title: Magnetic nanoparticle-mediated isolation of functional bacteria in a complex microbial community.
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 ((13)C-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 (13)C-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.
authors.affiliation: Department of Civil & Structural Engineering, Kroto Research Institute, University of Sheffield, Sheffield, England, UK.
authors.forename: Dayi
authors.initials: D
authors.lastname: Zhang
authors.affiliation: Department of Civil & Structural Engineering, Kroto Research Institute, University of Sheffield, Sheffield, England, UK.
authors.forename: James P
authors.initials: JP
authors.lastname: Berry
authors.affiliation: Department of Civil & Structural Engineering, Kroto Research Institute, University of Sheffield, Sheffield, England, UK.
authors.forename: Di
authors.initials: D
authors.lastname: Zhu
authors.affiliation: Single-Cell Centre, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.
authors.forename: Yun
authors.initials: Y
authors.lastname: Wang
authors.affiliation: School of Life Sciences, University of Warwick, Coventry, England, UK.
authors.forename: Yin
authors.initials: Y
authors.lastname: Chen
authors.affiliation: School of Environment, Tsinghua University, Beijing, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Jiang
authors.affiliation: Single-Cell Centre, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.
authors.forename: Shi
authors.initials: S
authors.lastname: Huang
authors.affiliation: Department of Civil & Structural Engineering, Kroto Research Institute, University of Sheffield, Sheffield, England, UK.
authors.forename: Harry
authors.initials: H
authors.lastname: Langford
authors.affiliation: School of Environment, Tsinghua University, Beijing, China.
authors.forename: Guanghe
authors.initials: G
authors.lastname: Li
authors.affiliation: Department of Civil & Structural Engineering, Kroto Research Institute, University of Sheffield, Sheffield, England, UK.
authors.forename: Paul A
authors.initials: PA
authors.lastname: Davison
authors.affiliation: Single-Cell Centre, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Xu
authors.affiliation: Tata Steel, Environment Technology, Group Environment, Swinden Technology Centre, Rotherham, UK.
authors.forename: Eric
authors.initials: E
authors.lastname: Aries
authors.affiliation: Department of Civil & Structural Engineering, Kroto Research Institute, University of Sheffield, Sheffield, England, UK.
authors.forename: Wei E
authors.initials: WE
authors.lastname: Huang
mesh_terms: D020562:Betaproteobacteria / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D001673:Biodegradation, Environmental; D004269:DNA, Bacterial / Q000235:genetics; D008280:Magnetics / Q000379:methods*; D058185:Magnetite Nanoparticles / Q000737:chemistry*; D019800:Phenol / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012722:Sewage / Q000737:chemistry / Q000382:microbiology; D062065:Wastewater / Q000737:chemistry / Q000382:microbiology*
chemical_list: D004269:DNA, Bacterial; D058185:Magnetite Nanoparticles; D019800:Phenol; D012336:RNA, Ribosomal, 16S; D012722:Sewage; D062065:Wastewater