Chemical Extraction of Microorganisms from Water‐Saturated, Packed Sediment

Abstract

Microbial characterization of aquifers should combine collection of suspended and attached microorganisms (biofilms). This study investigated chemical extraction of microorganisms from water-saturated, packed sediment containing established biofilms. It compares the use of different detachment-promoting agent (DPA) solutions with tap water as eluent in column experiments. Extraction efficiency was determined from cell concentrations in the column effluent. Adenosine triphosphate concentrations were measured to confirm cell extraction and as an indicator of cell membrane integrity. Quality of extracted bacterial communities was assessed by comparing their terminal restriction fragment length polymorphism profiles with destructively sampled sediment-community profiles. Extraction efficiency increased more than 8-fold when deionized water, D-amino acids, or enzymes were used as a DPA. Community profiles recovered by individual DPA solutions showed more pronounced differences at the level of rare microbial groups, whereas abundant groups appeared ubiquitous across treatments. These results suggest that comparison of communities extracted by different DPAs can provide improved information on the occurrence of rare microbial groups in biofilms.

Flow-cytometric quantification of microbial cells on sand from water biofilters

“…observed that solutions of NaCl and CaCl 2 showed a slower and more prolonged response similar to that described in this paper (Ugolini et al, 2013). Each of the solutions employed in this study promotes biofilm detachment and dispersal through different mechanisms.…”

“…The five dispersants used clustered according to three different extraction patterns similar to those previously observed by Ugolini et al, (2013), where a Tween mix (1% Tween 80 in 0.1 M EDTA and 0.1M TSPP 2 ) was tested, among other dispersants, to detach biofilm from freshwater sediment columns. The solution released the majority of cells shortly after application, followed by drastic, rapid attenuation of its extraction efficiency.…”

“…However, it is still not clear why in this experiment, a completely different behaviour, and a significantly lower extraction efficiency, was observed for Triton X-100. The increased extraction efficiency of TWEEN-PP might be explained by the fact that when the two dispersants are combined they may act through two different mechanisms: TWEEN dissolves hydrophobic molecules (as described above) and PP acts as a chelating agent, scavenging bivalent cations such as Ca 2þ and Mg 2þ that crosslink the negatively charged groups on the surface of EPS constituents (Ugolini et al, 2013;Velji and Albright, 1984). Mechanical treatment: We found that four cycles of highenergy sonication in a TWEEN-PP solution are the most effective treatment for optimal cell counts among all the treatments tested.…”

Substratum‐Associated Microbiota

“…Miscellaneous. Ugolini et al (2013) investigated chemical extraction of microorganisms from watersaturated, packed sediment containing established biofilms.…”

In‐Situ Sonication for Enhanced Recovery of Aquifer Microbial Communities

“…Thus, both increasing the external force (e.g., by mechanical shear or sonication) or reducing the biofilm cohesiveness (e.g., by application of heat or chemical treatment) may promote detachment. Chemical detachment of biofilms from water saturated, undisturbed sediment has been previously tested in column experiments under controlled laboratory conditions (Ugolini et al ), yielding up to 8‐fold increase in cell‐extraction efficiency, and showing substantial variability in the extracted microbial community composition related to the chemical agent employed for the detachment. Conversely, detachment mediated by physical means was more effective, and resulted in a better representation of the biofilm community, especially when ultrasonication was used to promote detachment (Ugolini et al submitted).…”