Evolution in progress: How ocean microbes shed genes to survive

In some of the leanest waters on Earth, life survives by teaming up. Microscopic algae known as diatoms and nitrogen-fixing cyanobacteria strike a bargain. The bacteria pull nitrogen from the air and hand it to their hosts, while the diatoms – ace photosynthesizers – pay in sugars powered by sunlight.

A new study led by Stockholm University shows these alliances don’t just keep the ocean’s pantry stocked. They also capture evolution in the act, offering rare, step-by-step snapshots of how symbiotic bacteria shed genes and slide into deeper dependence on their hosts.

The researchers examined partnerships between diatoms and cyanobacteria in the genus Richelia. By comparing Richelia genomes at different host intimacy levels, the team mapped stages of increasing symbiont integration.

From free-living to dependent

Not all Richelia bacteria occupy the same address. Some cling to the diatom’s exterior, others tuck into the narrow space beneath the silica shell (the frustule), and the most committed residents move right in.

That gradient of living arrangements – the “continuum of integration” – maps neatly onto a classic evolutionary pattern in symbiosis. The more a symbiont relies on its host, the more it tends to live inside, and the more of its own genome it can afford to discard.

“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,” said Professor Rachel Foster, a co-author of the study.

Having multiple, coexisting stages in a single system gives researchers something they rarely get in nature: different time points of the same evolutionary process, all available for side-by-side comparison.

Ocean genes in transition

Using comparative genomics, postdoctoral researcher Vesna Grujcic and colleagues parsed which genes Richelia keep and which they lose as they lean more on their diatom partners.

A pangenome analysis identified the core set shared by all Richelia, as well as accessory genes that vary among lineages.

The team also tracked hallmarks of genome streamlining. These included overall genome size, the fraction of DNA devoted to protein-coding regions, the length of intergenic spacers, and the prevalence of pseudogenes (broken genes that no longer function).

“As Richelia become more dependent on their hosts, the set of genes they carry changes a lot,” said Grujcic. “We can see which genes disappear and which stay – giving us a rare view of how these partnerships evolve step by step.”

Shrinking genomes, bigger dependence

Comparing Richelia to other nitrogen-fixing cyanobacterial symbionts revealed both shared themes in gene loss and ocean-specific lineage quirks. This underscores that there isn’t a single recipe for becoming a symbiont – there are family styles.

Crucially, deeper integration doesn’t just trim the parts list; it reshapes the genome’s architecture. More integrated Richelia typically have smaller genomes, a higher proportion of coding DNA, and fewer long non-coding stretches.

Those features point to a streamlined lifestyle in which the host picks up more of the metabolic slack, allowing the symbiont to jettison pathways it no longer needs to handle alone.

Genome clutter hides gene loss

One puzzle stood out. In Richelia that live squeezed between the diatom’s wall and membrane – a halfway house on the road to full integration – the genome wasn’t much smaller. It was comparable to that of the least integrated, free-surface dwellers.

In fact, despite missing many of the same metabolic pathways as the most internal symbionts, these “semi-internal” genomes hadn’t shrunk as expected.

The culprit, it turns out, was genomic clutter. Researcher Theo Vigil-Stenman cataloged a surge of insertion sequences and transposons in these partially integrated strains. These so-called “jumping genes” can copy and paste themselves around the genome.

That extra cargo inflates genome size even as functional content falls, masking the underlying trend toward streamlining. In other words, a genome on a diet can still look bulky if it’s stuffed with mobile DNA.

A living window into symbiosis

For evolutionary biologists, this system is a gift. Transitional symbioses are notoriously hard to catch; most known partnerships are either relatively loose or ancient and fully locked in.

Diatom–Richelia alliances capture multiple rungs on the ladder at once, letting scientists connect lifestyle, location in or on the host, and the fine-scale mechanics of genome change.

“What excites me is different steps on the way to a fully integrated symbiont exist at the same time,” said Daniel Lundin from Linnaeus University. “This allowed us to study the genetics behind how evolution towards complete dependence happened.”

From ocean genes to future crops

Beyond satisfying curiosity, the findings have practical resonance. Nitrogen fixation – the trick Richelia perform for their hosts – underpins marine productivity and global nutrient cycles.

Understanding how these symbioses assemble and are maintained can sharpen models of ocean ecology, especially in nutrient-poor regions where partnerships like these sustain food webs from the bottom up.

There’s also an applied horizon. Agriculture has long dreamed of cereals that fix nitrogen, reducing farmers’ costs and the environmental toll of fertilizers.

Though not crops, diatoms reveal principles for stabilizing low-oxygen niches for nitrogenase, offering valuable lessons for biology. Managing gene-loss cascades in symbionts could guide synthetic biology to engineer plants with similar nitrogen-fixing services.

Mysteries of symbiosis

The study focuses on the symbionts; the hosts have their own evolutionary stories to tell. How has living with Richelia reshaped diatom genomes? Which host genes facilitate the different levels of bacterial integration, from attachment to full residency?

How do environmental shifts – warming seas, stratification, nutrient changes—drive these partnerships toward or away from tighter dependence?

Answering those questions will require more genomes, more environmental sampling, and experiments that probe how host and symbiont negotiate the terms of their living arrangement.

But this much is clear already: in the ocean’s smallest alliances, we can see evolution’s gears turning – one lost gene, one mobile element, one deepening dependency at a time.

The study is published in the journal Current Biology.

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