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Magnetic nanoparticle-mediated isolation of functional bacteria in a complex microbial community
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Zhang, Dayi, Berry, James, Zhu, Di, Wang, Yun, Chen, Yin, Jiang, Bo, Huang, Shi, Langford, Harry, Li, Guanghe, Davison, Paul A., Xu, Jian, Aries, Eriv and Huang, Wei E. (2015) Magnetic nanoparticle-mediated isolation of functional bacteria in a complex microbial community. ISME Journal, 9 . pp. 603-614. doi:10.1038/ismej.2014.161 ISSN 1751-7362.
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Official URL: http://dx.doi.org/10.1038/ismej.2014.161
Abstract
Although uncultured microorganisms have important roles in ecosystems, their ecophysiology in situ remains elusive owing to the difficulty of obtaining live cells from their natural habitats. In this study, we employed a novel magnetic nanoparticle-mediated isolation (MMI) method to recover metabolically active cells of a group of previously uncultured phenol degraders, Burkholderiales spp., from coking plant wastewater biosludge; five other culturable phenol degraders—Rhodococcus sp., Chryseobacterium sp. and three different Pseudomonas spp.—were also isolated from the same biosludge using traditional methods. The kinetics of phenol degradation by MMI-recovered cells (MRCs) was similar to that of the original sludge. Stable isotope probing (SIP) and pyrosequencing of the 16S rRNA from the ‘heavy’ DNA (13C-DNA) fractions indicated that Burkholderiales spp. were the key phenol degraders in situ in the biosludge, consistent with the results of MRCs. Single-cell Raman micro-spectroscopy was applied to probe individual bacteria in the MRCs obtained from the SIP experiment and showed that 79% of them were fully 13C-labelled. Biolog assays on the MRCs revealed the impact of various carbon and nitrogen substrates on the efficiency of phenol degradation in the wastewater treatment plant biosludge. Specifically, hydroxylamine, a metabolite of ammonia oxidisation, but not nitrite, nitrate or ammonia, inhibited phenol degradation in the biosludge. Our results provided a novel insight into the occasional abrupt failure events that occur in the wastewater treatment plant. This study demonstrated that MMI is a powerful tool to recover live and functional cells in situ from a complex microbial community to enable further characterisation of their physiology.
Item Type: | Journal Article | ||||||||||
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Alternative Title: | Recovering live uncultured bacteria in-situ | ||||||||||
Subjects: | Q Science > QD Chemistry Q Science > QP Physiology Q Science > QR Microbiology |
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Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||||||||
Library of Congress Subject Headings (LCSH): | Raman spectroscopy, Microbial ecology , Stable isotopes, Biodegradation, Plant physiology -- Research, Hydroxylamine , Nanostructured materials -- Magnetic properties | ||||||||||
Journal or Publication Title: | ISME Journal | ||||||||||
Publisher: | Nature Publishing Group | ||||||||||
ISSN: | 1751-7362 | ||||||||||
Official Date: | March 2015 | ||||||||||
Dates: |
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Volume: | 9 | ||||||||||
Page Range: | pp. 603-614 | ||||||||||
DOI: | 10.1038/ismej.2014.161 | ||||||||||
Status: | Peer Reviewed | ||||||||||
Publication Status: | Published | ||||||||||
Access rights to Published version: | Restricted or Subscription Access | ||||||||||
Date of first compliant deposit: | 28 July 2016 | ||||||||||
Date of first compliant Open Access: | 28 July 2016 | ||||||||||
Funder: | European Union (EU), Engineering and Physical Sciences Research Council (EPSRC), Zhongguo ke xue yuan [Chinese Academy of Sciences] (CAS), China. Guo jia ke xue ji shu bu [Ministry of Science and Technology] (CMST), Natural Environment Research Council (Great Britain) (NERC), Gordon and Betty Moore Foundation (GBMF) | ||||||||||
Grant number: | RFCR-CT-2010-00010 (EU), EP/H04986X/1 (EPSRC), XDB15040100 (CAS), 2011IM030100 (CMST), NE/H016236/1 (NERC), 3303 (GBMF) |
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