Research

▪️ Next-generation marine probiotics  

Our ongoing research highlights the development of population genomic approaches that allow the selection of powerful coral probiotic strains that could facilitate their incorporation and retention into coral tissue, therefore minimizing the need for reapplication and the associated cost. Our model microbial system is coral holobiont-associated Ruegeria, a famous genus in the marine Roseobacter group (Roseobacteraceae, Alphaproteobacteria). We are building a big collection of coral-associated Ruegeria isolates from which we identified evolutionarily young, facultative endosymbiotic Ruegeria members and are using them for probiotic intervention.

As Ruegeria members are broadly and abundantly associated with marine invertebrate groups, we are extending our work to the development of novel probiotics for other important marine organisms, notably bivalves (e.g., oysters, mussels, scallops).

We actively collaborate with marine biologists to illustrate probiotic effects on stressed marine hosts through laboratory trials. We are looking for short-term reproducible systems that allow testing and comparing the efficacy of multiple probiotic strains. 

As a key component of proof of concept, testing the efficacy of probiotic strains in the real world is part of our main interest. We are always keen for field-based methods that allow measuring the effect of probiotic inoculations on marine organisms in the real world, and currently working with a few marine ecologists to perform field trials.

We are also very interested in the mechanistic processes underlying probiotic functioning. We use a variety of microbiome methods and work with geneticists and cell biologists to explore probiotic - host interactions.

▪️ Evolutionary genetics of genome-reduced marine bacterioplankton

We are interested in the adaptive evolution of marine bacterioplankton lineages that carry small genomes and dominate in marine bacterioplankton communities. Mechanistic understanding of the evolutionary processes requires knowing the magnitude of their effective population sizes (Ne). This can be determined by measuring genomic mutation rate through mutation accumulation experiments followed by genome sequencing the mutant lines, delineating population boundaries such that cells from within a population have higher recombination rates than those from different populations, and calculating neutral genetic diversity carried by delineated populations. The emerging pattern is interesting - the high-light-adapted clade II Prochlorococcus has its Ne at only ~1.7×107, which is smaller than originally thought by several orders of magnitude.

Our representative work in this area is theorizing random genetic drift as a key mechanism driving Prochlorococcus evolution. As the most abundant photosynthetic carbon-fixing organisms responsible for 10% of global oxygen production, Prochlorococcus was generally accepted to have extremely large effective population sizes (Ne). As the strength of genetic drift is the inverse of Ne, genetic drift was believed to be negligible in their evolution. Additionally, Prochlorococcus is known to have undergone a major genome reduction event during its early evolution, and natural selection was believed to have acted to drive this important event that largely shaped the reduced genome sizes of most lineages of today’s Prochlorococcus.

We provided evidence against this prevailing selective theory. Over the past several years, we demonstrated a few things. i) The early Prochlorococcus genome reduction was accompanied by genome-wide accumulation of a more deleterious type of mutations, suggesting population bottlenecks occurred at that time (Nat Microbiol 2017); ii) The early population bottlenecks were linked to the Snowball Earth icehouse climate conditions eponymous with the Cryogenian Period during 720 to 635 million years ago (Proceedings B 2021); iii) The early population bottlenecks reduced its Ne down to 104-105, which, together with the decreased opportunity of genetic recombination during the Snowball Earth conditions, leads to a new hypothesis - Muller’s ratchet is likely to be a main mechanism driving early genome reduction of Prochlorococcus (ISME Journal 2024); iv) Extant Prochlorococcus species have small Ne at the order of 107, suggesting genetic drift is also a major force driving the Prochlorococcus evolution in the modern ocean (Nat Ecol Evol 2022).

Key published/submitted papers in this area:

▪️ Leveraging abundant eukaryotic fossils to calibrate bacterial evolution

Making accurate inferences of bacterial ages is very challenging, mainly due to the great scarcity of appropriate fossils. We have developed a series of new approaches that ‘borrow’ the rich timing information associated with eukaryotic fossils to calibrate bacterial evolution. This includes calibrating Alphaproteobacteria evolution based on the mitochondrial endosymbiosis in which eukaryotic mitochondria is sister to Alphaproteobacteria, as well as calibrating Cyanobacteria evolution based on the plastid endosymbiosis in which eukaryotic plastid is phylogenetically embedded in Cyanobacteria. More recently, we leveraged the idea of host-symbiont coevolution and developed a probabilistic framework that allows constraining the origin of bacterial symbionts as postdating the origin of their eukaryotic hosts while also considering the uncertainty of the ancestral lifestyle and host identity of the modern symbionts.

Key published / submitted papers in this area: