A study led by researchers from the Centre for Advanced Studies of Blanes (CEAB-CSIC) reveals how early sponges living in primordial oceans transformed an environmental constraint into an evolutionary advantage. The work, published in Molecular Biology and Evolution and highlighted among its most relevant recent articles, explains how the abundance of dissolved silicon in ancestral oceans drove, more than 500 million years ago, the emergence of the unique glass-like skeletons of these animals.
Sponges (Porifera) are the oldest group of animals on the planet and the only ones capable of building skeletons composed of silica, the same material used in human-made glass. To achieve this, they take up dissolved silicon from seawater and transform it into thousands of minute solid pieces that together provide skeletal support.
This process, known as biosilicification, occurs in two stages. First, dissolved silicon in seawater is transported into sponge cells by transporter proteins; then, other proteins, known as silicifying proteins, precipitate it as solid silica (glass), forming the characteristic skeletal elements of these animals.
“Our study reconstructs the evolutionary history of transporter proteins through the analysis of multiple sponge genomes, as well as hundreds of genetic sequences from numerous organisms, from microbes to humans. Previous knowledge about the evolution of silicon transporters in sponges consisted of only a few disconnected pieces of information, a kind of collection of evolutionary anecdotes. However, we suspected that this limited information might just be the tip of a huge iceberg, and we have now demonstrated that silicon transporters have been central elements in the evolutionary history and diversification of these animals,” explain CEAB-CSIC researchers Manuel Maldonado and Laia Leria.
Genomic analyses indicate that the ability to precipitate silicon to form skeletal silica arose independently in at least four different sponge subgroups. Each subgroup not only developed its own silicifying proteins, but within each group, silicon transporter proteins followed very different evolutionary trajectories.
A key genetic innovation in the evolutionary success of sponges
One of the most notable examples is that heteroscleromorph sponge subgroup, which comprises about three-quarters of all currently known sponges, all of which possess siliceous skeletons. The study revealed that these sponges acquired, via gene transfer from a symbiotic bacterium, a novel type of silicon transporter that was added to those they already possessed. This acquisition, together with the mutation of a digestive enzyme into a silicifying protein, appears to have acted synergistically as a key innovation that likely drove the extraordinary evolutionary radiation and high degree of skeletonization observed in this large subgroup.
In contrast, sponge subgroups that did not acquire silicifying proteins eventually also lost their silicon transport system, and these groups have persisted to the present day without producing siliceous skeletons. Among these non-siliceous sponges are the soft-bodied bath sponges, and in general they are poorly diversified groups, consisting of only dozens or a few hundred species, compared to the more than 7,000 species that make up the heteroscleromorph sponges.
From an environmental threat to a driver of biological innovation
The discovery that sponges lacking silicifying proteins eventually lost their transporter proteins was crucial, as it allowed researchers to infer the cause that led to the emergence of biosilicification. In ancient oceans, which were extremely rich in dissolved silicon, this element likely entered sponge cells accidentally through transporter proteins originally designed to take up essential substances such as water, sugars, and alcohols—but not silicon. In fact, these ancestral sponges still lacked siliceous skeletons, and the environmental silicon entering their cells was actually toxic. Thus, cells had to expel it at a high energetic cost, because silicon concentrations outside were very high and it would re-enter continuously. However, at some point around 520 million years ago, random mutations caused some proteins in certain sponges to change function and begin precipitating dissolved silicon as solid silica. This not only detoxified silicon in a more energy-efficient way, but also generated a new biomineral material within the sponge. This new material likely contributed to the ecological success of these species, as it not only reduced the energetic cost of managing toxic silicon, but also provided structural support (a skeleton) that favored increasing body size, protection against predation, and other benefits that promoted further diversification of these sponge groups.
In this way, sponges transformed an environmental threat into a driver of biological innovation. Sponges that failed to develop silicifying proteins lost their membrane transporters to prevent the entry of silicon, as they could not detoxify it by precipitation. This represents an extraordinary example of how random mutations and other processes generating genetic diversity (such as the acquisition of bacterial genes), together with the need to survive in a hostile environment, can drive remarkable evolutionary innovations and ecological adaptations.
Maldonado and Leria note that this new knowledge also opens potential avenues for collaboration with the silicon industry: “a deeper understanding on how silicon transporters work could help develop new biotechnological ways to produce silicon for semiconductors”.
This work continues a long-standing line of research by the same team, whose recent discovery of new silicifying proteins demonstrated that the ability to produce silica emerged independently in several animal lineages (Nature Communications, 2024). While that previous study focused on the protein machinery responsible for silica polymerization, the new work adds another key piece to this evolutionary puzzle: how sponges learned to manage silicon toxicity within their cells and how this process influenced their subsequent evolutionary success.
