Research

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. 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

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