last updated 2025-09-22

The pelagic zone occupies approximately 1.3 billion km3 (1). Moreover, these aquatic environments hold a large biodiversity, most of it in the form of uncultivated planktonic microorganisms (2-5). This vast pelagic microbial biodiversity is essential to planetary health (6). Aquatic microorganisms have heavily influenced biogeochemical cycles for at least a billion years (7). Moreover, their long-term co-evolutionary history has led, in many cases, to reduced genome size (8), which leaves pelagic microorganisms depending on interactions with other organisms (9, 10). This makes the study of their ecology relevant to update fluxes in biogeochemical cycles (11), to update climate models (6), to design biotechnological tools that are more robust (12), among others.

Figure 1. Different levels of life organization for microorganisms (modified from 13). Credit for the beautiful illustrations: Dr. Tusso.

Our goal as a research group is to characterize the production and consumption of some essential metabolites (such as vitamins) at the cellular level and from a microbial community perspective. Our work will unravel the unseen nuances of cycles of some of these essential metabolites in the ocean, from molecular mechanisms to a global perspective (Figure 1).

Figure 2. In this simplified scheme, different taxa are represented with different colors and are responsible for the transformation of carbon. Moreover, these different taxa interact through production of essential metabolites for which some other taxa are dependent. One of the aims of our research is to understand the microbial interaction networks in the carbon cycle through anabolic dependencies and essential metabolites.

Topic one: Interactions and metabolic dependencies on the pelagic microbial world at different scales of microbiological organization.

Aquatic microorganisms and their complex ecological interactions (Figure 2) are responsible for fixing about half of the carbon dioxide on Earth (14-16). Among microbial interactions, auxotrophies are important, and yet key questions about them remain unanswered. Auxotrophy is defined as the inability to produce an essential metabolite (17). As environmental microorganisms evolved auxotrophies, they also developed dependencies and division of labor (18, 19). This untapped ecological knowledge has significant potential applications in biotechnology.

Topic two: Elucidate patterns of biogeography of abundant aquatic microorganisms, including micro-diversity and co-evolution of abundant lineages.

Microorganisms are extremely diverse (20) and perform many fundamental elemental transformations in the biogeochemical cycles (15). Many pelagic microorganisms remain uncultivated (3, 4), and their biogeography patterns are underexplored (21).

Through the analysis of large metagenomic datasets in time series (22) or multi-geographic characteristics, we aim to answer questions regarding ecology and evolution across time and space.

Topic three: Key microbial players in the carbon and nitrogen cycle of aquatic environments.

In an era of increasing anthropogenic greenhouse gas emissions, decreasing food security, and increasing need for clean energy sources, understanding the carbon cycle is crucial and relevant (Figure 3). Photoautotrophy by aquatic microorganisms is one of the largest contributors to carbon and nitrogen fixation in the atmosphere (23-25). However, the biogeochemical cycles have been severely affected by a new agent for change: humans. It is time for humans to seek and understand the balance that microorganisms brought to Earth and to take hold of their rich biodiversity to build a sustainable green bioeconomy (26, 27).

Figure 3. Integration of all research topics and vision. The carbon cycle in aquatic environments is linked through microbial interactions. The importance of primary producers and the flux of carbon between them and the heterotrophs. The vision of the scientific knowledge gained through the different scientific topics, leading to applied research in the future in biotechnology. The Global Goals reached through the research.

Topic four: Learn the fundamentals of microbial ecology and evolution that can lead to the improvement of politics, economy, and biotechnological tools

One long-term ambition is that all the ecological concepts and knowledge will eventually lead to the development of a better education system, political and economic system, and also biotechnological tools (12). I strongly believe that our oceans and our lakes hold wisdom in their pelagic microorganisms that we can harvest to build a bioeconomy that is sustainable. It takes a village…

References

1. Costello MJ, Cheung A, De Hauwere N. Surface area and the seabed area, volume, depth, slope, and topographic variation for the world’s seas, oceans, and countries. Environ Sci Technol. 2010;44(23):8821-8.
2. Menden-Deuer S, Rowlett J. Many ways to stay in the game: individual variability maintains high biodiversity in planktonic microorganisms. J R Soc Interface. 2014;11(95):20140031.
3. Rodriguez-Gijon A, Nuy JK, Mehrshad M, Buck M, Schulz F, Woyke T, et al. A Genomic Perspective Across Earth’s Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy. Frontiers in microbiology. 2021;12:761869.
4. Steen AD, Crits-Christoph A, Carini P, DeAngelis KM, Fierer N, Lloyd KG, et al. High proportions of bacteria and archaea across most biomes remain uncultured. ISME J. 2019;13(12):3126-30.
5. Del Campo J, Guillou L, Hehenberger E, Logares R, Lopez-Garcia P, Massana R. Ecological and evolutionary significance of novel protist lineages. European journal of protistology. 2016;55(Pt A):4-11.
6. Cavicchioli R, Ripple WJ, Timmis KN, Azam F, Bakken LR, Baylis M, et al. Scientists’ warning to humanity: microorganisms and climate change. Nature reviews Microbiology. 2019;17(9):569-86.
7. Sanchez-Baracaldo P, Bianchini G, Wilson JD, Knoll AH. Cyanobacteria and biogeochemical cycles through Earth history. Trends Microbiol. 2022;30(2):143-57. 8. Rodríguez-Gijón A, Pacheco-Valenciana A, Milke F, Dharamshi JE, Hampel JJ, Damashek J, et al. The ecological success of freshwater microorganisms is mediated by streamlining and biotic interactions. bioRxiv. 2025.
9. Kost C, Patil KR, Friedman J, Garcia SL, Ralser M. Metabolic exchanges are ubiquitous in natural microbial communities. Nat Microbiol. 2023;8(12):2244-52. 10. Pacheco-Valenciana A, Tausch A, Veseli I, Dharamshi JE, Bergland F, Delgado Zambrano LF, et al. Low anabolic independence emerges when cultivating more than three bacterial species together. bioRxiv. 2025.
11. Breitbart M, Bonnain C, Malki K, Sawaya NA. Phage puppet masters of the marine microbial realm. Nat Microbiol. 2018;3(7):754-66.
12. Giri S, Shitut S, Kost C. Harnessing ecological and evolutionary principles to guide the design of microbial production consortia. Curr Opin Biotechnol. 2020;62:228-38.
13. Milke F, Garcia SL, Simon M, Pacheco-Valenciana A, Lennartz ST. Microbial Cohorts: Bringing Ecological Meaning to the Modularity Concept of Co-Occurrence Networks. ISME Communications. 2026; 10.1093/ismeco/ycag037
14. Jardillier L, Zubkov MV, Pearman J, Scanlan DJ. Significant CO2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean. ISME J. 2010;4(9):1180-92.
15. Falkowski PG, Fenchel T, Delong EF. The Microbial Engines That Drive Earth’s Biogeochemical Cycles. Science. 2008;320(5879):1034-9.
16. Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, et al. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun. 2016;7:13219.
17. Droop MR. Auxotrophy and organic compounds in the nutrition of marine phytoplankton. J gen Microbiol. 1957;16:286-93.
18. Zengler K, Zaramela LS. The social network of microorganisms – how auxotrophies shape complex communities. Nature reviews Microbiology. 2018;16(6):383-90.
19. Pacheco AR, Moel M, Segre D. Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems. Nat Commun. 2019;10.
20. Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, et al. A new view of the tree of life. Nature Microbiology. 2016;1(5):16048.
21. Becker JW, Hogle SL, Rosendo K, Chisholm SW. Co-culture and biogeography of Prochlorococcus and SAR11. ISME J. 2019;13(6):1506-19.
22. Rohwer RR, Kirkpatrick M, Garcia SL, Kellom M, McMahon KD, Baker BJ. Two decades of bacterial ecology and evolution in a freshwater lake. Nat Microbiol. 2025;10(1):246-57.
23. Bar-On YM, Phillips R, Milo R. The biomass distribution on Earth. PNAS. 2018;115(25):6506-11.
24. Peura S, Buck M, Aalto SL, Morales SE, Nykanen H, Eiler A. Novel autotrophic organisms contribute significantly to the internal carbon cycling potential of a boreal lake. Mbio. 2018;9(4):e00916-18.
25. Delmont TO, Quince C, Shaiber A, Esen OC, Lee ST, Rappe MS, et al. Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat Microbiol. 2018;3(7):804-13.
26. D’Amato D, Droste N, Allen B, Kettunen M, Lähtinen K, Korhonen J, et al. Green, circular, bio economy: A comparative analysis of sustainability avenues. Journal of Cleaner Production. 2017;168:716-34.
27. Ducklow H. Microbial services: challenges for microbial ecologists in a changing world. Aquatic Microbial Ecology. 2008;53:13-9.