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.

Identification of Benzo[ a ]pyrene-Metabolizing Bacteria in Forest Soils by Using DNA-Based Stable-Isotope Probing

“…In our study, SIP results could not directly relate the Gram-positive PAH-RHD␣ genes to the functional Gram-negative host and therefore were not able to prove horizontal gene transfer. Further work is suggested for the single-cell isolation and genome amplification of individual BaP degraders (54) and deeper investigation on the PAH-RHD␣ genes within the targeting functional species.…”

Ligand‐Induced Evolution of Intrinsic Fluorescence and Catalytic Activity from Cobalt Ferrite Nanoparticles

“…CoFe 2 O 4 NPs were prepared by using at emplate-free wet chemical process following ap revious report with some modification, [12] which involves the high-temperature (270 8C) reflux of Co(ac) 2 and Fe(acac) 3 …”

“…The development of multifunctional nanoparticles (NPs) with both magnetic and fluorescent properties has attracted immense attention from researchers to address the shortcomings of traditional disease diagnostic and therapeutic agents, [1] owing to their prominence in magnetic resonance imaging (MRI) as well as excellence in pathogen detection, [2] cell separation, [3] hyperthermia, [4] NIR photothermal ablation, [5] and targeted gene and drugd elivery. [6] Moreover, the required size of the NPs is lesst han 10 nm, so that they can reach the intracellular markerso fd iseases or viral infections at ap reliminary stage before proliferation, [7] enhancer elaxation time in MRI because of the very large magnetic moments in the presence of as tatic magnetic field, and invoke dipolar interactions between the superparamagnetic cores and surrounding solventp rotons.…”

Raman‐activated cell sorting and metagenomic sequencing revealing carbon‐fixing bacteria in the ocean

“…Raman‐stable isotope probing (Raman‐SIP) has been employed to probe bacterial function at the single cell level (Huang et al ., ; Bankevich et al ., ; Li et al ., b; Wang et al ., a). To link the function to its underlying genotypes, we have developed a series of Raman‐Activated Cell Sorting (RACS) techniques, such as Raman‐activated cell ejection (RACE) (Wang et al ., ) and Raman‐activated microfluidic sorting (RAMS) (Zhang et al ., b; McIlvenna et al ., 2016; Song et al ., 2017), to isolate individual cells based on their SCRS characteristics. After RACS, genomic DNA from single cells was amplified by multiple displacement amplification (MDA) and subsequently processed for sequencing (Song et al ., ).…”