Advertisement

A Practical Guide to Studying the Microbiology of Karst Aquifers

  • Olivia S. Hershey
  • Jens Kallmeyer
  • Hazel A. BartonEmail author
Chapter
Part of the The Handbook of Environmental Chemistry book series (HEC, volume 68)

Abstract

Examination of microbial communities within karst aquifers is an important aspect of determining the quality of the drinking water obtained from groundwater. While past work has been based on culture-based assays, a more complete view of the microbial community within karst aquifers can be achieved using molecular approaches based on DNA sequencing. Due to a reduced cell number when compared to surface environments, collecting sufficient microbial cells for analysis in karst aquifers can be problematic. In addition to issues of cell density, particulates due to the geologic location, technological limitations of equipment that can be hand-carried and work for extended periods underground, and even the physical access to some of these subsurface sites, all contribute to making examination of the microbiology in karst aquifers a challenge. This chapter highlights some of the approaches we have used to successfully isolate microbial cells for DNA extraction from an aquifer accessed in a remote cave location. The methods we developed can aid other researchers to evaluate the microbiology of similar isolated karst aquifers.

Keywords

Cave Karst aquifer Low biomass Microbiology 

References

  1. 1.
    Griebler C, Lueders T (2009) Microbial biodiversity in groundwater ecosystems. Freshw Biol 54:649–677CrossRefGoogle Scholar
  2. 2.
    Kallmeyer J, Pockalny R, Adhikari RR, Smith DC, D’Hondt S (2012) Global distribution of microbial abundance and biomass in subseafloor sediment. Proc Natl Acad Sci U S A 109:16213–16216CrossRefGoogle Scholar
  3. 3.
    Gray CJ, Engel AS (2013) Microbial diversity and impact on carbonate geochemistry across a changing geochemical gradient in a karst aquifer. ISME 7(2):325–337CrossRefGoogle Scholar
  4. 4.
    Hug LA, Thomas BC, Brown CT, Frischkorn KR, Williams KH, Tringe SG, Banfield JF (2015) Aquifer environment selects for microbial species cohorts in sediment and groundwater. ISME J 9:1846–1856CrossRefGoogle Scholar
  5. 5.
    Cho JC, Kim SJ (2000) Increase in bacterial community diversity in subsurface aquifers receiving livestock wastewater input. Appl Environ Microbiol 66:956–965CrossRefGoogle Scholar
  6. 6.
    U.S. Environmental Protection Agency (USEPA) (2006) Volunteer estuary monitoring manual, a methods manual, 2nd edn. EPA Office of Water, Washington. EPA-842-B-06-003Google Scholar
  7. 7.
    Pronk M, Goldscheider N, Zopfi J (2006) Dynamics and interaction of organic carbon, turbidity and bacteria in a karst aquifer system. Hydrogeol J 14:473–484CrossRefGoogle Scholar
  8. 8.
    Dojka M, Hugenholtz P, Haack S, Pace N (1998) Microbial diversity in a hydrocarbon-and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microbiol 64:3869–3877Google Scholar
  9. 9.
    North NN, Dollhopf SL, Petrie L, Istok JD, Balkwill DL, Kostka JE (2004) Change in bacterial community structure during in situ biostimulation of subsurface sediment contaminated with uranium and nitrate. Appl Environ Microbiol 70:4911–4920CrossRefGoogle Scholar
  10. 10.
    Abed RMM, Safi NMD, Köster J, El-nahhal Y, Rullkötter J, De Beer D, Garcia-Pichel F (2002) Microbial diversity of a heavily polluted microbial mat and its community changes following degradation of petroleum compounds. Appl Environ Microbiol 68:1674–1683CrossRefGoogle Scholar
  11. 11.
    Ashbolt NJ, Grabow WOK, Snozzi M (2001) Indicators of microbial water quality. In: Fewtrell L, Bartram J (eds) Water quality: guidelines, standard and health. IWA Publishing, London, pp 289–316Google Scholar
  12. 12.
    Amann RI, Ludwig W, Schleifer KH, Amann RI, Ludwig W (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169Google Scholar
  13. 13.
    Gray ND, Head IM (2001) Linking genetic identity and function in communities of uncultured bacteria. Environ Microbiol 3:481–492CrossRefGoogle Scholar
  14. 14.
    Iker BC, Kambesis P, Oehrle SA, Groves C, Barton HA (2010) Microbial atrazine breakdown in a karst groundwater system and its effect on ecosystem energetics. J Environ Qual 39:509CrossRefGoogle Scholar
  15. 15.
    GSchV (1998) Water protection ordinance, SR 814.201. Swiss Federal Law, BernGoogle Scholar
  16. 16.
    Goldscheider N, Hunkeler D, Rossi P (2006) Review: microbial biocenoses in pristine aquifers and an assessment of investigative methods. Hydrogeol J 14:926–941CrossRefGoogle Scholar
  17. 17.
    Palmer AN, Palmer M (2000) Speleogenesis of the Black Hills maze caves, South Dakota, USA. In: Speleogenesis: evolution of karst aquifers. NSS, Hunstville, pp 274–281Google Scholar
  18. 18.
    Long AJ, Valder JF (2011) Multivariate analyses with end-member mixing to characterize groundwater flow: Wind Cave and associated aquifers. J Hydrol 409:315–327CrossRefGoogle Scholar
  19. 19.
    Lehman RM (2007) Understanding of aquifer microbiology is tightly linked to sampling approaches. Geomicrobiol J 24:331–341CrossRefGoogle Scholar
  20. 20.
    Elshahed MS, Senko JM, Najar FZ, Kenton SM, Roe BA, Dewers TA, Spear JR, Krumholz LR (2003) Bacterial diversity and sulfur cycling in a bacterial diversity and sulfur cycling in a mesophilic sulfide-rich spring. Appl Environ Microbiol 69:5609–5621CrossRefGoogle Scholar
  21. 21.
    Pinowska A, Stevenson RJ, Albertin A, Sickman JO, Anderson M (2007) Integrated interpretation of survey for determining nutrient thresholds for macroalgae in Florida springs: macroalgal relationships to water, sediment and macroalgae nutrients, diatom indicators and land use. Florida Department of Environmental Protection, TallahasseeGoogle Scholar
  22. 22.
    Kallmeyer J, Smith DC, Spivack AJ, D’Hondt S (2008) New cell extraction procedure applied to deep subsurface sediments. Limnol Oceanogr Methods 6:236–245CrossRefGoogle Scholar
  23. 23.
    Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science 276:734–740CrossRefGoogle Scholar
  24. 24.
    Garrido-Cardenas JA, Manzano-Agugliaro F (2017) The metagenomics worldwide research. Curr Genet 63:819–829CrossRefGoogle Scholar
  25. 25.
    Mirete S, Morgante V, Gonzalez-Pastor J (2016) Functional metagenomics of extreme environments. Curr Opin Biotechnol 38:143–149CrossRefGoogle Scholar
  26. 26.
    Miller CS, Baker BJ, Thomas BC, Singer SW, Banfield J (2011) EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome Biol 12:R44CrossRefGoogle Scholar
  27. 27.
    Suzuki MT, Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62:625–630Google Scholar
  28. 28.
    Pinto AJ, Raskin L (2012) PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS One 7:1–16Google Scholar
  29. 29.
    Head SR, Kiyomi Komori H, LaMere SA, Whisenant T, Van Nieuwerburgh F, Salomon DR, Ordoukhanian P (2014) Library construction for next-generation sequencing: overviews and challenges. BioTechniques 56:61–77CrossRefGoogle Scholar
  30. 30.
    Bowers RM, Clum A, Tice H, Lim J, Singh K, Ciobanu D, Ngan CY, Cheng J-F, Tringe SG, Woyke T (2015) Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community. BMC Genomics 16:856CrossRefGoogle Scholar
  31. 31.
    So A, Pel J, Rajan S, Marziali A (2010) Efficient genomic DNA extraction from low target concentration bacterial cultures using SCODA DNA extraction technology. Cold Spring Harb Protoc 5(10):1150–1198Google Scholar
  32. 32.
    Claassen S, du Toit E, Kaba M et al (2013) A comparison of the efficiency of five different commercial DNA extraction kits for extraction of DNA from faecal samples. J Microbiol Methods 94:103–110CrossRefGoogle Scholar
  33. 33.
    Farnleitner AH, Wilhartitz I, Ryzinska G et al (2005) Bacterial dynamics in spring water of alpine karst aquifers indicates the presence of stable autochthonous microbial endokarst communities. Environ Microbiol 7:1248–1259CrossRefGoogle Scholar
  34. 34.
    Newton RJ, Mcmahon KD (2011) Seasonal differences in bacterial community composition following nutrient additions in a eutrophic lake. Environ Microbiol 13:887–899CrossRefGoogle Scholar
  35. 35.
    Schauer M, Massana R, Pedrôs-Alio C (2000) Spatial differences in bacterioplankton composition along the Catalan coast (NW Mediterranean) assessed by molecular fingerprinting. FEMS Microbiol Ecol 33:51–59CrossRefGoogle Scholar
  36. 36.
    Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB (2005) Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc Natl Acad Sci 102:14683–14688CrossRefGoogle Scholar
  37. 37.
    Luef B, Frischkorn KR, Wrighton KC et al (2015) Diverse uncultivated ultra-small bacterial cells in groundwater. Nat Commun 6:6372CrossRefGoogle Scholar
  38. 38.
    Miyoshi T, Iwatsuki T, Naganuma T (2005) Phylogenetic characterization of 16S rRNA gene clones from deep-groundwater microorganisms that pass through 0.2-micrometer-pore-size filters. Appl Environ Microbiol 71:1084–1088CrossRefGoogle Scholar
  39. 39.
    Miteva VI, Brenchley JE (2005) Detection and isolation of ultrasmall microorganisms from a 120,000-year-old Greenland glacier ice core. Appl Environ Microbiol 71:7806–7818CrossRefGoogle Scholar
  40. 40.
    Ghai R, Mizuno CM, Picazo A et al (2013) Metagenomics uncovers a new group of low GC and ultra-small marine actinobacteria. Sci Rep 3:2471CrossRefGoogle Scholar
  41. 41.
    Maniloff J (1997) Nannobacteria: size limits and evidence. Science 276:1776–1777CrossRefGoogle Scholar
  42. 42.
    Li X, Li J (2015) Dead-end filtration. In: Droli E, Giorno L (eds) Encyclopedia of membranes. Springer, Berlin, pp 1–3Google Scholar
  43. 43.
    Petruševski B, Bolier G, Van Breemen AN, Alaerts GJ (1995) Tangential flow filtration: a method to concentrate freshwater algae. Water Res 29:1419–1424CrossRefGoogle Scholar
  44. 44.
    Marcy Y, Ouverney C, Bik EM et al (2007) Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci 104:11889–11894CrossRefGoogle Scholar
  45. 45.
    Rinke C, Schwientek P, Sczyrba A et al (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499:431–437CrossRefGoogle Scholar
  46. 46.
    Hedlund BP, Dodsworth JA, Murugapiran SK et al (2014) Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter”. Extremophiles 18:865–875CrossRefGoogle Scholar
  47. 47.
    Brown CT, Hug LA, Thomas BC et al (2015) Unusual biology across a group comprising more than 15% of domain bacteria. Nature 523:208–211CrossRefGoogle Scholar
  48. 48.
    Anantharaman K, Brown CT, Hug LA et al (2016) Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun 7:13219CrossRefGoogle Scholar
  49. 49.
    Engel AS, Randall KW (2011) Experimental evidence for microbially mediated carbonate dissolution from the saline water zone of the Edwards Aquifer, Central Texas. Geomicrobiol J 28:313–327CrossRefGoogle Scholar
  50. 50.
    Tringe S, Von MC, Kobayashi A et al (2005) Comparative metagenomics of microbial communities. Science 308:554–557CrossRefGoogle Scholar
  51. 51.
    Ward MH, deKok TM, Levallois P et al (2005) Workgroup report: drinking-water nitrate and health - recent findings and research needs. Environ Health Perspect 113:1607–1614CrossRefGoogle Scholar
  52. 52.
    Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A 95:6578–6583CrossRefGoogle Scholar
  53. 53.
    Freese HM, Karsten U, Schumann R (2006) Bacterial abundance, activity, and viability in the eutrophic river Warnow, northeast Germany. Microb Ecol 51:117–127CrossRefGoogle Scholar
  54. 54.
    Rowe JM, Debruyn JM, Poorvin L et al (2012) Viral and bacterial abundance and production in the Western Pacific Ocean and the relation to other oceanic realms. FEMS Microbiol Ecol 79:359–370CrossRefGoogle Scholar
  55. 55.
    Urbach E, Vergin KL, Young L et al (2001) Unusual bacterioplankton community structure in ultra-oligotrophic Crater Lake. Limnol Oceanogr 46:557–572CrossRefGoogle Scholar
  56. 56.
    Shabarova T, Pernthaler J (2010) Karst pools in subsurface environments: collectors of microbial diversity or temporary residence between habitat types. Environ Microbiol 12:1061–1074CrossRefGoogle Scholar
  57. 57.
    Karl DM, Bird DF, Bjorkman K et al (1999) Microorganisms in the accreted ice of Lake Vostok, Antarctica. Science 286:2144–2147CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2019

Authors and Affiliations

  • Olivia S. Hershey
    • 1
  • Jens Kallmeyer
    • 2
  • Hazel A. Barton
    • 1
    Email author
  1. 1.Department of BiologyUniversity of AkronAkronUSA
  2. 2.GFZ German Research Center for Geosciences, Section GeomicrobiologyPotsdamGermany

Personalised recommendations