Monitored natural attenuation at a coal-tar impacted aquifer in Northwestern Iowa: coupled biogeochemical and molecular microbiological approaches for establishing secondary and tertiary lines of evidence

Abstract

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Fluorescent In Situ Hybridization and Micro‐autoradiography Applied to Ecophysiology in Soil

“…These fi ndings support the selection of group-specifi c probes for exploration of soil microbial communities in the FISH studies reported above. Aside from bacteria, Zarda et al (1997), Chatzinotas et al (1998), and our own work with subsurface sediments (Rogers, 2004) indicate that Archaea in soils account for only a small fraction of the total population (<5%).…”

“…For more active microbial communities such as those derived from wastewater treatment plants or natural surface waters, short incubation times, generally ranging from 2 to 4 h, have been reported (Andreasen and Nielsen, 1997;Lee et al, 1999;Kindaichi et al, 2004;Ginige et al, 2004). In less active microbial communities or those consuming more challenging substrates such as xenobiotic compounds, longer incubation periods of up to 2 d have been required to achieve visible autoradiograms (Yang et al, 2003;Rogers, 2004). Due to these uncertainties, each new study should investigate the effects of incubation time on both the autoradiographic response and divergence of microbial communities from their initial structure.…”

“…Nielsen et al (2003a), however, examined the density of silver grains within either 1 μm of cells consuming 3 H-labeled substrates or 5 μm of cells consuming 14 C-labeled substrates, and defi ned clusters of silver grains as those that were 100 times denser than the background at 10 μm from either side of MAR+ cells. Their defi nitions are easily adapted for use in image analysis software to automate identifi cation of silver grain clusters by size exclusion (Rogers, 2004).…”

“…In a recent work, we applied FISH and MAR to characterize the microbial community of a coal-tar-impacted aquifer in which polycyclic aromatic hydrocarbons (PAHs) were the primary pollutants (Rogers, 2004). In this aquifer, the microbial community was three orders of magnitude greater in population in the coal-tar source region than in nearby unaffected sediments.…”

“…This is a signifi cant advancement over earlier MAR techniques based on morphology, general staining, or antibody staining because it allows investigators to answer questions regarding the metabolic state of microbial communities without a priori knowledge of the microbial community of interest, or when morphology and phylogeny may not refl ect well cellular physiology (Fliermans and Schmidt, 1975;Meyer-Reil, 1978;Fuhrman and Azam, 1982;Neihof, 1982, 1984;Andreasen and Nielsen, 1997). The FISH-MAR technique has proven useful for the study of diverse environments including marine and fresh waters and sediments, hot-spring microbial mats, and contaminated aquifer sediments (Lee et al, 1999;Ouverney and Fuhrman, 1999;Otte et al, 1999;Gray et al, 2000;Nübel et al, 2002;Ito et al, 2002;Glaeser and Overmann, 2003;Malmstrom et al, 2004;Villa et al, 2004;Rogers, 2004). This review examines these techniques and describes their application to soils and sediments.…”