Molecular Analysis of theIn SituGrowth Rates of Subsurface Geobacter Species

Abstract

dMolecular tools that can provide an estimate of the in situ growth rate of Geobacter species could improve understanding of dissimilatory metal reduction in a diversity of environments. Whole-genome microarray analyses of a subsurface isolate of Geobacter uraniireducens, grown under a variety of conditions, identified a number of genes that are differentially expressed at different specific growth rates. Expression of two genes encoding ribosomal proteins, rpsC and rplL, was further evaluated with quantitative reverse transcription-PCR (qRT-PCR) in cells with doubling times ranging from 6.56 h to 89.28 h. Transcript abundance of rpsC correlated best (r 2 ‫؍‬ 0.90) with specific growth rates. Therefore, expression patterns of rpsC were used to estimate specific growth rates of Geobacter species during an in situ uranium bioremediation field experiment in which acetate was added to the groundwater to promote dissimilatory metal reduction. Initially, increased availability of acetate in the groundwater resulted in higher expression of Geobacter rpsC, and the increase in the number of Geobacter cells estimated with fluorescent in situ hybridization compared well with specific growth rates estimated from levels of in situ rpsC expression. However, in later phases, cell number increases were substantially lower than predicted from rpsC transcript abundance. This change coincided with a bloom of protozoa and increased attachment of Geobacter species to solid phases. These results suggest that monitoring rpsC expression may better reflect the actual rate that Geobacter species are metabolizing and growing during in situ uranium bioremediation than changes in cell abundance.

The influence of sludge retention time on mixed culture microbial fuel cell start-ups

“…Because of the lack of organic substrate, it was difficult for the electrogenic microorganisms to compete efficiently, in particular taking into account the origin of the seeded sludge. This observation has been previously reported in the literature [34][35][36][37][38][39]. Because of that, it was decided to increase the concentration of COD from 4000 to 10000 ppm, in order to give electrogenic microorganisms more opportunities to grow in this system.…”

“…In the particular case of two well-known electroactive microorganisms: Shewanella and Geobacter, it has been reported [37,39,41] that a maximum growth rate of 2.4 d -1 can occur, whereas other anaerobic non electrogenic microorganisms present higher maximum specific growth rate values [34,42]. The different growth rates would lead to mixed cultures, enriched in electrogenic microorganisms when operating at the high SRT.…”

Evidence of Geobacter-associated phage in a uranium-contaminated aquifer

“…Analysis of Geobacter growth during bioremediation of uranium-contaminated groundwater revealed that growth rates estimated from gene transcript abundance were much higher than the actual increase in cell numbers in the groundwater (Holmes et al, 2013a). Furthermore, rates of subsurface Geobacter growth were significantly lower than the rates predicted by genome-scale metabolic models (Scheibe et al, 2009;Fang et al, 2011;Lovley et al, 2011;Zhuang et al, 2011).…”

In Situ Determination of Bacterial Growth in Mixing Zone of Hydrothermal Vent Field on the Hatoma Knoll, Southern Okinawa Trough

“…Several parameters without traditional cultivation methods have been used to estimate microbial growth rate, e.g. microscopic cell density and cell size, adenosine 5 0 -triphosphate (ATP), assimilation rate of isotope labeled substrates (Karl et al 1980;Kirchman 2001;Malmstrom et al 2005;Torrton and Dufour 1996), microbial mat formation based on time-series observation (Taylor et al 1999), frequency of dividing cells (Newell and Christian 1981), macromolecular synthesis (Torrton and Dufour 1996), whole-genome microarray analysis (Holmes et al 2013). These methods were applied in the hydrothermal environments (Jannasch and Mottl 1985;Karl et al 1980) as well as general oceanic environments, and the calibration methods to convert growth rate or doubling time from these parameters have been developed (Kirchman 2001;Sherr et al 1999;Torrton and Dufour 1996;Yokokawa et al 2004).…”