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 these next-generation probiotics for 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 use a standardized, short-term, reproducible system called CBASS to compare the efficacy of different probiotic strains on inoculated cnidarian hosts. We are looking for such short-term systems to test bivalves and other marine invertebrate hosts.
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
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.
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.
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.
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.
Extant Prochlorococcus species have their Ne at the order of 107, which are smaller than originally thought by several orders of magnitude, suggesting genetic drift is also an important force driving the Prochlorococcus evolution in the modern ocean.
Our new work highlights a direct experimental test of the famous “genome streamlining” theory. This theory posits that positive selection is the key driver of bacterial genome reduction in surface oceans. The underlying principle is straightforward - cells with smaller genomes require fewer resources and thus are more favorable in surface ocean habitats in which nutrients are very limited. Testing this theory requires determining and comparing Ne across bacterioplankton lineages that are evolutionarily related but vary substantially in genome size, which has never been done. Our recent cultivation of a new bacterioplankton lineage, “CHUG” (2.6 Mbp), in the globally dominant marine Roseobacter group which typically have large and variable genomes (typically >4 Mbp) provides a unique opportunity to test this prevailing theory. A key prediction of the genome streamlining theory is that genome-reduced bacterioplankton lineages should have larger effective population sizes (Ne) compared to bacterioplankton lineages that carry large genomes. We report a reverse trend – Ne scales positively with genome size. It means random genetic drift, rather than natural selection, is a key driver of their genome reduction.
Key published / submitted papers in this area:
H. Luo. 2024. How big is big? The effective population size of marine bacteria. Annual Review of Marine Science (invited review; submitted)
X. Wang, M. Xie, K.E.Y.K Ho, Y. Sun, X. Chu, S. Zhang, V. Ringel, H. Wang, X-H Zhang, Z. Shao, Y. Zhao, T. Brinkhoff, J. Petersen, I. Wagner-Döbler, and H. Luo. 2024. A neutral process of genome reduction in marine bacterioplankton. (on bioRxiv)
H. Zhang, F.L. Hellweger, and H. Luo. 2024. Genome reduction occurred in early Prochlorococcus with an unusually low effective population size. The ISME Journal (in press)
Z. Chen, X. Wang, Y. Song, Q. Zeng, Y. Zhang, and H. Luo. 2022. Prochlorococcus have low global mutation rate and small effective population size. Nature Ecology & Evolution 6(2): 183-194
H. Zhang, Y. Sun, Q. Zeng, S.A. Crowe, and H. Luo. 2021. Snowball Earth, population bottleneck and Prochlorococcus evolution. Proceedings of the Royal Society B 288(1963): 20211956
H. Luo, Y. Huang, R. Stepanauskas, and J. Tang. 2017. Excess of non-conservative amino acid changes in marine bacterioplankton lineages with reduced genomes. Nature Microbiology 2: 17091
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:
S. Wang and H. Luo. 2023. Dating the bacterial tree of life based on ancient symbiosis. (on bioRxiv)
T. Liao, S. Wang, H. Zhang, E.E. Stüeken, and H. Luo. 2024. Dating ammonia-oxidizing bacteria with abundant eukaryotic fossils. (on bioRxiv)
H. Zhang, S. Wang, T. Liao, S.A. Crowe, and H. Luo. 2023. Emergence of Prochlorococcus in the Tonian oceans and the initiation of Neoproterozoic oxygenation. (on bioRxiv)
S. Wang and H. Luo. 2021. Dating Alphaproteobacteria evolution with eukaryotic fossils. Nature Communications 12: 3324