. The richness of the bacteria taxa in the microbial community of the groundwater spring sources was shaped by pH level and the beta diversity was shaped by geographic locations.

Klíčová slova:

Bacteria – Bacterial biofilms – Ecosystems – Spring – Surface water – Iceland – Archaea – Lava


1. Svavarsson J, Kristjánsson BK. Crangonyx islandicus sp nov., a subterranean freshwater amphipod (Crustacea, Amphipoda, Crangonyctidae) from springs in lava fields in Iceland. Zootaxa. 2006;1365:1–17.

2. Kristjánsson BK, Svavarsson J. Subglacial refugia in Iceland enabled groundwater amphipods to survive glaciations. The American Naturalist. 2007;170(2):292–6. doi: 10.1086/518951 17874379

3. Kornobis E, Pálsson S, Kristjánsson BK, Svavarsson J. Molecular evidence of the survival of subterranean amphipods (Arthropoda) during Ice Age underneath glaciers in Iceland. Mol Ecol. 2010;19(12):2516–30. doi: 10.1111/j.1365-294X.2010.04663.x 20465590.

4. Geirsdóttir Á, Miller GH, Andrews JT. Glaciation, erosion, and landscape evolution of Iceland. Journal of Geodynamics. 2007;43(1):170–86.

5. Buckland PC, Perry DW, Gislason GM, Dugmore AJ. The pre-Landnám fauna of Iceland: a palaeontological contribution. Boreas. 1986;15:173–84.

6. Kreiling AK, Olafsson JS, Palsson S, Kristjansson BK. Chironomidae fauna of springs in Iceland: Assessing the ecological relevance behind Tuxen's spring classification. J Limnol. 2018;77:145–54. doi: 10.4081/jlimnol.2018.1754 WOS:000453842300019.

7. Griebler C, Mindl B, Slezak D, Geiger-Kaiser M. Distribution patterns of attached and suspended bacteria in pristine and contaminated shallow aquifers studied with an in situ sediment exposure microcosm. Aquat Microb Ecol. 2002;28:117–29.

8. Hancock PJ, Boulton AJ, Humphreys WF. Aquifers and hyporheic zones: Towards an ecological understanding of groundwater. Hydrogeology Journal. 2005;13(1):98–111. doi: 10.1007/s10040-004-0421-6

9. Simon KS, Gibert J, Petitot P, Laurent R. Spatial and temporal patterns of bacterial density and metabolic activity in a karst aquifer. Archiv für Hydrobiologie. 2001;151(1):67–82.

10. Farnleitner AH, Wilhartitz I, Ryzinska G, Kirschner AK, Stadler H, Burtscher MM, et al. Bacterial dynamics in spring water of alpine karst aquifers indicates the presence of stable autochthonous microbial endokarst communities. Environ Microbiol. 2005;7(8):1248–59. doi: 10.1111/j.1462-2920.2005.00810.x 16011762.

11. Davey ME, O'Toole G A. Microbial biofilms: from ecology to molecular genetics. Microbiol Mol Biol Rev. 2000;64(4):847–67. Epub 2000/12/06. doi: 10.1128/mmbr.64.4.847-867.2000 11104821; PubMed Central PMCID: PMC99016.

12. Besemer K, Peter H, Logue JB, Langenheder S, Lindstrom ES, Tranvik LJ, et al. Unraveling assembly of stream biofilm communities. ISME J. 2012;6(8):1459–68. Epub 2012/01/13. doi: 10.1038/ismej.2011.205 22237539; PubMed Central PMCID: PMC3400417.

13. van der Kamp G. The Hydrogeology of Springs in Relation to the Biodiversity of Spring Fauna: A Review. J Kans Entomol Soc. 1995;68(2):4–17.

14. Szczucińska AM, Wasielewski H. Seasonal Water Temperature Variability of Springs From Porous Sediments in Gryżynka Valley, Western Poland. Quaestiones Geographicae. 2013;32(3):111–7. doi: 10.2478/quageo-2013-0019

15. Glazier DS. Springs. In: Likens GE, editor. Encyclopedia of Inland Waters: Academic Press; 2009. p. 734–55.

16. Gibert J, Stanford JA, Dole-Olivier M-J, Ward JV. Basic attributes of Groundwater Ecosystems and Prospects for Research. In: Thorp JH, editor. Aquatic biology series (USA). Groundwater ecology. San Diego, Ca: Academic Press, Inc.; 1994.

17. Gibert J, Deharveng L. Subterranean ecosystems: A truncated functional biodiversity. Bioscience. 2002;52(6):473–81.

18. Foulquier A, Simon L, Gilbert F, Fourel F, Malard F, Mermillod-Blondin F. Relative influences of DOC flux and subterranean fauna on microbial abundance and activity in aquifer sediments: new insights from 13C-tracer experiments. Freshwat Biol. 2010;55(7):1560–76. doi: 10.1111/j.1365-2427.2010.02385.x

19. Sarbu SM, Kane TC, Kinkle BK. A Chemoautotrophically Based Cave Ecosystem. Science. 1996;272(5270):1953–5. doi: 10.1126/science.272.5270.1953 8662497

20. Flot J-F, Bauermeister J, Brad T, Hillebrand-Voiculescu A, Sarbu SM, Dattagupta S. Niphargus–Thiothrix associations may be widespread in sulphidic groundwater ecosystems: evidence from southeastern Romania. Mol Ecol. 2014;23(6):1405–17. doi: 10.1111/mec.12461 24044653

21. Por FD. Ophel: a groundwater biome based on chemoautotrophic resources. The global significance of the Ayyalon cave finds, Israel. Hydrobiologia. 2007;592(1):1–10. doi: 10.1007/s10750-007-0795-2

22. Por FD, Dimentman C, Frumkin A, Naaman I. Animal life in the chemoautotrophic ecosystem of the hypogenic groundwater cave of Ayyalon (Israel): A summing up. Natural Science. 2013;05(04):7–13. doi: 10.4236/ns.2013.54A002

23. Dattagupta S, Schaperdoth I, Montanari A, Mariani S, Kita N, Valley JW, et al. A novel symbiosis between chemoautotrophic bacteria and a freshwater cave amphipod. ISME J. 2009;3(8):935–43. doi: 10.1038/ismej.2009.34 19360027.

24. Bauermeister J, Ramette A, Dattagupta S. Repeatedly evolved host-specific ectosymbioses between sulfur-oxidizing bacteria and amphipods living in a cave ecosystem. PLoS One. 2012;7(11):e50254. doi: 10.1371/journal.pone.0050254 23209690; PubMed Central PMCID: PMC3510229.

25. Lascu C. Paleogeographical and hydrogeological hypothesis regarding the origin of a peculiar cave fauna. Misc speol Rom Bucharest. 1989;1:13–8.

26. Galdenzi S, Cocchioni M, Morichetti L, Amici V, Scuri S. Sulfidic ground-water chemistry in the Frasassi caves, Italy. J Cave Karst Stud. 2008;70(2):94–107.

27. Bach W, Edwards KJ. Iron and sulfide oxidation within the basaltic ocean crust: Implications for chemolithoautotrophic microbial biomass production. Geochim Cosmochim Acta. 2003;67(20):3871–87. doi: 10.1016/s0016-7037(03)00304-1

28. Santelli CM, Orcutt BN, Banning E, Bach W, Moyer CL, Sogin ML, et al. Abundance and diversity of microbial life in ocean crust. Nature. 2008;453(7195):653–6. doi: 10.1038/nature06899 18509444.

29. Orcutt BN, Sylvan JB, Knab NJ, Edwards KJ. Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol Mol Biol Rev. 2011;75(2):361–422. doi: 10.1128/MMBR.00039-10 21646433; PubMed Central PMCID: PMC3122624.

30. Orcutt BN, Sylvan JB, Rogers DR, Delaney J, Lee RW, Girguis PR. Carbon fixation by basalt-hosted microbial communities. Front Microbiol. 2015;6:904. doi: 10.3389/fmicb.2015.00904 26441854; PubMed Central PMCID: PMC4561358.

31. Barquín J, Scarsbrook M. Management and conservation strategies for coldwater springs. Aquat Conserv: Mar Freshwat Ecosyst. 2008;18(5):580–91. doi: 10.1002/aqc.884

32. Cantonati M, Gerecke R, Bertuzzi E. Springs of the Alps–Sensitive Ecosystems to Environmental Change: From Biodiversity Assessments to Long-term Studies. Hydrobiologia. 2006;562(1):59–96. doi: 10.1007/s10750-005-1806-9

33. Cantonati M, Füreder L, Gerecke R, Jüttner I, Cox EJ. Crenic habitats, hotspots for freshwater biodiversity conservation: toward an understanding of their ecology. Freshwater Science. 2012;31(2):463–80. doi: 10.1899/11-111.1

34. Power JF, Carere CR, Lee CK, Wakerley GLJ, Evans DW, Button M, et al. Microbial biogeography of 925 geothermal springs in New Zealand. Nat Commun. 2018;9(1):2876. doi: 10.1038/s41467-018-05020-y 30038374; PubMed Central PMCID: PMC6056493.

35. Árnason B. Groundwater systems in Iceland traced by deuterium. Reykjavík: Vísindafélag Íslendinga; 1976. 236 p.

36. Koreimann C, Grath J, Winkler G, Nagy W, Vogel WR. Groundwater monitoring in Europe. Copenhagen: European Environmental Agency, 1996 Contract No.: Topic report No 14/1996.

37. Sveinbjörnsdóttir ÁE, Johnsen SJ. Stable isotope study of the Thingvallavatn area. Groundwater origin, age and evaporation models. Oikos. 1992;64:136–50.

38. Sigurdsson O, Stefansson V. Porosity structure of Icelandic basalt. Proceedings of the Estonian Academy of Sciences, Geology. 2002;51(1):33–46.

39. Tuxen SL. The hot springs, their animal communities and their zoogeographical significance. Friðriksson Á, Tuxen SL, editors. Copenhagen and Reykjavík: Carsberg-Fond, Rask-Ørsted-Fond and Sáttmálasjóður; 1944.

40. Govoni DP, Kristjánsson BK, Ólafsson JS. Spring type influences invertebrate communities at cold spring sources. Hydrobiologia. 2018;808:315–25. doi: 10.1007/s10750-017-3434-6

41. Taberlet P, Coissac E, Hajibabaei M, Rieseberg LH. Environmental DNA. Mol Ecol. 2012;21:1789–93. doi: 10.1111/j.1365-294X.2012.05542.x 22486819

42. Voisin J, Cournoyer B, Mermillod-Blondin F. Assessment of artificial substrates for evaluating groundwater microbial quality. Ecol Indicators. 2016;71:577–86. doi: 10.1016/j.ecolind.2016.07.035

43. Eiríksdóttir ES, Gíslason SR. Efnasamsetning Þingvallavatns 2007–2012. Reykjavík: Jarðvísindastofnun Háskólans, 2013.

44. Bartrons M, Einarsson Á, Nobre RLG, Herren CM, Webert KC, Brucet S, et al. Spatial patterns reveal strong abiotic and biotic drivers of zooplankton community composition in Lake Mývatn, Iceland. Ecosphere. 2015;6(6):art105. doi: 10.1890/es14-00392.1

45. Neufeld JD, Schafer H, Cox MJ, Boden R, McDonald IR, Murrell JC. Stable-isotope probing implicates Methylophaga spp and novel Gammaproteobacteria in marine methanol and methylamine metabolism. ISME J. 2007;1(6):480–91. doi: 10.1038/ismej.2007.65 18043650.

46. Herlemann DP, Labrenz M, Jurgens K, Bertilsson S, Waniek JJ, Andersson AF. Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J. 2011;5(10):1571–9. doi: 10.1038/ismej.2011.41 21472016; PubMed Central PMCID: PMC3176514.

47. Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41(1):e1. doi: 10.1093/nar/gks808 22933715; PubMed Central PMCID: PMC3592464.

48. Boyer F, Mercier C, Bonin A, Le Bras Y, Taberlet P, Coissac E. OBITools: a UNIX-inspired software package for DNA metabarcoding. Mol Ecol Resour. 2016;16(1):176–82. doi: 10.1111/1755-0998.12428 25959493.

49. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41(Database issue):D590–6. doi: 10.1093/nar/gks1219 23193283; PubMed Central PMCID: PMC3531112.

50. Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, et al. The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucleic Acids Res. 2014;42(Database issue):D643–8. doi: 10.1093/nar/gkt1209 24293649; PubMed Central PMCID: PMC3965112.

51. Oksanen J, Guillaume Blanchet F, Friendly M, Kindt R, Legendre P, McGlinn D, et al. vegan: Community Ecology Package. 2017:R package version 2.4–3

52. R Core Team. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing; 2017.

53. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A. 2011;108 Suppl 1:4516–22. doi: 10.1073/pnas.1000080107 20534432; PubMed Central PMCID: PMC3063599.

54. Chen H. VennDiagram: Generate High-Resolution Venn and Euler Plots. 2016:R package version 1.6.17

55. P. L, L. L. Numerical ecology. 2nd ed. Amsterdam: Elsevier science B.V.; 1998.

56. Paradis E., Claude J., K. S. APE: analyses of phylogenetics and evolution in R language. Bioinformatics. 2004;20:289–90. doi: 10.1093/bioinformatics/btg412 14734327

57. Schmidt SI, Hahn HJ. What is groundwater and what does this mean to fauna?—An opinion. Limnologica. 2012;42(1):1–6. doi: 10.1016/j.limno.2011.08.002 WOS:000298779100001.

58. Guðmundsson K. Environmental microbial diversity and anthropogenic impact on Lake Thingvallavatn basin: University of Iceland; 2014.

59. Lauber CL, Hamady M, Knight R, Fierer N. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol. 2009;75(15):5111–20. doi: 10.1128/AEM.00335-09 19502440; PubMed Central PMCID: PMC2725504.

60. Bartram AK, Jiang X, Lynch MD, Masella AP, Nicol GW, Dushoff J, et al. Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm. FEMS Microbiol Ecol. 2014;87(2):403–15. doi: 10.1111/1574-6941.12231 24117982.

61. Yun Y, Wang H, Man B, Xiang X, Zhou J, Qiu X, et al. The Relationship between pH and Bacterial Communities in a Single Karst Ecosystem and Its Implication for Soil Acidification. Front Microbiol. 2016;7:1955. doi: 10.3389/fmicb.2016.01955 28018299; PubMed Central PMCID: PMC5159436.

62. Fritscher J. Untersuchungen über Sulfid-Schwefelquellen in Bayern Beiträge zum ökologischen Monitoring und zur Entwicklung von biotechnologischen Methoden für die Grundwasserreinigung [PhD Thesis]. Nürnberg, Germany: Universität Erlangen; 2004.

63. Cockell CS, Kelly LC, Summers S, Marteinsson V. Following the kinetics: iron-oxidizing microbial mats in cold icelandic volcanic habitats and their rock-associated carbonaceous signature. Astrobiology. 2011;11(7):679–94. doi: 10.1089/ast.2011.0606 21895443.

64. Trias R, Menez B, le Campion P, Zivanovic Y, Lecourt L, Lecoeuvre A, et al. High reactivity of deep biota under anthropogenic CO2 injection into basalt. Nat Commun. 2017;8(1):1063. doi: 10.1038/s41467-017-01288-8 29051484; PubMed Central PMCID: PMC5648843.

65. Falasco E, Ector L, Isaia M, Wetzel C, Hoffmann L, Bona F. Diatom flora in subterranean ecosystems: a review. International Journal of Speleology. 2014;43(3):231–51. doi: 10.5038/1827-806x.43.3.1

66. Mogna M, Cantonati M, Andreucci F, Angeli N, Berta G, Miserere L. Diatom communities and vegetation of springs in the south-western Alps. Acta Bot Croat. 2015;74(2):265–85. doi: 10.1515/botcro-2015-0024

67. Ortiz-Alvarez R, Casamayor EO. High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes. Environ Microbiol Rep. 2016;8(2):210–7. doi: 10.1111/1758-2229.12370 26711582.

68. Apprill A, McNally S, Parsons R, Weber L. Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton. Aquat Microb Ecol. 2015;75(2):129–37. doi: 10.3354/ame01753

69. Koskinen K, Pausan MR, Perras AK, Beck M, Bang C, Mora M, et al. First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin. mBio. 2017;8(6):e00824–17. doi: 10.1128/mBio.00824-17 29138298

70. Narrowe AB, Angle JC, Daly RA, Stefanik KC, Wrighton KC, Miller CS. High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils. Environ Microbiol. 2017;19(6):2192–209. doi: 10.1111/1462-2920.13703 28217877.

71. Vreeland RH. Halomonas. Bergey's Manual of Systematics of Archaea and Bacteria: John Wiley & Sons, Ltd; 2015.

72. Gavish Y, Kedem H, Messika I, Cohen C, Toh E, Munro D, et al. Association of host and microbial species diversity across spatial scales in desert rodent communities. PLoS One. 2014;9(10):e109677. doi: 10.1371/journal.pone.0109677 25343259; PubMed Central PMCID: PMC4208758.

73. Manzari C, Fosso B, Marzano M, Annese A, Caprioli R, D´Erichia AM, et al. The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy. Biol Invasions. 2015;17:923–40. doi: 10.1007/s10530-014-0810-2).

74. Simon-Colin C, Raguenes G, Cozien J, Guezennec JG. Halomonas profundus sp. nov., a new PHA-producing bacterium isolated from a deep-sea hydrothermal vent shrimp. J Appl Microbiol. 2008;104(5):1425–32. doi: 10.1111/j.1365-2672.2007.03667.x 18179545.

75. Newsome L, Lopez Adams R, Downie HF, Moore KL, Lloyd JR. NanoSIMS imaging of extracellular electron transport processes during microbial iron(III) reduction. FEMS Microbiol Ecol. 2018;94(8). doi: 10.1093/femsec/fiy104 29878195; PubMed Central PMCID: PMC6041951.

76. Bowman JP. Shewanella. Bergey's Manual of Systematics of Archaea and Bacteria: John Wiley & Sons, Ltd; 2015.

77. Bowman JP, McCammon SA, Nichols DS, Skerratt JH, Rea SM, Nichols PD, et al. Shewanella gelidimarina sp. nov. and Shewanella figidimarina sp. nov., Novel Antarctic Species with the Ability To Produce Eicosapentaenoic Acid (20:503) and Grow Anaerobically by Dissimilatory Fe (111) Reduction Int J Syst Bacteriol. 1997;47(4).

78. Lysnes K, Thorseth IH, Steinsbu BO, Ovreas L, Torsvik T, Pedersen RB. Microbial community diversity in seafloor basalt from the Arctic spreading ridges. FEMS Microbiol Ecol. 2004;50(3):213–30. doi: 10.1016/j.femsec.2004.06.014 19712362.

79. Chang HW, Roh SW, Kim KH, Nam YD, Jeon CO, Oh HM, et al. Shewanella basaltis sp. nov., a marine bacterium isolated from black sand. Int J Syst Evol Microbiol. 2008;58(8):1907–10. doi: 10.1099/ijs.0.65725–0 18676478.

80. Gislason SR, Arnorsson S, Armannsson H. Chemical weathering of basalt in southwest Iceland: Effects of runoff, age of rocks and vegetative/glacial cover. Am J Sci. 1996;296:837–907.

81. Lutz RA, Kennish MJ. Ecology of deep-sea hydrothermal vent communities: A review. Rev Geophys. 1993;31(3):211–42.

82. Tandberg AH, Rapp HT, Schander C, Vader W, Sweetman AK, Berge J. Exitomelita sigynae gen. et sp. nov.: a new amphipod from the Arctic Loki Castle vent field with potential gill ectosymbionts. Polar Biol. 2011;35(5):705–16. doi: 10.1007/s00300-011-1115-x

83. Jan C, Petersen JM, Werner J, Teeling H, Huang S, Glockner FO, et al. The gill chamber epibiosis of deep-sea shrimp Rimicaris exoculata: an in-depth metagenomic investigation and discovery of Zetaproteobacteria. Environ Microbiol. 2014;16(9):2723–38. doi: 10.1111/1462-2920.12406 24447589.

84. Pakes JM, Mejía-Ortiz L, Weis AK. Arthropods host intracellular chemosynthetic symbionts, too: cave study reveals an unusual form of symbiosis. J Crust Biol. 2014;34(3):334–41. doi: 10.1163/1937240x-00002238

Článek vyšel v časopise


2019 Číslo 10
Nejčtenější tento týden