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Physical Extraction of Microorganisms From Water‐Saturated, Packed Sediment
Author(s) -
Ugolini Fabio,
Schroth Martin H.,
Bürgmann Helmut,
Zeyer Josef
Publication year - 2014
Publication title -
water environment research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.356
H-Index - 73
eISSN - 1554-7531
pISSN - 1061-4303
DOI - 10.2175/106143013x13807328848216
Subject(s) - sonication , chromatography , extraction (chemistry) , microorganism , sediment , environmental chemistry , aquifer , chemistry , water column , terminal restriction fragment length polymorphism , effluent , environmental science , environmental engineering , geology , bacteria , restriction fragment length polymorphism , biology , ecology , groundwater , biochemistry , polymerase chain reaction , paleontology , geotechnical engineering , gene
Microbial characterization of aquifers should include samples of both suspended and attached microorganisms (biofilms). We investigated the effect of shear, sonication, and heat on the extraction of microorganisms from water‐saturated, packed sediment columns containing established biofilms. Shear was studied by increasing flow velocity of the column eluent, sonication by treating the columns with ultrasound at different power levels, and heat by warming up the column eluent to different temperatures. Effluent cell concentrations were used as a measure of extraction efficiency. Dissolved organic carbon and adenosine tri‐phosphate (ATP) concentrations were used to corroborate cell‐extraction results. Additionally, ATP was used as an indicator of cell‐membrane integrity. Extraction quality was determined by comparing terminal‐restriction fragment length polymorphism (T‐RFLP) profiles of extracted bacterial communities with destructively sampled sediment‐community profiles. Sonication and heat increased the extraction efficiency up to 200‐fold and yielded communities comparable to the sediment community. These treatments showed high potential for in‐situ application in aquifers.