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An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing
Published on: May 23, 2018
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High-throughput single-cell sequencing of activated sludge microbiome
Yulin Zhang1, Bingjie Xue1,2,3, Yanping Mao3
1Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China.
Environmental Science and Ecotechnology
|October 21, 2024
Summary
Single-cell sequencing of activated sludge (AS) revealed novel microbial species and extensive horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). This method enhances understanding of microbial communities in wastewater treatment plants (WWTPs) and aids in health risk assessment.
Area of Science:
- Environmental microbiology
- Biotechnology
- Genomics
Background:
- Wastewater treatment plants (WWTPs) are crucial for environmental protection and public health, utilizing activated sludge (AS) for contaminant removal.
- Metagenomics offers insights into microbial communities but struggles with genomic heterogeneity, microbial dark matter, and host-cell genetic links.
- Single-cell sequencing provides high resolution to overcome these limitations in studying complex microbiomes.
Purpose of the Study:
- To apply high-throughput single-cell sequencing to the activated sludge (AS) microbiome.
- To characterize the genomic diversity and identify novel species within AS.
- To investigate the prevalence and transfer of antibiotic resistance genes (ARGs), plasmids, and phages in AS.
Main Methods:
- High-throughput single-cell sequencing of 15,110 individual cells from AS.
- Clustering of single-amplified genomes (SAGs) into 2,454 SAG bins.
- Analysis of ARGs, plasmid fragments, and phage contigs.
- Complementary analysis using 1,529 metagenome-assembled genomes (MAGs).
Main Results:
- Clustering yielded 2,454 SAG bins, with 27.5% representing potential novel species (microbial dark matter).
- Identified 1,137 ARGs, 10,450 plasmid fragments, and 1,343 phage contigs, with broad host distribution indicating frequent horizontal gene transfer (HGT).
- Taxonomically classified 98 previously unclassified SAG bins using MAGs.
Conclusions:
- Single-cell sequencing is feasible and effective for characterizing the AS microbiome.
- The study provides novel insights into AS ecological dynamics and HGT, especially concerning ARGs.
- This approach can monitor ARG distribution and host association, contributing to health risk evaluation within a One Health framework.
