Microorganisms in soils & sediments. Detection, quantification and activity. Deliverable 2.2


Artificial groundwater recharge (AR) is used as semi-natural pre-treatment for drinking water production in Berlin and many other sites world-wide. Earlier research has focussed on the degradation of organic substances in these recharge systems (NASRI final reports 1 – 6), and has improved our knowledge of AR in the specific sites in Berlin. Nevertheless, a process understanding which might enable a transfer to other sites and boundary conditions is still lacking. Since biodegradation – which is assumed to be the main removal process of organic compounds – depends on the presence and activity of microorganisms, characterisation experiments with respect to biological activity will help to interpret results from soil column experiments simulating AR. In this stage of the OXIRED project, it will be of interest to link biological activity to degradation patterns in soil columns. Therefore, the following questions related to microorganisms could be necessary to answer: 1) How many are there? 2) How active are they? 3) Who is living there? A review of published literature yielded that in general, soils and sediments contain great numbers of microorganisms. Whereas in surface soils concentrations of culturable microorganisms can be found in the range of 108 per gram of dry soil, the number of culturable organisms in the subsurface are dependent on depth and are generally lower. In order to analyse them, adapted sampling methods and a sound sampling strategy are necessary for a reliable overview of microbial life. Another important aspect of microbial investigations is the detachment of organisms from biofilms for which enzymatic based methods have proven to be very useful. Different microbiological and biomolecular methods were described and assessed with respect to their suitability: 1) Cultivation: Since less than 1% of the microorganisms in natural environments can be cultured they will not be useful when one aims to get more insight into the microbial community. 2) Nucleic acid based techniques: Whereas DNA based primers can be used to detect specific species, general primers can be used to get a broad overview of the microbial life within a sample. Furthermore, active organisms can be detected by the use of RNA based primers. 3) Physiological technique: Microbial activity can be estimated indirectly based on AOC or BDOC measurements. To assess the micro-organisms present in soil columns and their activity the following methods are recommended: (i) Substrate degradation assessments by BDOC (or AOC) measurements (normally done in column studies) (ii) Direct counts (DAPI/ Acridine Orange) of direct extracted organisms and organisms present on buried slides. (iii) DGGE with universal primers (iv) qPCR (v) Direct counts with LIFE/DEAD staining and (vi) CTC redox dye o Clone libraries constructed from DGGE bands In addition to an extensive literature database of references for further details the results are summarized in a table with an overview of methods for detection, quantification and activity assessments of microbial communities in soils and sediments.

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