Suppr超能文献

地下 Geobacter 种原位生长速率的分子分析。

Molecular analysis of the in situ growth rates of subsurface Geobacter species.

机构信息

Department of Physical and Biological Sciences, Western New England University, Springfield, MA, USA.

出版信息

Appl Environ Microbiol. 2013 Mar;79(5):1646-53. doi: 10.1128/AEM.03263-12. Epub 2012 Dec 28.

Abstract

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.

摘要

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。

相似文献

1
Molecular analysis of the in situ growth rates of subsurface Geobacter species.
Appl Environ Microbiol. 2013 Mar;79(5):1646-53. doi: 10.1128/AEM.03263-12. Epub 2012 Dec 28.
2
Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwater.
ISME J. 2013 Jul;7(7):1286-98. doi: 10.1038/ismej.2013.20. Epub 2013 Feb 28.
3
Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments.
ISME J. 2009 Feb;3(2):216-30. doi: 10.1038/ismej.2008.89. Epub 2008 Oct 9.
6
Stimulating the in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer.
Appl Environ Microbiol. 2003 Oct;69(10):5884-91. doi: 10.1128/AEM.69.10.5884-5891.2003.
7
Potential for Methanosarcina to Contribute to Uranium Reduction during Acetate-Promoted Groundwater Bioremediation.
Microb Ecol. 2018 Oct;76(3):660-667. doi: 10.1007/s00248-018-1165-5. Epub 2018 Mar 2.
8
Evidence of Geobacter-associated phage in a uranium-contaminated aquifer.
ISME J. 2015 Feb;9(2):333-46. doi: 10.1038/ismej.2014.128. Epub 2014 Aug 1.
9
Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation.
Microb Biotechnol. 2009 Mar;2(2):274-86. doi: 10.1111/j.1751-7915.2009.00087.x.

引用本文的文献

2
On Modeling Ensemble Transport of Metal Reducing Motile Bacteria.
Sci Rep. 2019 Oct 10;9(1):14638. doi: 10.1038/s41598-019-51271-0.
3
Potential for Methanosarcina to Contribute to Uranium Reduction during Acetate-Promoted Groundwater Bioremediation.
Microb Ecol. 2018 Oct;76(3):660-667. doi: 10.1007/s00248-018-1165-5. Epub 2018 Mar 2.
5
Metagenomic applications in environmental monitoring and bioremediation.
J Ind Microbiol Biotechnol. 2016 Oct;43(10):1345-54. doi: 10.1007/s10295-016-1809-8. Epub 2016 Aug 24.
7
Evidence of Geobacter-associated phage in a uranium-contaminated aquifer.
ISME J. 2015 Feb;9(2):333-46. doi: 10.1038/ismej.2014.128. Epub 2014 Aug 1.
8
Fluctuations in species-level protein expression occur during element and nutrient cycling in the subsurface.
PLoS One. 2013;8(3):e57819. doi: 10.1371/journal.pone.0057819. Epub 2013 Mar 5.
9
Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwater.
ISME J. 2013 Jul;7(7):1286-98. doi: 10.1038/ismej.2013.20. Epub 2013 Feb 28.

本文引用的文献

1
Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwater.
ISME J. 2013 Jul;7(7):1286-98. doi: 10.1038/ismej.2013.20. Epub 2013 Feb 28.
2
Electromicrobiology.
Annu Rev Microbiol. 2012;66:391-409. doi: 10.1146/annurev-micro-092611-150104. Epub 2012 Jun 28.
3
Geobacter: the microbe electric's physiology, ecology, and practical applications.
Adv Microb Physiol. 2011;59:1-100. doi: 10.1016/B978-0-12-387661-4.00004-5.
4
Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation.
Microb Biotechnol. 2009 Mar;2(2):274-86. doi: 10.1111/j.1751-7915.2009.00087.x.
5
Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model.
J Contam Hydrol. 2011 Mar 25;122(1-4):96-103. doi: 10.1016/j.jconhyd.2010.11.007. Epub 2010 Nov 28.
6
In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling.
Nat Rev Microbiol. 2011 Jan;9(1):39-50. doi: 10.1038/nrmicro2456. Epub 2010 Dec 6.
9
How Geobacteraceae may dominate subsurface biodegradation: physiology of Geobacter metallireducens in slow-growth habitat-simulating retentostats.
Environ Microbiol. 2009 Sep;11(9):2425-33. doi: 10.1111/j.1462-2920.2009.01971.x. Epub 2009 Jul 22.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验