The microscopic alliance between algae and bacteria offers rare, step-by-step snapshots of how bacteria lose genes and adapt to increasing host dependence. This groundbreaking discovery is highlighted in a new study led by researchers from Stockholm University, in collaboration with the Swedish University of Agricultural Sciences and Linnaeus University, and published in Current Biology.
In some of the most nutrient-poor waters of our oceans, tiny partnerships are hard at work sustaining life. These partnerships, known as symbioses, occur between microscopic algae called diatoms and a specific type of bacteria known as cyanobacteria, which can convert atmospheric nitrogen into a form usable by living organisms. Among these cyanobacteria, the genus Richelia plays a crucial role by supplying nitrogen to their diatom hosts, which are highly active photosynthesizers. Photosynthesis, a process common to all plants, algae, and some bacteria, uses sunlight to convert carbon dioxide into chemical energy, typically in the form of sugars.
A Continuum of Integration
The physical interaction between Richelia and their diatom hosts varies widely. Some Richelia attach to the outside of their host, others live in the space between the diatom’s outer cell wall, known as a frustule, and the inner cell membrane, while some reside fully inside. This “continuum” of integration reflects different stages of the partnerships and provides researchers with a unique opportunity to examine the evolutionary process at various points in their relationship.
“In general, as symbionts become more dependent on their hosts, they become more integrated into the host, for example, live inside the host cell, and start to lose genomic information that is redundant with their hosts,” explains Professor Rachel Foster at Stockholm University.
Genomes in Transition
Using a comparative genomics approach, postdoctoral researcher Dr. Vesna Grujcic identified several genomic features of the different Richelia that reflect key transitional stages in the evolutionary process.
“As Richelia become more dependent on their hosts, the set of genes they carry changes a lot. We can see which genes disappear and which stay – giving us a rare view of how these partnerships evolve step by step. Moreover, by comparing Richelia to other nitrogen-fixing cyanobacterial symbionts, we found both shared patterns of gene loss and unique changes that reflect each lineage’s evolutionary path,”
says Vesna Grujcic.
Daniel Lundin from Linnaeus University adds, “What excites me most with this research is that different steps on the way to a fully integrated symbiont exist at the same time. This allowed us to study the genetics behind how evolution towards a lifestyle characterized by complete dependence of the symbiont on its host happened.”
Grujcic led the pangenome analysis, identifying the set of genes shared by all Richelia (the core genome) as well as the accessory genes that differ between species. Together with Maliheh Mehrshad from the Swedish University of Agricultural Sciences, Grujcic also examined patterns of genome reduction, the size and distribution of spaces between genes known as intergenic spacers, and the extent of pseudogenization – when genes accumulate mutations and lose their function.
“The level of integration between Richelia and their hosts affects not only genome size and gene content, but also the proportion of coding regions – the parts of DNA that carry instructions for making proteins. Looking at the non-coding DNA, such as the intergenic spacers and broken genes that no longer work (pseudogenes), also tells us a lot about their evolutionary journey,” says Maliheh Mehrshad.
The Role of ‘Jumping Genes’
Another intriguing result emerged from the work of researcher Theo Vigil-Stenman, a former postdoc at Stockholm University, who characterized all the insertion sequences and transposons – pieces of DNA known as “jumping genes” because they can move genetic information within the genome.
The researchers had previously observed that the genome of the partially integrated symbiont, which resides between the outer cell wall of the diatom and the inner cell membrane, was only slightly smaller than that of the symbiont attached to the outside of the host diatom. This was despite missing similar metabolic pathways as the most internal symbiont. Typically, genome size decreases as symbionts become more integrated, or live further inside their respective hosts.
“We didn’t understand why it could maintain this genome size despite lacking several functional metabolic pathways,” reflects Foster. “Theo Vigil-Stenman identified that these partially integrated symbiont genomes were full of insertion sequences which inflated their genome size.”
A Model for Studying Evolution in Action
The research group suggests that these diatom-Richelia symbioses represent a valuable model for studying symbiont genome evolution. The work offers a unique glimpse into evolution in action, as there are few known examples of symbioses caught in transitional stages. Such comparative analysis is rare among planktonic systems and places the diatom–Richelia partnership alongside other notable models of symbiosis.
Much remains to be learned about how living in symbioses has impacted the evolutionary trajectory of the host diatom genomes and how such models of nitrogen-fixing symbioses can be utilized in other fields. For example, can such systems lend valuable insights to synthetic biology for creating nitrogen-fixing crops?
As scientists continue to unravel the complexities of these microscopic partnerships, the potential applications of their findings could extend far beyond marine biology, offering innovative solutions to agricultural and ecological challenges.
