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Hydrogeology Journal

, Volume 14, Issue 6, pp 926–941 | Cite as

Review: Microbial biocenoses in pristine aquifers and an assessment of investigative methods

  • Nico GoldscheiderEmail author
  • Daniel Hunkeler
  • Pierre Rossi
Report

Abstract

The current knowledge of microbial biocenoses (communities) in pristine aquifers is presented in a review, which also discusses their relevance for questions of groundwater protection. Aquifers are heterogeneous on all scales and structured in a variety of habitats. The void spaces in many aquifers are small. The biocenoses are thus predominantly composed of microorganisms and, often, microinvertebrates. Larger voids and macroorganisms occur in karst cavities. Due to the absence of light, the biocenoses depend on chemical energy resources, which are, however, scarce in non-contaminated groundwater. The microorganisms thus show small cell sizes, low population densities and reduced activity; they developed specific strategies to survive oligotrophic conditions. The review also discusses the impact of contamination on the biocenoses, and the potential use of the biocenoses or specific organisms as indicators for groundwater quality, and the limits of this approach. Bacteria are either planktonic or attached to aquifer material, which requires both fluid and solid phase sampling. Most groundwater bacteria are viable but non-culturable. Consequently, cultivation techniques give an incomplete picture of the biocenoses, while methods from molecular microbiology provide genetic fingerprints of the entire community. Different analytical methods are available to count microorganisms, identify species, characterise microbial diversity, and measure activity.

Keywords

Non-contaminated aquifer Groundwater protection Environmental microbiology Micro-ecology Microbial community 

Résumé

Cette revue expose l’état actuel des connaissances concernant les biocénoses microbiennes présentes dans les aquifères oligotrophes. L’impact d’une contamination sur les biocénoses est discuté, ainsi que le potentiel que représentent les communautés ou un organisme spécifique, en tant qu’indicateur de qualité des eaux souterraines. En dernier lieu les méthodes à disposition en microbiologie sont examinées.

Les aquifères sont hétérogènes à de nombreuses échelles et sont structurés en une grande variété d’habitats. Les espaces vides sont très souvent de petite taille. De ce fait, les biocénoses sont composées de manière prédominante par des microorganismes et parfois quelques micro-invertébrés. Les espaces plus larges, notamment les cavités karstiques, sont peuplés de macro-organismes également.

En l’absence de toute forme d’énergie lumineuse, les biocénoses dépendent de sources d’énergie chimiques, présentes en faible quantité dans les aquifères non contaminés. Les microorganismes développent ainsi de petites tailles, une densité de population faible et une activité réduite. La physiologie des organismes est adaptée à la survie en conditions oligotrophes.

Les bactéries sont planctoniques ou attachées aux matériaux de l’aquifère, ce qui demande un échantillonnage à la fois de l’eau et du substrat. De nombreuses méthodes sont aujourd’hui disponibles pour le comptage, l’identifi-cation et la caractérisation de la diversité, ainsi que la mesure des activités des organismes des aquifères. Comme la grande majorité des bactéries est viable mais non cultivable, les techniques de cultures actuelles ne donnent qu’une image incomplète des communautés, alors que les méthodes moléculaires développées récemment offrent la possibilité d’obtenir un profil de la communauté plus complet.

Resumen

Se presenta una reseña crítica del conocimiento actual de biocenosis microbiana (comunidades) en acuíferos prístinos la cual también discute su relevancia en términos de protección de aguas subterráneas. Los acuíferos son heterogéneos en todas las escalas y estructurados en una variedad de habitats. Los espacios vacíos en muchos acuíferos son pequeños. La biocenosis está por lo tanto compuesta predominantemente por microorganismos y, frecuentemente, microinvertebrados. Espacios más grandes y macroorganismos ocurren en cavidades kársticas. Debido a la ausencia de luz la biocenosis depende de recursos energéticos químicos los cuales, sin embargo, son escasos en agua subterránea no contaminada. Los microorganismos muestran entonces tamaños de células pequeñas, bajas densidades de población y actividad reducida por lo que desarrollan estrategias específicas para sobrevivir en condiciones oligotróficas. Esta reseña crítica también discute el impacto de la contaminación en la biocenosis y el uso potencial de la biocenosis o de organismos específicos como indicadores de la calidad del agua subterránea, así como los límites de este enfoque. Las bacterias se encuentran ya sea en forma planctónica o ligadas al material acuífero lo cual requiere muestreo de la fase sólida y la fase fluida. La mayoría de bacterias de agua subterránea son viables pero no cultivables. Por lo tanto, las técnicas de cultivo aportan un cuadro incompleto de la biocenosis mientras que los métodos de microbiología molecular aportan señales genéticas de toda la comunidad. Existen diferentes métodos analíticos para contar microorganismos, identificar especies, caracterizar diversidad microbiana, y medir actividad.

Notes

Acknowledgement

The Swiss Federal Office for the Environment (FOEN) funded this study. We thank Dr. Ronald Kozel and Dr. Benjamin Meylan for the good cooperation. We are particularly grateful to Dr. Jakob Zopfi (Neuchâtel) for numerous valuable suggestions and fruitful discussions. We acknowledge Christine Burn's contribution to the literature search. We also thank Dr. Franziska Zibuschka (Vienna) and Dr. Patrick Höhener (Lausanne) for useful comments. We thank Dr. Sascha Oswald (Associate Editor), Dr. Ralph David and an anonymous reviewer for their valuable comments and suggestions, and Dr. David Drew (Dublin) for the language check.

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Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • Nico Goldscheider
    • 1
    Email author
  • Daniel Hunkeler
    • 1
  • Pierre Rossi
    • 2
  1. 1.Centre of Hydrogeology (CHYN)University of NeuchâtelNeuchâtelSwitzerland
  2. 2.EPFL-LBELaboratory for Environmental BiotechnologyLausanneSwitzerland

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