Periodic Reporting for period 1 - Si-ORHIGENS (Unravelling the Silicification prOcess in RHIzaria through GENetics and Skeletal growth)
Reporting period: 2022-11-01 to 2024-10-31
Silicon (Si) is a critical nutrient in the global ocean, essential for the growth of a wide range of organisms, including microalgae, sponges, and rhizarians. Silicifying Rhizaria were among the first protists to inhabit the ocean and, alongside sponges, dominated biogenic silica production during the Cambrian era. Despite their significance, these organisms remain poorly understood as key components of marine ecosystems. In today’s ocean, diatoms are widely recognized as the primary contributors to the Si cycle within the planktonic realm. However, recent research has uncovered that Rhizaria exhibit unexpectedly high individual Si production rates and biogenic silica content, indicating that their role in marine Si and carbon cycles may have been underestimated.
This project seeks to elucidate the process of silicification in Rhizaria and to identify the factors driving variability in silicic acid uptake. To achieve this, the work is divided into three integrated components. The first involves analyzing global transcriptomic data and individual transcriptomes of isolated Rhizaria to investigate the diversity of Si transporters. The second focuses on examining silica deposition using fluorescence markers across a wide range of Rhizaria. The third component quantifies gene expression during silicification, employing primers developed from the first component.
This interdisciplinary project leverages bioinformatics, molecular biology, and physiology, presenting a unified approach to studying plankton. Its outcomes will significantly enhance our understanding of Si transport in Rhizaria and their role in the ocean's biogeochemical Si cycle.
This project seeks to elucidate the process of silicification in Rhizaria and to identify the factors driving variability in silicic acid uptake. To achieve this, the work is divided into three integrated components. The first involves analyzing global transcriptomic data and individual transcriptomes of isolated Rhizaria to investigate the diversity of Si transporters. The second focuses on examining silica deposition using fluorescence markers across a wide range of Rhizaria. The third component quantifies gene expression during silicification, employing primers developed from the first component.
This interdisciplinary project leverages bioinformatics, molecular biology, and physiology, presenting a unified approach to studying plankton. Its outcomes will significantly enhance our understanding of Si transport in Rhizaria and their role in the ocean's biogeochemical Si cycle.
Overall, the project is progressing as expected, despite some adjustments along the way.
The Objective 1 of the project is progressing as planned. The researcher successfully generated transcriptomes of these rare organisms and identified transporters using a compiled dataset created at the beginning of the project. Combining the transcriptomes of all silicifiers has allowed for meaningful analysis of environmental datasets, yielding important insights into the role of these organisms in the biogeochemical silicon cycle in the ocean. The phylogenetic tree encompassing all the silicon transporters genes provides deeper insights into the evolutionary relationship among silicifiers. Phaeodaria have a similar trajectory of SIT evolution as diatoms, with a diverse multicopy gene family, but evolved independently. Adaptation to environmental changes likely drove similar outcomes in both lineages. Findings revealed that Phaeodaria have 5 transmembrane domains compared to diatoms, which have 10 transmembrane domains. This supports the hypothesis that the modern silicon transporters evolved from ancestral partial proteins through gene fusion. In the ocean, about half of the silicon transporters expressed iare from organisms other than diatoms, including Phaeodaria. This is not really incorporated into our concepts of the silicon cycle.
Objective 2 encountered more challenges, as it became clear that the unculturable cells did not survive as long as needed to conduct the experiments. Various taxonomic groups of Rhizaria were collected in the Monterey Bay. Specimens were maintained in specially designed tanks (e.g. roller tanks) to prolong their survival and conduct experiments. The researcher used a fluorescent marker to trace the incorporation of silicic acid but due to the difficulty of keeping these organisms alive for a long time, additional stains were also used to reveal the cellular structures of these unicellular protists. The use of alternative stains, did not only overcome this issue but also added new opportunities to explore the cellular structure. The integration of both new (confocal) and established (scanning electron) microscopy techniques has provided valuable details on the skeletal growth.
Objective 3 has not yet been fully initiated, although the collection and extraction of samples for transcriptomes and genomes during the outgoing phase of the project are crucial steps. Fieldwork opportunities have allowed the researcher to explore the silicification process from a different perspective, particularly by studying Collodaria, colonial Rhizaria that host symbionts in the surface ocean. These organisms can either be siliceous or not, and comparing DNA data with detailed images of their skeletons may offer new insights into the evolution of silicifiers and the silicification process.
The Objective 1 of the project is progressing as planned. The researcher successfully generated transcriptomes of these rare organisms and identified transporters using a compiled dataset created at the beginning of the project. Combining the transcriptomes of all silicifiers has allowed for meaningful analysis of environmental datasets, yielding important insights into the role of these organisms in the biogeochemical silicon cycle in the ocean. The phylogenetic tree encompassing all the silicon transporters genes provides deeper insights into the evolutionary relationship among silicifiers. Phaeodaria have a similar trajectory of SIT evolution as diatoms, with a diverse multicopy gene family, but evolved independently. Adaptation to environmental changes likely drove similar outcomes in both lineages. Findings revealed that Phaeodaria have 5 transmembrane domains compared to diatoms, which have 10 transmembrane domains. This supports the hypothesis that the modern silicon transporters evolved from ancestral partial proteins through gene fusion. In the ocean, about half of the silicon transporters expressed iare from organisms other than diatoms, including Phaeodaria. This is not really incorporated into our concepts of the silicon cycle.
Objective 2 encountered more challenges, as it became clear that the unculturable cells did not survive as long as needed to conduct the experiments. Various taxonomic groups of Rhizaria were collected in the Monterey Bay. Specimens were maintained in specially designed tanks (e.g. roller tanks) to prolong their survival and conduct experiments. The researcher used a fluorescent marker to trace the incorporation of silicic acid but due to the difficulty of keeping these organisms alive for a long time, additional stains were also used to reveal the cellular structures of these unicellular protists. The use of alternative stains, did not only overcome this issue but also added new opportunities to explore the cellular structure. The integration of both new (confocal) and established (scanning electron) microscopy techniques has provided valuable details on the skeletal growth.
Objective 3 has not yet been fully initiated, although the collection and extraction of samples for transcriptomes and genomes during the outgoing phase of the project are crucial steps. Fieldwork opportunities have allowed the researcher to explore the silicification process from a different perspective, particularly by studying Collodaria, colonial Rhizaria that host symbionts in the surface ocean. These organisms can either be siliceous or not, and comparing DNA data with detailed images of their skeletons may offer new insights into the evolution of silicifiers and the silicification process.
The results from the first objective provide valuable insights into conspicuous silicifiers that are currently overlooked in our understanding of the silicon cycle. These findings include detailed information on the protein structure of silicon transporters and their evolutionary relationships with other silicifiers. Such knowledge contributes to refining our understanding of the diversity and role of silicifiers in marine ecosystems.
However, advancing the remaining objectives would greatly benefit from addressing the key challenge of maintaining these delicate organisms in laboratory conditions for extended periods of time. This requires significant experimental efforts, as little is known about their feeding behaviors or life strategies. Developing methods to sustain these organisms in the laboratory is essential for further exploration of their physiology and ecological roles.
Notably, during this project, the researcher had the rare and unique opportunity to observe Phaeodaria in their natural habitat. This firsthand observation of these deep-water inhabitants provided critical insights into their behavior and ecology, offering a foundation for future research. These findings highlight the importance of integrating field observations with experimental approaches to deepen our understanding of the life processes and ecological functions of silicifying organisms.
Further research in this area, including demonstration studies, will be pivotal to unlocking their full biogeochemical significance and ensuring the broader uptake of these results into models of the silicon cycle.
However, advancing the remaining objectives would greatly benefit from addressing the key challenge of maintaining these delicate organisms in laboratory conditions for extended periods of time. This requires significant experimental efforts, as little is known about their feeding behaviors or life strategies. Developing methods to sustain these organisms in the laboratory is essential for further exploration of their physiology and ecological roles.
Notably, during this project, the researcher had the rare and unique opportunity to observe Phaeodaria in their natural habitat. This firsthand observation of these deep-water inhabitants provided critical insights into their behavior and ecology, offering a foundation for future research. These findings highlight the importance of integrating field observations with experimental approaches to deepen our understanding of the life processes and ecological functions of silicifying organisms.
Further research in this area, including demonstration studies, will be pivotal to unlocking their full biogeochemical significance and ensuring the broader uptake of these results into models of the silicon cycle.