Research – Yung Lab

New Study Reveals Microbial Dynamics in Coastal South China Sea

We’re proud to announce that Wenqian Xu, PhD candidate, from our group has published a paper in Science of the Total Environment. The study, “Revealing the intricate temporal dynamics and adaptive responses of prokaryotic and eukaryotic microbes in the coastal South China Sea,” offers new insights into marine microbial communities.

Wenqian’s two-year study combined metagenomics and metatranscriptomics to explore how microbial communities adapt to environmental changes. The research uncovered seasonal shifts in microbial composition and analyzed 37 phytoplankton metagenome-assembled genomes.

Congratulations to Wenqian and the team on this significant contribution to marine microbiology!

Prasinovirus diversity in the South China Sea

A collaborative study between researchers from Yung lab and the GENOPHY group at the Observatoire Océanologique de Banyuls has been accepted for publication in ISME Communications. The paper, titled “Unveiling Prasinovirus diversity and host specificity through targeted enrichment in the South China Sea,” sheds new light on the complex relationships between prasinoviruses and their algal hosts in marine ecosystems (https://doi.org/10.1093/ismeco/ycae109).

Using an innovative virus enrichment and sequencing method, our team successfully assembled 80 prasinovirus genomes from samples collected in the South China Sea. This research provides the first direct estimation of genome similarity correlating to host range with 94% accuracy.

Some key findings include:

Unexpected host-switching across diverse algal lineages
Detection of horizontal gene transfer between viruses and hosts
Evidence of ongoing coevolutionary dynamics through diversifying selection on viral proteins

This work not only expands our understanding of prasinovirus genomic diversity but also highlights the intricate evolutionary mechanisms shaping virus-host interactions in marine environments.

Congratulations to all the authors on this significant contribution to the field of marine microbial ecology!

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Congratulations, Ruixian!

We are delighted to announce that Ruixian has successfully defended her MPhil thesis titled ‘Unveiling Virus-Host Interactions in the Dynamic Marine Ecosystem of the Pearl River Estuary.’ Her research involved a comprehensive metagenomic analysis of samples, examining prokaryotes, eukaryotes, and viruses. Ruixian also made significant strides in predicting virus-host interactions based on genetic data. We eagerly anticipate the publication of her findings in a peer-reviewed journal. Ruixian’s academic journey doesn’t end here – she will be continuing her studies as a PhD student in the Yung Lab. We have every confidence in her ability to make further valuable contributions to the field of marine microbiology.

Congratulations, Ruixian, on this impressive achievement. We look forward to witnessing your continued growth and success in your doctoral studies!

New Study Reveals Hidden Diversity in Marine Picophytoplankton

We’re excited to announce that our manuscript “Hidden genomic diversity drives niche partitioning in a cosmopolitan eukaryotic picophytoplankton” has been published in The ISME Journal (https://doi.org/10.1093/ismejo/wrae163). Xu et al recovered and analyzed 37 genomes from the picophytoplankton genus Bathycoccus, revealing four distinct evolutionary clades with well-differentiated ecological niches and biogeographic distributions shaped by environmental factors. The study uncovered clade-specific genomic traits contributing to niche adaptation, highlighted temperature as a major driver of genome diversification, and identified potential cold-adaptation mechanisms in polar-adapted clades, providing insights into the microdiversity and adaptive evolution of this crucial marine eukaryotic phytoplankton.

Invited talk at NUS, Singapore

Charmaine delivered an insightful presentation titled ‘Unraveling Virus-Phytoplankton Interactions Using Integrated Cultivation and Multi-omics Approaches’ at the School of Biological Sciences, National University of Singapore. The invitation came from Prof. Steve Pointing, Charmaine’s former MPhil advisor from her time at the University of Hong Kong (HKU).

The visit provided a valuable opportunity to reconnect with Steve and meet his talented team members, Christaline and Thirumaran. Charmaine appreciated the chance to engage with these bright minds and explore their current research endeavors. Beyond the presentation, the visit facilitated discussions on potential collaborations with NUS scientists, opening doors for future joint research projects.

The day concluded with a delightful dinner hosted by Prof. Pointing. Charmaine expressed her gratitude for both the invitation and the delicious meal, which provided a fitting end to a productive and inspiring visit.

Discovery of a novel Mamiellophycean green alga

We’re pleased to announce the publication of our study ‘Genomic characterisation and ecological distribution of Mantoniella tinhauana: a novel Mamiellophycean green alga from the Western Pacific’ in Frontiers in Microbiology (https://doi.org/10.3389/fmicb.2024.1358574). In this research, Rey Redondo et al. isolated and characterized a new species of Mamiellophyceae, Mantoniella tinhauana, from subtropical coastal waters in the South China Sea. We sequenced and assembled its genome for the first time, uncovering significant differences from previously studied Mamiellophyceae species. Our global metagenomic analysis revealed that M. tinhauana exhibits a cosmopolitan distribution with low-level prevalence worldwide. This study underscores the importance of understanding the intricate relationship between Mamiellophyceae and their environment, which is crucial for accurately predicting their response to future environmental changes.

Jun-Aug 2012: Meeting the GENOPHY group

Charmaine recently visited the Observatoire Océanologique de Banyuls-sur-Mer, meeting her collaborator Gwenael in person for the first time since their partnership began in 2020. This collaboration, supported by the Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), focuses on prasinovirus diversity.

During her visit, Charmaine engaged in productive discussions with Gwenael, Sheree, and Julie about their joint project. Unexpectedly, Charmaine’s brief visit turned into an extended summer stay in France, allowing for deeper research collaboration and cultural exploration.

Charmaine expressed gratitude for her colleagues’ hospitality, which made this unplanned extension both possible and enriching. This experience highlights the value of in-person interactions in fostering scientific partnerships and the unexpected opportunities that can arise from international collaborations.

Comprehensive Review on Mamiellophyceae Diversity and Evolution Published

A collaborative effort between the YUNG group and the GENOPHY group has resulted in a comprehensive review titled “Diversity and Evolution of Mamiellophyceae: Early-Diverging Phytoplanktonic Green Algae Containing Many Cosmopolitan Species,” published in the Journal of Marine Science and Engineering. This in-depth review synthesizes current knowledge on the diversity, ecology, and evolution of Mamiellophyceae and their associated large double-stranded DNA prasinoviruses. The authors integrate insights from cutting-edge genomic and metagenomic analyses, including data from 26 metabarcoding environmental studies and major oceanic expeditions such as the Global Ocean Sampling (GOS) and Tara Oceans. This review offers a state-of-the-art understanding of these important marine microorganisms, highlighting their global distribution and ecological significance. For those interested in marine microbial ecology, phytoplankton diversity, or algal virology, this article serves as an essential resource. The full review can be accessed at: https://doi.org/10.3390/jmse10020240.

Intensive Diel Sampling Reveals Temporal Dynamics of Coastal Marine Microbes

Our research team conducted a 48-hour sampling campaign to investigate the temporal dynamics of coastal marine microbial communities. The study involved collecting water samples at six-hour intervals, providing a high-resolution snapshot of microbial activity over two full day-night cycles. This sampling protocol was designed to capture the diel variations in marine prokaryotes, eukaryotes, and viruses.

Water samples were carefully filtered to isolate different microbial components, allowing for comprehensive analysis of the diverse marine microbial ecosystem. Concurrent with biological sampling, we recorded crucial physico-chemical parameters to contextualize the microbial data within the changing environmental conditions.

This intensive effort aims to shed light on the short-term fluctuations in microbial populations and their potential drivers in coastal marine environments. The resulting dataset promises to offer valuable insights into the complex interplay between marine microbes and their dynamic coastal habitat over diurnal cycles.