Research

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 next-generation probiotic functioning. We use a variety of microbiome methods and work with geneticists and cell biologists to explore mechanisms underlying probiotic-host interactions. 

While manuscripts in this new probiotic area are still under preparation, a few interesting studies in other areas of Ruegeria ecology and evolution have been completed over the past several years. The key references are listed below.

X. Lin, X. Feng, X. Wang, H. Long, S.A. Crowe, and H. Luo. 2024. Sulfur oxidation through rDsr in a novel Sox-free marine Roseobacter lineage. (on bioRxiv)

X. Lin, J. McNichol, X. Chu, Y. Qian, and H. Luo. 2022. Cryptic niche differentiation of novel sediment ecotypes of Ruegeria pomeroyi correlates with nitrate respiration. Environmental Microbiology 24(1): 390-403

D. Luo, X. Wang, X. Feng, M. Tian, S. Wang, S-L. Tang, P. Ang, A. Yan, and H. Luo. 2021. Population differentiation of Rhodobacteraceae along coral compartments. The ISME Journal 15(11): 3286-3302

X. Chu, S. Li, S. Wang, D. Luo, and H. Luo. 2021. Gene loss through pseudogenization contributes to the ecological diversification of a generalist Roseobacter lineage. The ISME Journal 15(2): 489-502

F.L. Hellweger, Y. Huang, and H. Luo. 2018. Carbon limitation drives GC content evolution of a marine bacterium in an individual-based genome-scale model. The ISME Journal 12(5): 1180-1187

Y. Sun, K.E. Powell, W. Sung, M. Lynch, M.A. Moran, and H. Luo. 2017. Spontaneous mutations of a model heterotrophic marine bacterium. The ISME Journal 11(7): 1713-1718

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.

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. 2025. How big is big? The effective population size of marine bacteria. Annual Review of Marine Science (invited review article; in press)

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

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. 2024. Dating the bacterial tree of life based on ancient symbiosis. Systematic Biology (under revision; on bioRxiv)

T. Liao, S. Wang, H. Zhang, E.E. Stüeken, and H. Luo. 2024. Dating ammonia-oxidizing bacteria with abundant eukaryotic fossils. Molecular Biology and Evolution (in press)

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)

T. Liao, S. Wang, E.E. Stüeken, and H. Luo. 2022. Phylogenomic evidence for the origin of obligately anaerobic Anammox bacteria around the Great Oxidation Event. Molecular Biology and Evolution 39(8): msac170

S. Wang and H. Luo. 2021. Dating Alphaproteobacteria evolution with eukaryotic fossils. Nature Communications 12: 3324

Free-living N2-fixing (diazotrophic) soil bacteria contribute substantively to nitrogen budget in terrestrial ecosystems and have great potential for application in green agriculture. Unlike the overwhelming research on symbiotic N2-fixing bacteria that carry nod genes that allows for nodulation of legume plants, there is a huge knowledge gap in free-living soil diazotrophs, particularly in areas of their ecology and evolution. An interesting example is the genus Bradyrhizobium. It has been a classical model system for symbiotic nitrogen fixation, but it was not until recently that Bradyrhizobium started to be known as the most abundant member in soil diazotrophic communities. 

Our lab has initiated large-scale cultivation and genome-sequencing of free-living Bradyrhizobium from soil and crop ecosystems. We reported a unique genomic island that accommodates the nif genes and other important genes potentially involved in coping with oxygen tension and temperature fluctuation. These free-living members are phylogenetically dispersed in the genome tree of the Bradyrhizobium, but the nif genes derived from these free-living isolates form phylogenetic clusters, indicating a role of horizontal gene transfer. We are now putting together a manuscript that is focused on the environmental controls of the free-living diazotrophic Bradyrhizobium through amplicon-based and genomic analyses. 

In another area of free-living Bradyrhizobium research, we focused on an unusual Bradyrhizobium phylogroup that, despite being nod-free, can nodulate tropical legumes in the Aeschynomene genus. Using amplicon-based analysis we show that this phylogroup is particularly abundant in rice field compared to typical soil ecosystems such as grassland and forest. We then isolated a few hundred strains of this phylogroup predominantly from rice fields and discovered a new deeply branching clade, thereby supplementing the two previously known clades. We further show that the ability to nodulate Aeschynomene appears to be a common trait among this phylogroup members regardless of their ecological origin, but the three major clades differ in symbiosis efficiency in a way aligning with their phylogenetic branching order.  

Key published / submitted papers in this area:

L. Ling, A. Camuel, S. Wang, X. Wang, T. Liao, J. Tao, X. Lin, N. Nouwen, E. Giraud, and H. Luo. 2024. Correlating phylogenetic and functional diversity of the nod-free but nodulating Bradyrhizobium phylogroup. (on bioRxiv)

J. Tao, S. Wang, T. Liao, and H. Luo. 2021. Evolutionary origin and ecological implication of a unique nif island in free-living Bradyrhizobium lineages. The ISME Journal 15(11): 3195-3206