Phase Preference by Active, Acetate-Utilizing Bacteria at the Rifle, CO Integrated Field Research Challenge Site

Abstract

ABSTRACT. Previous experiments at the Rifle, Colorado Integrated Field Research Challenge (IFRC)site demonstrated that field-scale addition of acetate to groundwater reduced the ambient soluble uranium concentration. In this report, sediment samples collected before and after acetate field addition were used to assess the active microbes via 13 C acetate stable isotope probing on 3 phases [coarse sand, fines (8-approximately 150 micron), groundwater (0.2-8 micron)] over a 24 -day time frame. TRFLP results generally indicated a stronger signal in 13 C-DNA in the "fines" fraction compared to the sand and groundwater. Before the field-scale acetate addition, a Geobacter-like group primarily synthesized 13 C-DNA in the groundwater phase, an alpha Proteobacterium primarily grew on the fines/sands, and an Acinetobacter sp. and Decholoromonas-like OTU utilized much of the 13 C acetate in both groundwater and particle-associated phases. At the termination of the field-scale acetate addition, the Geobacter-like species was active on the solid phases rather than the groundwater while the other bacterial groups had very reduced newly synthesized DNA signal. These findings will help to delineate the acetate utilization patterns of bacteria in the field and can lead to improved methods for stimulating distinct microbial populations in situ.

Crenarchaeal heterotrophy in salt marsh sediments

“…Approximately 10 g of sediment was placed in 170 ml glass serum vials, filled to the top with sterile-filtered (0.2 mm Supor, Pall, Port Washington, NY, USA) site water as in Kerkhof et al (2011). To determine heterotrophic activity, the SIP microcosms were amended with a single 13 C-labeled compound (acetate, glycine or urea) or a single 13 C-labeled biopolymer (methanol extract of algal lipids/pigments, extract of algal proteins) or complex growth medium (ISOGRO, Sigma-Aldrich, St Louis, MO, USA).…”

Bacterial genome replication at subzero temperatures in permafrost

“…These 12 C and 13 C-DNA bands were collected by pipette, rather than fractionating the entire gradient. This approach has been shown to reduce contamination and ensure clean 12 C-control amplifications (Padmanabhan et al, 2003;Gallagher et al, 2005;Kerkhof et al, 2011). This does not imply that 12 C DNA contamination is not present throughout the gradient.…”

“…Individual colonies from the libraries (240 clones per temperature treatment) were individually screened by TRFLP to identify partial 16S rRNA genes corresponding to specific TRFLP peaks in the active permafrost-community fingerprints as previously described (Gallagher et al, 2005;Kerkhof et al, 2011). Plasmid preps of recombinant clones corresponding to specific TRFLP peaks were performed using Zyppy Plasmid Miniprep Kits (Zymo, Irvine, CA, USA), and sequenced by the Sanger method (Genewiz, South Plainfield, NJ, USA).…”

Evaluation of a Genome-Scale In Silico Metabolic Model for Geobacter metallireducens by Using Proteomic Data from a Field Biostimulation Experiment

“…In addition, the genomescale metabolic model is used to analyze the metabolic behavior of microorganisms as an individual cell and does not include mechanisms to handle external biological stresses (e.g., overpopulation or interaction with other organisms) or account for other microorganisms present in the aquifer that also utilize the electron donor and other key essential elements (26). Furthermore, protein extraction from biological membranes still poses technical challenges during global protein sample preparations and can sometimes result in missed identifications.…”