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Microbial communities in karst groundwater and their potential use for biomonitoring

Potentiel d’utilisation des communautés microbiennes pour le suivi biologique des eaux de karst

Las comunidades microbianas en aguas subterráneas cársticas y su uso potencial para biomonitoreo

喀斯特地区地下水中的细菌群落以及它们在生态监测中的潜在应用

Comunidades microbiológicas em águas subterrâneas cársicas e seu uso potencial para biomonitorização

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Abstract

The structure, diversity and dynamics of microbial communities from a swallow hole draining agricultural land and two connected karst springs (Switzerland) were studied using molecular microbiological methods and related to hydrological and physicochemical parameters. Storm responses and an annual hydrological cycle were monitored to determine the short- and long-term variability, respectively, of bacterial communities. Statistical analysis of bacterial genetic fingerprints (16S rDNA PCR-DGGE) of spring water samples revealed several clusters that corresponded well with different levels of the allochthonous swallow hole contribution. Microbial communities in spring water samples highly affected by the swallow hole showed low similarities among them, reflecting the high temporal variability of the bacterial communities infiltrating at the swallow hole. Conversely, high similarities among samples with low allochthonous contribution provided evidence for a stable autochthonous endokarst microbial community. Three spring samples, representative for low, medium and high swallow hole contribution, were analysed by cloning/sequencing in order to identify the major bacterial groups in the communities. The autochthonous endokarst microbial community was mainly characterized of δ-Proteobacteria, Acidobacteria and Nitrospira species. A high percentage of unknown sequences suggested further that many karst aquifer bacteria are still undiscovered. Finally, the potential use of groundwater biomonitoring using microbial communities is discussed.

Résumé

La structure, la diversité et la dynamique des communautés microbiennes d’un aven et de deux résurgences associées en contexte agricole (Suisse) ont été étudiées par microbiologie moléculaire et mis en relation avec des paramètres hydrologiques et physico-chimiques. Un cycle hydrologique annuel complet, incluant les impacts d’orages, a été suivi afin de déterminer la variabilité à court et à long terme des communautés bactériennes. L’analyse statistique des signatures génétiques bactériennes (16S rDNA PCR-DGGE) des résurgences a mis en évidence plusieurs groupes correspondant à une contribution allochtone depuis l’aven. Les communautés microbiennes des eaux de source marquées par une forte contribution de l’aven ont montré peu de similitudes entre elles, soulignant ainsi une forte variabilité temporelle des populations bactériennes infiltrées. Réciproquement, les fortes similitudes observées entre les échantillons à faible composante allochtone mettent en évidence une communauté microbienne stable en provenance de l’endokarst. Trois échantillons d’eaux de source représentatifs de contributions allochtones faible, moyenne et forte ont été analysés par clonage/séquençage afin d’identifier les principaux groupes bactériens. La communauté microbienne autochtone de l’endokarst est principalement characterisé par des espèces δ- Proteobacteria, Acidobacteria et Nitrospira. De plus, l’existence d’un fort pourcentage de séquences inconnues suggère que nombre de bactéries karstiques restent à découvrir. En conclusion, l’utilisation potentielle des communautés microbiennes pour le suivi biologique des eaux souterraines est discutée.

Resumen

La estructura, diversidad y dinámica de las comunidades microbianas en una cavidad que drena tierras agrícolas y dos manantiales cársticos conectados (Suiza) han sido estudiados usando métodos microbiológicos moleculares y han sido relacionadas son los parámetros hidrológicos y físico-químicos. Las respuestas a tormentas y al ciclo hidrológico annual han sido monitoreadas para determinar la variabilidad de las comunidades bacterianas a corto y largo plazo, respectivamente. El análisis estadístico de las huellas genéticas de las bacterias (16S rDNA PCR-DGGE) a partir de muestras de agua de los manantiales revela agrupamientos que se corresponden bien con los diferentes niveles de la contribución alóctona de la cavidad drenante. Las comunidades microbianas en las muestras de agua de los manantiales que están fuertemente afectadas por la cavidad muestran bajas similitudes entre sí, lo que refleja la alta variabilidad temporal de las comunidades de bacterias que se infiltran en la cavidad. De forma inversa, las altas similitudes entre muestras con baja contribución alóctona provee evidencias de una comunidad microbiana endocárstica autóctona estable. Tres muestras de manantiales, representativas de baja, media y alta contribución de la cavidad fueron analizadas por medio de clonado y secuenciación para identificar los grupos bacterianos predominantes en las comunidades. La comunidad microbiana autóctona endocárstica está caracterizado principalmente de especies de δ-Proteobacteria, Acidobacteria y Nitrospira. El alto porcentaje da secuencias desconocidas sugiere que muchas bacterias del acuífero no han sido todavía descubiertas. Finalmente, se discute el uso potencial de las comunidades microbianas para el biomonitoreo de aguas subterráneas.

摘要

利用分子生物学中微生物学的方法研究了一个由农田排水形成的落水洞和两个相互连通的岩溶泉眼 (瑞士) 中的细菌群落的结构、多样性和动态, 并且与水文学和物理化学的参数相对比。而细菌群落的短期和长期变化分别通过监测其对暴风雨和年度水文循环的响应加以确定。通过对泉水样中细菌遗传指纹图谱的统计分析揭示了几种不同集群的存在, 且它们与外来落水洞的水量的贡献程度相关。泉水样品中, 受落水洞强烈影响的细菌群落相似性差, 反映了渗入落水洞的水其细菌群落具有极高的时间变异性。相反, 外来水贡献较小的水样中的细菌群落的相似性较高, 这说明了喀斯特原地的微生物群落较为稳定。为了识别各群落里主要的细菌种类, 文中选取了三个泉水样品的细菌进行克隆和基因测序, 分别代表落水洞补给水量较少、中等和较多的这三种情况。喀斯特地区本地内生的细菌群落主要由δ变型菌、嗜酸细菌和硝化螺菌组成。但一大部分未知的遗传序列表明喀斯特地区含水层仍有多数细菌未被发现。最后, 文章讨论了利用细菌群落来进行地下水生态监测的可能性。

Resumo

A estrutura, diversidade e dinâmica das comunidades microbiológicas de uma dolina que drena terrenos agrícolas e de duas nascentes cársicas conectadas (Suiça) foram estudadas utilizando métodos moleculares microbiológicos e relacionadas com parâmetros hidrológicos e físico-químicos. Respostas a tempestades e um ciclo hidrológico anual foram monitorizados para determinar a variabilidade de curto e longo prazo, respectivamente, das comunidades bacterianas. Análises estatísticas das impressões genéticas das bactérias (16S rDNA PCR-DGGE) de amostras de água das nascentes mostram vários grupos que têm correspondência com diferentes níveis de contribuição alóctone da dolina. As comunidades microbianas nas amostras de água das nascentes altamente afectadas pela dolina mostraram baixa similaridade entre elas, reflectindo a elevada variabilidade temporal das comunidades bacterianas que se infiltram na dolina. Pelo contrário, a elevada similaridade entre amostras com pouca contribuição alóctone mostram à evidência uma comunidade microbiana autóctone estável no endocarso. Três amostras de nascente, representativas de baixa, média e elevada contribuição da dolina, foram analisadas através de clonagem/sequenciação, de modo a identificar os principais grupos de bactérias nas comunidades. A comunidade microbiana autóctone do endocarso era fundamentalmente composta pelas espécies δ-Proteobacteria, Acidobacteria e Nitrospira. Uma elevada percentagem de sequências desconhecidas sugerem que muitas bactérias de aquíferos cársicos estão ainda por identificar. Finalmente, é discutido o uso potencial da biomonitorização da água subterranean utilizando as comunidades microbiológicas.

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References

  • Alfreider A, Krössbacher M, Psenner R (1997) Groundwater samples do not reflect bacterial densities and activity in subsurface systems. Water Res 31(4):832–840

    Article  Google Scholar 

  • APHA, AWWA, WEF (2005) Standard methods for the examination of water and wastewater, 21st edn. Water Environment Federation, Alexandria, VA, USA

    Google Scholar 

  • Barns SM, Cain EC, Sommerville L, Kuske CR (2007) Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within this phylum. Appl Environ Microbiol 73(9):3113–3116

    Article  Google Scholar 

  • Barton HA, Northup DE (2007) Geomicrobiology in cave environments: past, current and future perspectives. J Caves Karst Stud 69(1):163–178

    Google Scholar 

  • Canaveras JC, Hoyos M, Sanchez-Moral S, Sanz-Rubio E, Bedoya J, Soler V, Groth I, Schumann P, Laiz L, Gonzales I, Sainz-Jimenez C (1999) Microbial communities associated with hydromagnesite and needle-fiber aragonite deposits in a karstic cave (Altamira, northern Spain). Geomicrobiol J 16(1):9–25

    Article  Google Scholar 

  • Chandler DP, Jarrell AE (2004) Automated purification and suspension array detection of 16S rRNA from soil and sediment extracts by using tunable surface microparticles. Appl Environ Microbiol 70(5):2621–2631

    Article  Google Scholar 

  • Chapelle FH (2001) Groundwater microbiology and geochemistry. Wiley, New York

    Google Scholar 

  • Chelius MK, Moore JC (2004) Molecular phylogenetic analysis of archaea and bacteria in Wind Cave, South Dakota. Geomicrobiol J 21(2):123–134

    Article  Google Scholar 

  • Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, McGarrell DM, Bandela AM, Cardenas E, Garrity GM, Tiedje JM (2007) The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res 35(Database issue):D169-D172. doi:10.1093/nar/gkl889

  • Danielopol DL, Griebler C, Gunatilaka A, Notenboom J (2003) Present state and future prospects for groundwater ecosystems. Environ Conserv 30(2):104–130

    Article  Google Scholar 

  • Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA (2005) Diversity of the human intestinal microbial flora. Science 308(5728):1635–1638

    Article  Google Scholar 

  • Engel AS (2007) Observations on the biodiversity of sulfidic karst habitats. J Caves Karst Stud 69(1):187–206

    Google Scholar 

  • Farnleitner AH, Wilhartitz I, Ryzinska G, Kirschner AKT, Stadler H, Burtscher MM, Hornek R, Szewzyk U, Herndl G, Mach RL (2005) Bacterial dynamics in spring water of alpine karst aquifers indicates the presence of stable autochthonous microbial endokarst communities. Environ Microbiol 7(8):1248–1259

    Article  Google Scholar 

  • Felske A, Wolterink A, van Lis R, Akkermans ADL (1998) Phylogeny of the main bacterial 16S rRNA sequences in Drentse A grassland soils (The Netherlands). Appl Environ Microbiol 64(3):871–879

    Google Scholar 

  • Goldscheider N, Hunkeler D, Rossi P (2006) Review: microbial biocenoses in pristine aquifers and an assessment of investigative methods. Hydrogeol J 14(6):926–941

    Article  Google Scholar 

  • Green U, Kremer JH, Zillmer M, Moldaenke C (2003) Detection of chemical threat agents in drinking water by an early warning real-time biomonitor. Environ Toxicol 18(6):368–374

    Article  Google Scholar 

  • Griebler C, Mösslacher F (2003) Grundwasser-Ökologie [Groundwater ecology]. Facultas UTB, Vienna

    Google Scholar 

  • GSchV (1998) Water Protection Ordinance, SR 814.201, Swiss Federal Law, Bern

  • Hahn HJ, Friedrich E (1999) Brauchen wir ein faunistisch begründetes Grundwassermonitoring und was kann es leisten? [Do we need a fauna-based groundwater monitoring, and what is its potential?]. Grundwasser 4:147–154

    Article  Google Scholar 

  • Hancock PJ, Boulton AJ, Humphreys WF (2005) Aquifers and hyporheic zone: towards an ecological understanding of groundwater. Hydrogeol J 13(1):98–111

    Article  Google Scholar 

  • Hartmann M, Widmer F (2006) Community structure analyses are more sensitive to differences in soil bacterial communities than anonymous diversity indices. Appl Environ Microbiol 72(12):7804–7812

    Article  Google Scholar 

  • He Z, Gentry TJ, Schadt CW, Wu L, Liebich J, Chong SC, Huang Z, Wu W, Gu B, Jardine P, Criddle C, Zhou J (2007) GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J 1(1):67–77

    Article  Google Scholar 

  • Hose LD, Palmer AN, Palmer MV, Northup DE, Boston PJ, DuChene HR (2000) Microbiology and geochemistry in a hydrogen-sulphide-rich karst environment. Chem Geol 169(3–4):399–423

    Article  Google Scholar 

  • Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180(18):4765–4774

    Google Scholar 

  • Janssen PH (2006) Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72(3):1719–1728

    Article  Google Scholar 

  • Käss W (1998) Tracing technique in geohydrology. Balkema, Rotterdam, The Netherlands

    Google Scholar 

  • Lehman RM (2007) Understanding of aquifer microbiology is tightly linked to sampling approach. Geomicrobiol J 24(3–4):331–341

    Article  Google Scholar 

  • Macalady JL, Lyon EH, Koffman B, Albertson LK, Meyer K, Galdenzi S, Mariani S (2006) Dominant microbial populations in limestone-corroding stream biofilms, Frasassi cave system, Italy. Appl Environ Microbiol 72(8):5596–5609

    Article  Google Scholar 

  • Macalady JL, Jones DS, Lyon EH (2007) Extremely acidic, pendulous cave wall biofilms from the Frasassi cave system, Italy. Environ Microbiol 9(6):1402–1414

    Article  Google Scholar 

  • Malard F, Plenet S, Gibert J (1996) The use of invertebrates in groundwater monitoring: a rising research field. Ground Water Monit Remediat 16(2):103–113

    Article  Google Scholar 

  • Mösslacher F, Griebler C, Notenboom J (2001) Biomonitoring of groundwater systems: methods, applications and possible indicators among the groundwater biota. In: Griebler C, Danielopol DL, Gibert J, Nachtnebel HP, Notenboom J (eds) Groundwater ecology: a tool for management of water resources. Office for Official Publications of the European Communities, Luxemburg

    Google Scholar 

  • Muralt R (1999) Processus hydrogéologiques et hydrochimiques dans les circulations profondes des calcaires du Malm de l’arc jurassien [Hydrogeological and hydrochemical processes in the circulation system in the Malm limestones of the Jurassic belt]. Beiträge zur Geologie der Schweiz, Geotechnische Serie, Lieferung 82, Schweizerischen Geotechnischen Kommision, Zurich, 236 pp

  • Muyzer G (1999) DGGE/TGGE a method for identifying genes from natural ecosystems. Curr Opin Microbiol 2(3):317–322

    Article  Google Scholar 

  • Muyzer G, Dewaal EC, Uitterlinden AG (1993) Profiling of complex microbial-populations by denaturing gradient gel-electrophoresis analysis of polymerase chain reaction-amplified genes-coding for 16S ribosomal-RNA. Appl Environ Microbiol 59(3):695–700

    Google Scholar 

  • Muyzer G, Teske A, Wirsen CO, Jannasch HW (1995) Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch Microbiol 164(3):165–172

    Article  Google Scholar 

  • Nocker A, Burr M, Camper AK (2007) Genotypic microbial community profiling: a critical technical review. Microb Ecol 54(2):276–289

    Article  Google Scholar 

  • Northup DE, Lavoie KH (2001) Geomicrobiology of caves: a review. Geomicrobiol J 18(3):199–222

    Article  Google Scholar 

  • Ovreas L, Forney L, Daae FL, Torsvik V (1997) Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol 63(9):3367–3373

    Google Scholar 

  • Personné JC, Poty F, Mahler BJ, Drogue C (2004) Colonization by aerobic bacteria in karst: laboratory and in situ experiments. Ground Water 42(4):526–533

    Article  Google Scholar 

  • Pronk M, Goldscheider N, Zopfi J (2006) Dynamics and interaction of organic carbon, turbidity and bacteria in a karst aquifer system. Hydrogeol J 14(4):473–484

    Article  Google Scholar 

  • Pronk M, Goldscheider N, Zopfi J (2007) Particle-size distribution as indicator for fecal bacteria contamination of drinking water from karst springs. Environ Sci Technol 41(24):8400–8405

    Article  Google Scholar 

  • Roesch LF, Fulthorpe RR, Riva A, Casella G, Hadwin AKM, Kent AD, Daroub SH, Camargo FAO, Farmerie WG, Triplett EW (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1(4):283–290

    Google Scholar 

  • Rusterholtz KJ, Mallory LM (1994) Density, activity, and diversity of bacteria indigenous to a karstic aquifer. Microb Ecol 28(1):79–99

    Article  Google Scholar 

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

    Google Scholar 

  • Sommaruga A (1997) Geology of the central Jura and the Molasse Basin: new insight into an evaporite-based foreland fold and thrust belt. Mém Soc Neuchâteloise Sci Nat, XII edn., Société Neuchâteloise des Sciences Nat, La Chaux-de-Fonds, Switzerland

  • Vervier P, Gibert J (1991) Dynamics of surface-water groundwater ecotones in a karstic aquifer. Freshw Biol 26(2):241–250

    Article  Google Scholar 

  • Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73(16):5261–5267

    Article  Google Scholar 

  • Weiss JV, Cozzarelli M (2008) Biodegradation in contaminated aquifers: incorporating microbial/molecular methods. Ground Water 46(2):305–322

    Article  Google Scholar 

Download references

Acknowledgements

We are grateful to the water works of Yverdon-les-Bains for their cooperation, and for technical and logistical support. We thank the Swiss National Science Foundation (project BEKARST/KARSTDYN, grant No. 200020–113609/1) for funding and the three reviewers for their valuable comments.

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Authors and Affiliations

  1. Centre of Hydrogeology, University of Neuchâtel, Rue Emile-Argand 11, CP 158, CH-2009, Neuchâtel, Switzerland

    Michiel Pronk & Nico Goldscheider

  2. Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, CP 158, CH-2009, Neuchâtel, Switzerland

    Jakob Zopfi

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  1. Michiel Pronk
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Correspondence to Jakob Zopfi.

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Pronk, M., Goldscheider, N. & Zopfi, J. Microbial communities in karst groundwater and their potential use for biomonitoring. Hydrogeol J 17, 37–48 (2009). https://doi.org/10.1007/s10040-008-0350-x

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