Dr. Asimenia Gavriilidou

Another PhD in the group! Menia wrote a great thesis and confidently defended it: “Zooming into the sponge microbiome in the omics era”

Two chapters already published in journals:

Gavriilidou, A., Mackenzie, T.A., Sánchez, P., Tormo, J.R., Ingham, C., Smidt, H., Sipkema, D. (2021). Bioactivity screening and gene-trait matching across marine sponge-associated bacteria. Mar. Drugs 19, 75.

Gavriilidou, A., Gutleben, J., Versluis, D., Forgiarini, F., Van Passel, M.W.J., Ingham, C.J., Smidt, H., Sipkema, D. (2020). Comparative genomic analysis of Flavobacteriaceae: insights into carbohydrate metabolism, gliding motility and secondary metabolite biosynthesis. BMC Genomics 21, 569.

And the two most exciting ones are (of course) almost there….. we are expecting newly discovered bacterial taxa (order, families, genera and species) that are currently dark biological matter to see the light.


PhD position available on: Ecological Impact of Seaweed farming

Seaweed culture in the North Sea has high potential to sustainably produce commodities of the future. However, the step from small-scale pilot experiments to large scale offshore production has not yet materialized. Main reasons are insecurities about ecological consequences, strict regulations, variable yields and uncertainty about profitability and market potential. One cause underlying the aforementioned insecurities is the high loss (up to 90%) caused by detachment of seaweeds from culture lines in facilities. In the framework of a KIC aquatic food production consortium, we offer 4 PhD student positions in an interdisciplinary research team that aims to reduce seaweed (Saccharina latissima) detachment and study associated economic and ecological risks. You will work in close association with the different members from the team and partners from the Dutch seaweed industry and retail in a joint effort to boast seaweed culture. 

In this multidisciplinary project 4 PhD students will operate as a team and each focus on specific aspects of the project. The first PhD student focuses on economic risk management of seaweed farms. The second sub-project focuses on developing a method to quantify attachment of seaweed seedlings and explore the influence of environmental variables on attachment. The third PhD student focuses on identifying and employing the genetics that underlie attachment. This final sub-project (this one) aims to study the ecological consequences of large scale seaweed culture in the North Sea.

You will assess the pelagic residence time of detached fronds, seedlings and reproductive cells; The microbial community composition associated with Saccharina latissima culture facilities will be assessed; By using currents data, you will predict the traveling routes of detached seedlings, fronds and reproductive cells of seaweed and associated microbiota; You will assess changes in biodiversity associated with seaweed culture facilities; Together, these findings will serve as input for policy makers to develop safe and realistic regulations.

We’re looking for someone with an MSc in Microbiology / Marine Ecology

The research is embedded within the Laboratory of Microbiology, and you will be part of the Aquatic Microbial Ecology group, which is led by dr. Detmer Sipkema. You will be co-supervised by Reinier Nauta (Wageningen Marine Research) and dr. Tijs Ketelaar (Laboratory of Cell Biology).

To apply for this position, please have a look at:

SEASEEDS has been granted!

Within the NWO KIC call ‘Aquatic food production’, two research projects have been awarded funding. Consortia of researchers, companies and public organisations will carry out research into the production of biomass and protein-rich food in the sea. The projects have been awarded a total of more than 2.6 million euros.

Seaweeds are a promising though barely exploited source of biomass and proteins. Small scale cultivation trials show that large and variable detachment of seaweeds results in inefficient and unpredictable cultivation with high economic risks and an unknown impact on marine ecology. Consequently, the sector fails to attract investments, which complicates the upscaling required for profitability. In SEASEEDS we will improve attachment of sugar kelp (including the role of bacteria in attachment of seedlings), study the consequences of large-scale seaweed culture on the marine ecology and create business models for Dutch seaweed. Our efforts will yield economic opportunities in, and societal awareness for the transition towards a sustainable blue economy.

Our group in collaboration with Reinier Nauta (Wageningen Marine Research) aims to assess the environmental impact of seaweed losses on the surroundings by assessing (i) presence and development of harmful microorganisms on detached seaweed (fragments), (ii) risk on genetic intermingling of cultured and natural seaweed populations. This data will support policy makers on a national, but also international level, on a matter in which policy is largely lacking for both seaweed aquaculture in general and specifically the situation in the North Sea.

Hot Microbes that eat Carbon Monoxide?

Anastasia Galani is searching for novel thermophylic microbes that can eat carbon monoxide (CO) and as such contribute to carbon recycling from syngas to produce carbon-based commodities. CO, the main component of syngas, is highly toxic towards most organisms, but it is also a favorable energy and carbon source for specific carboxydotrophic microbes. From a biotechnological perspective, this is very interesting since these microbes can be used by industry for the production of biochemicals and biofuels.

The vast majority of currently known microorganisms that can convert CO into valuable products are mesophiles. However, many of these mesophilic species are susceptible to high CO concentrations and show low conversion rates limiting their biotechnological application. The few known thermophilic CO-utilising microbes have numerous advantages in that they have four times higher CO conversion rates. Furthermore, the use of thermophiles allows recovery of products with low boiling point from the off-gas via condensation. In this way, the products do not accumulate inside the reactor eliminating the risk of product toxicity and subsequent inhibition of the production pathways.

We now got a small KNAW Ecology grant to search for these microbes in hotsprings and hydrothermal sediments at the beautiful Azores! An expedition undertaken together with the Ettema Lab (Patricia Geesink and Guillaume Tahon).

More in Patricia’s blog at: https://www.wur.nl/nl/blogpost/Life-in-hot-springs-why-hot-springs-are-not-just-fun-to-bathe-in-.htm

EATFISH funded!!!

Wow!!!!!! We have been selected to coordinate a new Marie Curie ITN project on integrated innovation of European Aquaculture: EATFISH.

Together with many other high-level research groups we are allowed to collaborate on integrating biological, system, economic, law and maritime spatial planning to innovate aquaculture.

Our new review on algae-bacteria interactions

The effect of the Algal Microbiome on Industrial Production of Microalgae

Jie Lian, René H. Wijffels, Hauke Smidt & Detmer Sipkema,

Microbial Biotechnology, early view

Abstract: Microbes are ubiquitously distributed, and they are also present in algae production systems. The algal microbiome is a pivotal part of the alga holobiont and has a key role in modulating algal populations in nature. However, there is a lack of knowledge on the role of bacteria in artificial systems ranging from laboratory flasks to industrial ponds. Coexisting microorganisms, and predominantly bacteria, are often regarded as contaminants in algal research, but recent studies manifested that many algal symbionts not only promote algal growth but also offer advantages in downstream processing. Because of the high expectations for microalgae in a bio‐based economy, better understanding of benefits and risks of algal–microbial associations is important for the algae industry. Reducing production cost may be through applying specific bacteria to enhance algae growth at large scale as well as through preventing the growth of a broad spectrum of algal pathogens. In this review, we highlight the latest studies of algae–microbial interactions and their underlying mechanisms, discuss advantages of large‐scale algal–bacterial cocultivation and extend such knowledge to a broad range of biotechnological applications.