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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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
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
Ford DC, Williams PW (2007) Karst geomorphology and hydrology, 2nd edn. John Wiley & Sons, Chichester, U.K.
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
Zumft WG (1997) Cell biology and molecular basis of denitrification. Microbiol Mol Biol Reviews 61:533–616
Knowles R (1982) Denitrification. Microbio Rev 46:43–70
Schlesinger WH (2009) On the fate of anthropogenic nitrogen. Proc. Natl. Acad. Sci. U. S. A. 106:203–208
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
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
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
Smith RL, Howes BL, Duff JH (1991) Denitrification in nitrate contaminated groundwater: occurrence in steep vertical geochemical gradients. Geochim. Cosmochim. Acta 55:1815–1825
Morris JT, Whiting GJ, Chapelle FH (1988) Potential denitrification rates in deep sediments from the Southeastern Coastal Plain. Environ Sci Technol 22:832–836
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
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
Schippers A, Jozsa PG, Sand W (1996) Sulfur chemistry in bacterial leaching of pyrite. Appl. Environ. Microbiol. 62:3424–3431
Rimstidt JD, Vaughan DJ (2003) Pyrite oxidation: a state-of-the-art assessment of the reaction mechanism. Geochim. Cosmochim. Acta 67:873–880
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
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
Braker G, Dörsch P, Bakken Lars R (2012) Genetic characterization of denitrifier communities with contrasting intrinsic functional traits. FEMS Microbiol. Ecol. 79:542–554
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
Saarenheimo J, Tiirolaa MA, Rissanen AJ (2015) Functional gene pyrosequencing reveals core proteobacterial denitrifiers in boreal lakes. Frontiers Microbiol 6:674
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
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
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
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
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
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
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
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
Griebler C, Lueders T (2009) Microbial biodiversity in groundwater ecosystems. Freshw. Biol. 54:649–677
Griebler C, Avramov M (2015) Groundwater ecosystem services: a review. Freshwater Science 34:355–367
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
Bishop PL, Yu T (1999) A microelectrode study of redox potential changes in biofilms. Water Sci. Technol. 39:179–185
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
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
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
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
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
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
Grasshoff K, Ehrhardt M, Kremling K (1983) Methods of seawater analysis, 2nd edn. Chemie, Weinheim
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
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
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
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
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
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
Hallin S, Lindgren P (1999) PCR detection of genes encoding nitrite reductase in denitrifying bacteria. Appl. Environ. Microbiol. 65:1652–1657
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
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
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
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
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
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
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
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
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
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
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
Delong EF (1992) Archaea in coastal marine environments. Proc. Natl. Acad. Sci. U. S. A. 89:5685–5689
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
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
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
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
Emerson D, Moyer C (1997) Isolation and characterization of novel iron-oxidizing bacteria that grow at circumneutral pH. Appl. Environ. Microbiol. 63:4784–4792
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
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
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
Tesoriero AJ, Puckett LJ (2011) O2 reduction and denitrification rates in shallow aquifers. Water Resour. Res. 47:W12522
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
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
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
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
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
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
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
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
Schedel M, Trüper HG (1980) Anaerobic oxidation of thiosulfate and elemental sulfur in Thiobacillus denitrificans. Arch. Microbiol. 124:205–210
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
Eschenbach W, Well R (2013) Predicting the denitrification capacity of sandy aquifers from shorter-term incubation experiments and sediment properties. Biogeosciences 10:1013–1035
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
Poole RK (2011) Advances in microbial physiology, volume 59. Elsevier, London
Bulger PR, Kehew AE, Nelson RA (1989) Dissimilatory nitrate reduction in a waste water contaminated aquifer. Ground Water 27:664–671
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
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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DOI: https://doi.org/10.1007/s00248-017-0950-x