Department of Physical and Biological Sciences, Western New England University, Springfield, MA, USA.
Appl Environ Microbiol. 2013 Mar;79(5):1646-53. doi: 10.1128/AEM.03263-12. Epub 2012 Dec 28.
Molecular 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.
能够提供 Geobacter 种原位生长速率估计的分子工具可以提高对不同环境中异化金属还原的理解。对生长在各种条件下的地下分离株 Geobacter uraniireducens 的全基因组微阵列分析,鉴定出了许多在不同特定生长速率下差异表达的基因。用定量逆转录 PCR(qRT-PCR)进一步评估了编码核糖体蛋白 rpsC 和 rplL 的两个基因的表达,细胞倍增时间范围从 6.56 h 到 89.28 h。rpsC 的转录丰度与特定生长速率相关性最好(r(2) = 0.90)。因此,rpsC 的表达模式被用于估计在原位铀生物修复现场实验中 Geobacter 种的特定生长速率,该实验中向地下水添加乙酸盐以促进异化金属还原。最初,地下水中乙酸盐的可用性增加导致 Geobacter rpsC 的表达增加,与从原位 rpsC 表达水平估计的特定生长速率相比,用荧光原位杂交估计的 Geobacter 细胞数量增加情况良好。然而,在后期阶段,细胞数量的增加远低于 rpsC 转录丰度的预测。这种变化与原生动物的大量繁殖和 Geobacter 物种与固相的附着增加同时发生。这些结果表明,与细胞丰度的变化相比,监测 rpsC 表达可能更好地反映了 Geobacter 物种在原位铀生物修复过程中代谢和生长的实际速率。