Attached and Suspended Denitrifier Communities in Pristine Limestone Aquifers Harbor High Fractions of Potential Autotrophs Oxidizing Reduced Iron and Sulfur Compounds

Abstract

Oxygen and nitrate availability as well as the presence of suitable organic or inorganic electron donors are strong drivers of denitrification; however, the factors influencing denitrifier abundance and community composition in pristine aquifers are not well understood. We explored the denitrifier community structure of suspended and attached groundwater microorganisms in two superimposed limestone aquifer assemblages with contrasting oxygen regime in the Hainich Critical Zone Exploratory (Germany). Attached communities were retrieved from freshly crushed parent rock material which had been exposed for colonization in two groundwater wells (12.7 and 48 m depth). Quantitative PCR and amplicon pyrosequencing of nirK and nirS genes encoding copper-containing or cytochrome cd1 heme-type nitrite reductase, respectively, and of bacterial 16S ribosomal RNA genes showed a numerical predominance of nirS-type denitrifiers in both attached and suspended groundwater communities and a dominance of nirS-type denitrifiers closely related to the autotrophic thiosulfate- and hydrogen-oxidizing Sulfuritalea hydrogenivorans and the iron- and sulfide-oxidizing Sideroxydans lithotrophicus ES-1. Potential rates of nitrate reduction in association with exposed crushed rock material were higher with an inorganic electron donor (thiosulfate) compared to an organic electron donor (fumarate/acetate) in the upper aquifer assemblage but similar in the lower, oxic aquifer. Our results have clearly demonstrated that groundwater from pristine limestone aquifers harbors diverse denitrifier communities which appear to selectively attach to rock surfaces and harbor a high potential for nitrate reduction. Our findings suggest that the availability of suitable inorganic versus organic electron donors rather than oxygen availability shapes denitrifier communities and their potential activity in these limestone aquifers.

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References

  1. 1.

    Pucket LJ, Cowdery TK (2002) Transport and fate of nitrate in a glacial outwash aquifer in relation to ground water age, land use practices, and redox processes. J. Environ. Qual. 31:782–7965

    Article  Google Scholar 

  2. 2.

    Rivett MO, Buss SR, Morgan P, Smith JWN, Bemment CD (2008) Nitrate attenuation in groundwater: a review of biogeochemical controlling processes. Water Res. 42:4215–4232

    CAS  Article  PubMed  Google Scholar 

  3. 3.

    Ford DC, Williams PW (2007) Karst geomorphology and hydrology, 2nd edn. John Wiley & Sons, Chichester, U.K.

    Google Scholar 

  4. 4.

    Einsiedl F, Mayer B (2006) Hydrodynamic and microbial processes controlling nitrate in a fissured-porous karst aquifer of the Franconian Alb, Southern Germany. Environ Sci Technol 40:6697–6702

    CAS  Article  PubMed  Google Scholar 

  5. 5.

    Zumft WG (1997) Cell biology and molecular basis of denitrification. Microbiol Mol Biol Reviews 61:533–616

    CAS  Google Scholar 

  6. 6.

    Knowles R (1982) Denitrification. Microbio Rev 46:43–70

    CAS  Google Scholar 

  7. 7.

    Schlesinger WH (2009) On the fate of anthropogenic nitrogen. Proc. Natl. Acad. Sci. U. S. A. 106:203–208

    CAS  Article  PubMed  Google Scholar 

  8. 8.

    Rütting T, Boeckx P, Müller C, Klemedtsson L (2011) Assessment of the importance of dissimilatory nitrate reduction to ammonium for the terrestrial nitrogen cycle. Biogeosciences 8:1779–1791

    Article  Google Scholar 

  9. 9.

    Strous M, Fuerst JA, Kramer EHM, Logemann S, Muyzer G, van de Pas-Schoonen KT, Webb R, Kuenen JG, Jetten MSM (1999) Missing lithotroph identified as new planctomycete. Nature 400:446–449

    CAS  Article  PubMed  Google Scholar 

  10. 10.

    Mariotti A, Landreau A, Simon B (1988) 15N isotope biogeochemistry and natural denitrification process in groundwater: application ot the chalk aquifer of northern France. Geochim. Cosmochim. Acta 52:1869–1878

    CAS  Article  Google Scholar 

  11. 11.

    Smith RL, Howes BL, Duff JH (1991) Denitrification in nitrate contaminated groundwater: occurrence in steep vertical geochemical gradients. Geochim. Cosmochim. Acta 55:1815–1825

    CAS  Article  Google Scholar 

  12. 12.

    Morris JT, Whiting GJ, Chapelle FH (1988) Potential denitrification rates in deep sediments from the Southeastern Coastal Plain. Environ Sci Technol 22:832–836

    CAS  Article  PubMed  Google Scholar 

  13. 13.

    Neilsen ME, Fisk MR, Istok JD, Pedersen K (2006) Microbial nitrate respiration of lactate at in situ conditions in groundwater from a granitic aquifer situated 450 m underground. Geobiology 4:43–52

    Article  Google Scholar 

  14. 14.

    Böttcher J, Strebel O, Voerkelius S, Schmidt HL (1990) Using isotope fractionation of nitrate nitrogen and nitrate oxygen for evaluation of microbial denitrification in a sandy aquifer. J. Hydrol. 114:413–424

    Article  Google Scholar 

  15. 15.

    Schippers A, Jozsa PG, Sand W (1996) Sulfur chemistry in bacterial leaching of pyrite. Appl. Environ. Microbiol. 62:3424–3431

    CAS  PubMed  PubMed Central  Google Scholar 

  16. 16.

    Rimstidt JD, Vaughan DJ (2003) Pyrite oxidation: a state-of-the-art assessment of the reaction mechanism. Geochim. Cosmochim. Acta 67:873–880

    CAS  Article  Google Scholar 

  17. 17.

    Schwientek M, Einsiedl F, Stichler W, Stögbauer A, Strauss H, Maloszewski P (2008) Evidence for denitrification regulated by pyrite oxidation in a heterogeneous porous groundwater system. Chem. Geol. 255:60–67

    CAS  Article  Google Scholar 

  18. 18.

    Zhang Y-C, Slomp CP, Broers HP, Bostick B, Passier HF, Böttcher ME, Omoregie EO, Lloyd JR, Polya DA, Van Cappellen P (2012) Isotopic and microbiological signatures of pyrite-driven denitrification in a sandy aquifer. Chem. Geol. 300-301:123–132

    CAS  Article  Google Scholar 

  19. 19.

    Braker G, Dörsch P, Bakken Lars R (2012) Genetic characterization of denitrifier communities with contrasting intrinsic functional traits. FEMS Microbiol. Ecol. 79:542–554

    CAS  Article  PubMed  Google Scholar 

  20. 20.

    Palmer K, Horn MA (2015) Denitrification activity of a remarkably diverse fen denitrifier community in Finnish Lapland is N-oxide limited. PLoS One 10:e0123123

    Article  PubMed  PubMed Central  Google Scholar 

  21. 21.

    Saarenheimo J, Tiirolaa MA, Rissanen AJ (2015) Functional gene pyrosequencing reveals core proteobacterial denitrifiers in boreal lakes. Frontiers Microbiol 6:674

    Article  Google Scholar 

  22. 22.

    Kim OS, Imhoff JS, Witzel K-P, Junier P (2011) Distribution of denitrifying bacterial communities in the stratified water column and sediment–water interface in two freshwater lakes and the Baltic Sea. Aquat. Ecol. 45:99–112

    CAS  Article  Google Scholar 

  23. 23.

    Ward BB, Devol AH, Rich JJ, Chang BX, Bulow SE, Naik H, Pratihary A, Jayakumar A (2009) Denitrification as the dominant nitrogen loss process in the Arabian Sea. Nature 461:78–82

    CAS  Article  PubMed  Google Scholar 

  24. 24.

    Yan TF, Fields MW, Wu LY, Zu YG, Tiedje JM, Zhou JZ (2003) Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater. Environ. Microbiol. 5:13–24

    CAS  Article  PubMed  Google Scholar 

  25. 25.

    Barrett M, Jahangir MMR, Lee C, Smith CJ, Bhreathnach N, Collins G, Richards KG, O’Flaherty V (2013) Abundance of denitrification genes under different piezometer depths in four Irish agricultural groundwater sites. Environ. Sci. Pollut. Res. 20:6646–6657

    CAS  Article  Google Scholar 

  26. 26.

    Bellini I, Gutiérrez L, Tarlera S, Scavino AF (2013) Isolation and functional analysis of denitrifiers in an aquifer with highpotential for denitrification. Syst. Appl. Microbiol. 36:505–516

    CAS  Article  PubMed  Google Scholar 

  27. 27.

    Santoro A, Boehm AB, Francis CA (2006) Denitrifier community composition along a nitrate and salinity gradient in a coastal aquifer. Appl. Environ. Microbiol. 72:2102–2109

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  28. 28.

    Katsuyama C, Nashimoto H, Nagaosa K, Ishibashi T, Furuta K, Kinoshita T, Yoshikawa H, Aoki K, Asano T, Sasaki Y, Sohrin R, Komatsu DD, Tsunogai U, Kimura H, Suwa Y, Kato K (2013) Occurrence and potential activity of denitrifiers and methanogens in groundwater at 140 m depth in Pliocene diatomaceous mudstone of northern Japan. FEMS Microbiol. Ecol. 86:532–543

    CAS  Article  PubMed  Google Scholar 

  29. 29.

    Kölbelboelke J, Anders EM, Nehrkorn A (1988) Microbial communities in the saturated groundwater environment. 2. Diversity of bacterial communities in a pleistocene sand aquifer and their invitro activities. Microb Ecol 16:31–48

    Article  Google Scholar 

  30. 30.

    Griebler C, Lueders T (2009) Microbial biodiversity in groundwater ecosystems. Freshw. Biol. 54:649–677

    Article  Google Scholar 

  31. 31.

    Griebler C, Avramov M (2015) Groundwater ecosystem services: a review. Freshwater Science 34:355–367

    Article  Google Scholar 

  32. 32.

    Yu T, Bishop PL (1998) Stratification of microbial metabolic processes and redox potential change in an aerobic biofilm studied using microelectrodes. Water Sci. Technol. 37:195–198

    CAS  Article  Google Scholar 

  33. 33.

    Bishop PL, Yu T (1999) A microelectrode study of redox potential changes in biofilms. Water Sci. Technol. 39:179–185

    CAS  Article  Google Scholar 

  34. 34.

    Lehman RM, Roberto FF, Earley D, Bruhn DF, Brink SE, O’Connell SP, Delwiche ME, Colwell FS (2001) Attached and unattached bacterial communities in a 120-meter corehole in an acidic, crystalline rock aquifer. Appl. Environ. Microbiol. 67:2095–2106

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  35. 35.

    Besemer K, Moeseneder MM, Arrieta JM, Herndl GJ, Peduzzi P (2005) Complexity of bacterial communities in a river-floodplain system (Danube, Austria). Appl. Environ. Microbiol. 71:609–620

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  36. 36.

    Iribar A, Sanchez-Perez JM, Lyautey E, Garabetian F (2008) Differentiated free-living and sediment-attached bacterial community structure inside andoutside denitrification hotspots in the river-groundwater interface. Hydrobiologia 598:109–121

    CAS  Article  Google Scholar 

  37. 37.

    Küsel K, Totsche KU, Trumbore SE, Lehmann R, Steinhäuser C, Herrmann M (2016) How deep can surface signals be traced in the critical zone? Merging biodiversity with biogeochemistry research in a central German Muschelkalk landscape. Front. Earth Sci. 4:32. doi:10.3389/feart.2016.00032

    Article  Google Scholar 

  38. 38.

    Kohlhepp B, Lehmann R, Seeber P, Küsel K, Trumbore SE, Totsche KU (2016) Pedological and hydrogeological setting and subsurface flow structure of the carbonate-rock CZE Hainich in western Thuringia, Germany. Hydrology and Earth System Sciences. doi:10.5194/hess-2016-374

    Google Scholar 

  39. 39.

    DEV. 1975 Deutsche Einheitsverfahren zur Wasser-, Abwasser- und Schlammuntersuchung. Physikalische, chemische, biologische und bakteriologische Verfahren. Ed Fachgruppe Wasserchemie in der Gesellschaft Deutscher Chemiker in Gemeinschaft mit dem Normenausschuß Wasserwesen (NAW) im DIN Deutsches Institut für Normung e. V. VCH Verlagsgesellschaft Weinheim, Germany

  40. 40.

    Grasshoff K, Ehrhardt M, Kremling K (1983) Methods of seawater analysis, 2nd edn. Chemie, Weinheim

    Google Scholar 

  41. 41.

    Herrmann M, Rusznyak A, Akob DM, Schulze I, Opitz S, Totsche KU, Küsel K (2015) Large fractions of CO2-fixing microorganisms in pristine limestone aquifers appear to be involved in the oxidation of reduced sulfur and nitrogen compounds. Appl. Environ. Microbiol. 81:2384–2394

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  42. 42.

    Griebler C, Mindl B, Slezak D, Geiger-Kaiser M (2002) Distribution patterns of attached and suspended bacteria in pristine and contaminated shallow aquifers studied with an in situ sediment exposure microcosm. Aquat. Microb. Ecol. 28:117–129

    Article  Google Scholar 

  43. 43.

    Church MJ, Wai B, Karl DM, DeLong EF (2010) Abundances of crenarchaeal amoA genes and transcripts in the Pacific Ocean. Environ. Microbiol. 12:679–688

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  44. 44.

    Opitz S, Küsel K, Spott O, Totsche KU, Herrmann M (2014) Oxygen availability and distance to surface environments determine community composition and abundance of ammonia oxidizing prokaryotes in two superimposed pristine limestone aquifers in the Hainich region, Germany. FEMS Microbiol. Ecol. 9:39–53

    Article  Google Scholar 

  45. 45.

    Barton HA, Taylor NM, Lubbers BR, Pemberton AC (2006) DNA extraction from low-biomass carbonate rock: an improved method with reduced contamination and the low-biomass contaminant database. J. Microbiol. Methods 66:21–31

    CAS  Article  PubMed  Google Scholar 

  46. 46.

    Throbäck IN, Enwall K, Jarvis A, Hallin S (2004) Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiol. Ecol. 49:401–417

    Article  PubMed  Google Scholar 

  47. 47.

    Hallin S, Lindgren P (1999) PCR detection of genes encoding nitrite reductase in denitrifying bacteria. Appl. Environ. Microbiol. 65:1652–1657

    CAS  PubMed  PubMed Central  Google Scholar 

  48. 48.

    Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. John Wiley and Sons, New York, pp. 115–175

    Google Scholar 

  49. 49.

    Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:695–700

    CAS  PubMed  PubMed Central  Google Scholar 

  50. 50.

    Ludwig W, Strunk O, Westram R, Richter L, Meier H, Kumar Y, Buchner A, Lai T, Steppi S, Jobb G, Förster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, König A, Liss T, Lüßmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer K-H (2004) ARB: a software environment for sequence data. Nuc Acids Res 32:1363–1371

    CAS  Article  Google Scholar 

  51. 51.

    Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75:7537–7541

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  52. 52.

    Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  53. 53.

    Palmer K, Biasi C, Horn MA (2012) Contrasting denitrifier communities relate to contrasting N2O emission patterns from acidic peat soil in arctic tundra. ISME J 6:1058–1077

    CAS  Article  PubMed  Google Scholar 

  54. 54.

    Fish JA, Chai B, Wang Q, Sun Y, Brown CT, Tiedje JM, Cole JR (2013) FunGene: the functional gene pipeline and repository. Front. Microbiol. 4:291

    Article  PubMed  PubMed Central  Google Scholar 

  55. 55.

    Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41(D1):D590–D596

    CAS  Article  PubMed  Google Scholar 

  56. 56.

    Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD (2013) Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl. Environ. Microbiol. 79:5112–5120

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  57. 57.

    Daims H, Brühl A, Amann R, Schleifer K-H, Wagner M (1999) The domain-specific probe EUB338 is insufficient for the detection of all bacteria: development and evaluation of a more comprehensive probe set. Syst. Appl. Microbiol. 22:434–444

    CAS  Article  PubMed  Google Scholar 

  58. 58.

    Loy A, Lehner A, Lee N, Adamczyk J, Meier H, Ernst J, Schleifer K-H, Wagner M (2002) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl. Environ. Microbiol. 68:5064–5081

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  59. 59.

    Delong EF (1992) Archaea in coastal marine environments. Proc. Natl. Acad. Sci. U. S. A. 89:5685–5689

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  60. 60.

    Takai K, Horikoshi K (2000) Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes. Appl. Environ. Microbiol. 66:5066–5072

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  61. 61.

    Herrmann M, Hädrich A, Küsel K (2012) Predominance of thaumarchaeal ammonia oxidizer abundance and transcriptional activity in an acidic fen. Environ. Microbiol. 14:3013–3025

    CAS  Article  PubMed  Google Scholar 

  62. 62.

    Kojima H, Watanabe T, Fukui M (2016) Sulfuricaulis limicola gen. nov., sp. nov., a sulfur-oxidizer isolated from a lake. Int. J. Syst. Evol. Microbiol. 66:266–270

    CAS  Article  PubMed  Google Scholar 

  63. 63.

    Kojima H, Shinohara A, Fukui M (2015) Sulfurifustis variabilis gen. nov., sp. nov., a sulfur oxidizer isolated from a lake, and proposal of Acidiferrobacteraceae fam. nov. and Acidiferrobacterales ord. nov. Int. J. Syst. Evol. Microbiol. 65:3709–3713

    CAS  Article  PubMed  Google Scholar 

  64. 64.

    Emerson D, Moyer C (1997) Isolation and characterization of novel iron-oxidizing bacteria that grow at circumneutral pH. Appl. Environ. Microbiol. 63:4784–4792

    CAS  PubMed  PubMed Central  Google Scholar 

  65. 65.

    Willems A, Busse J, Goor B, Pot B, Falsen E, Jantzen E, Hoste B, Gillis M, Kersters K, Auling G, de Ley J (1989) Hydrogenophaga, a new genus of hydrogen-oxidizing bacteria that includes Hydrogenophaga flava comb. nov. (formerly Pseudomonas flava), Hydrogenophaga palleronii (formerly Pseudomonas palleronii), Hydrogenophaga pseudoflava (formerly Pseudomonas pseudoflava and “Pseudomonas carboxydoflava”), and Hydrogenophaga taeniospiralis (formerly Pseudomonas taeniospiralis). Int. J. Syst. Bacteriol. 39:319–333

    CAS  Article  Google Scholar 

  66. 66.

    Green CT, Bohlke JK, Bekins BA, Phillips SP (2010) Mixing effects on apparent reaction rates and isotope fractionation during denitrification in a heterogeneous aquifer. Water Resour. Res. 46:W08525

    Article  Google Scholar 

  67. 67.

    McMahon PB, Bohlke JK, Christenson SC (2004) Geochemistry, radiocarbon ages, and paleorecharge conditions along a transect in the central High Plains aquifer, southwestern Kansas, USA. Appl. Geochem. 19:1655–1686

    CAS  Article  Google Scholar 

  68. 68.

    Tesoriero AJ, Puckett LJ (2011) O2 reduction and denitrification rates in shallow aquifers. Water Resour. Res. 47:W12522

    Article  Google Scholar 

  69. 69.

    Ramsing NB, Kühl M, Jørgensen BB (1993) Distribution of sulfate-reducing bacteria, O2, and H2S in photosynthetic biofilms determined by oligonucleotide probes and microelectrodes. Appl. Environ. Microbiol. 59:3840–3849

    CAS  PubMed  PubMed Central  Google Scholar 

  70. 70.

    De Beer D, Stoodley P, Roe F, Lewandowski Z (1994) Effects of biofilm structures on oxygen distribution and mass transport. Biotechnol. Bioeng. 43:1131–1138

    CAS  Article  PubMed  Google Scholar 

  71. 71.

    Knapp C, Dodds WK, Wilson KC, O’Brien JM, Graham DW (2009) Spatial heterogeneity of denitrification genes in a highly homogenous urban stream. Environ Sci Technol 43:4273–4279

    CAS  Article  PubMed  Google Scholar 

  72. 72.

    Graham DW, Trippett C, Dodds WK, O’Brien JM, Banner EB, Head IM, et al. (2010) Correlations between in situ denitrification activity and nir- gene abundances in pristine and impacted prairie streams. Environ. Pollut. 158:3225–3229

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  73. 73.

    Tatariw C, Chapman EL, Sponseller RA, Mortazavi B, Edmonds JW (2013) Denitrification in a large river: consideration of geomorphic controls on microbial activity and community structure. Ecology 94:2249–2262

    Article  PubMed  Google Scholar 

  74. 74.

    Abell GCJ, Revill AT, Smith C, Bissett AP, Volkman JK, Robert SS (2010) Archaeal ammonia oxidizers and nirS-type denitrifiers dominate sediment nitrifying and denitrifying populations in a subtropical macrotidal estuary. ISME J 4:286–300

    CAS  Article  PubMed  Google Scholar 

  75. 75.

    Li M, Hong Y, Cao H, Klotz MG, Gu JD (2013) Diversity, abundance, and distribution of NO-forming nitrite reductase-encoding genes in deep-sea subsurface sediments of the South China Sea. Geobiology 11:170–179

    CAS  Article  PubMed  Google Scholar 

  76. 76.

    Kojima H, Fukui M (2011) Sulfuritalea hydrogenivorans gen. nov., sp. nov., a facultative autotroph isolated from a freshwater lake. Int. J. Syst. Evol. Microbiol. 61:1651–1655

    CAS  Article  PubMed  Google Scholar 

  77. 77.

    Schedel M, Trüper HG (1980) Anaerobic oxidation of thiosulfate and elemental sulfur in Thiobacillus denitrificans. Arch. Microbiol. 124:205–210

    CAS  Article  Google Scholar 

  78. 78.

    Kojima H, Fukui M (2010) Sulfuricella denitrificans gen. nov., sp. nov., a sulfur-oxidizing autotroph isolated from a freshwater lake. Int. J. Syst. Evol. Microbiol. 60:2862–2866

    CAS  Article  PubMed  Google Scholar 

  79. 79.

    Eschenbach W, Well R (2013) Predicting the denitrification capacity of sandy aquifers from shorter-term incubation experiments and sediment properties. Biogeosciences 10:1013–1035

    Article  Google Scholar 

  80. 80.

    Unden G, Bongaerts J (1997) Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors. Biochimica et Biophysica Acta (BBA) – Bioenergetics 1320:217–234

    CAS  Article  Google Scholar 

  81. 81.

    Poole RK (2011) Advances in microbial physiology, volume 59. Elsevier, London

    Google Scholar 

  82. 82.

    Bulger PR, Kehew AE, Nelson RA (1989) Dissimilatory nitrate reduction in a waste water contaminated aquifer. Ground Water 27:664–671

    CAS  Article  Google Scholar 

  83. 83.

    Schwab VF, Herrmann M, Roth V-N, Gleixner G, Lehmann R, Pohnert G, Trumbore S, Küsel K, Totsche KU (2016) Functional diversity of microbial communities in pristine aquifers inferred by PLFA- and sequencing-based approaches. Biogeosciences Discuss, doi:10.5194/bg-2016-442, 2016

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Acknowledgements

We thank Patricia Geesink, Erika Köhnke, Holger Hartmann, Robert Lehmann, and Heiko Minkmar for their help with the field and laboratory work. This work was financially supported by the Deutsche Forschungsgemeinschaft (CRC 1076 AquaDiva) and the Free State of Thuringia (ProExcellence Initiative “AquaDiv@Jena” and ProChance Programmlinie A1, Friedrich Schiller University Jena). Sequencing was financially supported by the German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, funded by the DFG (FZT118). The climate chambers to conduct experiments under controlled temperature conditions were financially supported by the Thüringer Ministerium für Wirtschaft, Wissenschaft und Digitale Gesellschaft (TMWWDG; project B 715-09075).

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Herrmann, M., Opitz, S., Harzer, R. et al. Attached and Suspended Denitrifier Communities in Pristine Limestone Aquifers Harbor High Fractions of Potential Autotrophs Oxidizing Reduced Iron and Sulfur Compounds. Microb Ecol 74, 264–277 (2017). https://doi.org/10.1007/s00248-017-0950-x

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Keywords

  • Groundwater
  • Denitrification
  • nirS
  • nirK