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Algal Microbiome: Friends or Foes (ALFF)

About us

About ALFF


Algae may not feature highly in our general human awareness but their importance in terms of ecology and industrial application can hardly be exaggerated. Recent studies highlight that the relationship between algae and the microbial community living with them (the algal microbiome) are of critical importance to algal biology - and as such to algal aquaculture. The Algal Microbiome: Friends of Foe (ALFF) project has been designed to improve our understanding of these relationships - ranging from the essential to the devastatingly harmful.

ALFF is a 4 year programme funded by the prestigious Marie Sklodowska-Curie Initial Training Networks (ITN) programme of the European Union to develop 15 outstanding researchers in algal biotechnology and aquaculture. Their work will contribute to the future development of these major growth industries.

ALFF combines multidisciplinary research-based projects, each with a focus on either pathogens, mutualistic symbionts, endosymbiotic micro-organisms, biofilms or bioinformatics.

ALFF also involves an ambitious outreach and public engagement programme in collaboration with highly renowned institutions such as the Flanders Marine Institute and the United Nations University. We are developing outreach materials for exhibitions, films, presentations and activities to help decision-makers and the public better understand the issues and opportunities relating to the sustainable use of our aquatic freshwater and marine resources.

ALFF is a multinational consortium consisting of universities, research institutes and companies based across Europe. This website contains information about the ALFF programme, the Consortium and our students. It also explains what we do, why we study algae and what we hope to achieve from our research into algal growth and aquaculture.

So, if you thought algae were slimy, smelly stuff on beaches...think again! They are diverse and beautiful, as they are multi-purpose, and they produce about 70% of the air we breath!

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Meet our 15 research students and their projects...

Noreen Hiegle (based at A4F, Portugal: Towards controlling chytrid pathogens in industrial cultures of Haematococcus sp 

This project investigates the life cycle and nutritional needs of a newly characterised fungal pathogen and its interaction with its high value algal host, the microalga Haematococcus, with the aim of developing control strategies for industrial environments. More... 

Emilio Cirri (based at the University of Jena, Germany): Bacteria as adverse modulators of signal molecules from benthic diatoms

This project examines the cross-kingdom effects of bacteria on diatom signalling. A growing number of studies show that lytic bacteria are capable of directly interfering with diatom growth and propagation. In this project we will examine how bacteria exploit the pheromone chemistry of the algae to support pathogenicity, and how the alga reacts to and adapts its pheromone chemistry to the presence of these bacteria. More...

Andrea Garvetto (based at SAMS, UK): Do phytoplankton parasites affect marine water quality? A pioneering investigation with a focus on a dominant toxin-producing diatom

The hypothesis underpinning this area of research is that parasitism of phytoplankton is an under-estimated driver of marine ecosystem functioning. In a pilot study, we unveiled many unreported parasites infecting pelagic diatoms. A notable example was the toxin producing, dominant diatom bloom forming Pseudo-nitzschia, which was frequently subjected to epidemic outbreaks of an Ectrogella-like oomycete pathogen during the three consecutive years investigated. This diatom undergoes unexplained inter-annual variations in abundance and toxicity, making our observations particularly relevant to the regulatory framework of water quality monitoring in Scotland. This project is investigating experimentally and in silico the biodiversity and ecological impact of the parasites of diatoms, in particular on the abundance and toxicity of Pseudo-nitschzia sp. More...

Miriam Bernard (based at the Station Biologique de Roscoff (CNRS), France): Defence and resistance against endophytic pathogens in the brown macroalga Saccharina latissima

In response to recent observations of disease outbreak in seaweed cultivation facilities and wild kelp populations, this area of research is currently exploring the defence and resistance processes of the kelp Saccaharina latissima against pathogens with a focus on brown algal endophytes. More...

 Tatiana Yurchenko (based at the University of Ostrava, Czech Republic): Functional and Evolutionary aspects of novel Rickettsia-related endosymbionts of eustigmatophyte algae

This project explores the role of Eustigmatophytes in biotechnology development. A previously neglected area of mainstream biology, it is now recognised that Eustigmatophytes, particularly Nannochloropsis, are extremely promising candidates for biotechnology due to their ability to accumulate large amounts of lipids. However, biological knowledge of Eustigmatophytes, especially outside the Nannochloropsis, remains fragmentary. The objective of this project is to define the existence, evolution, biological and practical significance of newly discovered Rickettsia-related endosymbiotic bacteria in Eustigmatophytes. More...

Katherine Morrisey (based at the University of Ghent, Belgium): Functional diversity of endosymbiotic bacterial communities in marine green algae

This project examines the role of siphonous green seaweeds. These seaweeds are amongst the morphologically most complex algae and also one of the most notorious  invasive species in many parts of the world. Their ecological success has repeatedly been linked to their association with endo- as well as epiphytic bacteria. Indeed, recent studies based on 16S rDNA barcoding revealed rich associated bacterial communities. However, little is known about their functional diversity as well as the principles underlying their assembly. More...

Frederike Stock (based at the University of Ghent, Belgium): Inter-Kingdom cross talk via quorum sensing compounds in bacteria-diatom biofilms

The objective of this project is to examine the natural and biological functions of inter-kingdom cross talk quorum sensing compounds produced by bacteria and diatoms, and to test the use of these compounds as anti-fouling agents in photobioreactors. More...

Javier Giraldo (based at Proviron, Belgium) Signalling and constitutive compounds of biofilms as targets to prophylaxis/remediation of bio-fouling during cultivation of planktonic microalgae in a closed photobioreactor system

This industry based project examines strategies for preventing the build-up and removal of biofilms at the liquid to plastic polymer surface interface during the (non-axenic) cultivation of Nannochchloropsis sp. in the proprietary ProviAPT photobioreactors. Although data is available on bacterial communities in Nannochloropsis open production systems, little is known about the origin and nature of bio-films occuring in closed photo-bioreactors such as the proprietary ProviAPT system. More... 

Lachlan Dow (based at the University of Konstanz, Germany): Characterization of the role of bacteria on photo-trophic bio-film formation

This project is based at the University of Konstanz in Germany. We have previously shown that bacteria or substances secreted by bacteria can have a strong impact on diatom growth, attachment and carbohydrate secretion. Therefore this project is aimed at characterizing the organismic syntrophic interactions as well as bio-chemically signalling processes in photo-autotrophic bio-films, and more specifically the role of bacteria for induction of diatom growth, movement, carbohydrate secretion and bio-film formation. More...

Hetty Kleinjan (based at the Station Biologique de Roscoff, France): The influence of bacteria on the adaptation to changing environments in Ectocarpus: a systems biology approach

Ectocarpus siliculosus is a genomic model for brown algae. The closely related species E. subulatus is currently being established as comparative genomic model, notably because of its high tolerance to abiotic stress, especially low salinity. Recent experiments show that the ability of E. subulatus to colonize freshwater is conditional to the presence of bacteria: it can be removed by antibiotic treatments and restored by contact with xenic cultures. 16S metabarcoding of the bacteria associated with E. subulatus under different conditions has revealed 56 bacterial operational taxonomic units in the cultures.

While this project is based at Roscoff in Brittany, the student will also work at Marine Science Scotland (MARLAB in Aberdeen), the Flanders Institute for Biotechnology (VIB) and Friedrich-Schiller University (in Jena, Germany). More...

Gianmaria Califano (based at the University of Jena, Germany): Growth and morphogenesis of Ulva mutabilis in a changing bacterial environment

Based at the University of Jena in Germany, the concept underlying this area of research is: the green seaweed Ulva (sea lettuce) develops into callus-like cell colonies and other aberrant phenotypes under axenic conditions, or in the presence of an innappropriate bacterial flora. To study this cross-kingdom interaction, a unique tripartite system of Ulva and its associated bacteria Roseobacter sp. and Cytophaga sp. was established. Functionally, the Roseobacter- and Cytophaga-factors act similar to plant growth regulators and recover the complete algal morphogenesis. In addition, certain bacteria are chemotactically attracted by the rhizoid cells of the settled germlings to induce algal growth and maintain complete morphogenesis. More...

Frederick de Boever (based at SAMS, UK): Marinobacter as an algal panacea

Recent work at SAMS has shown that bacteria (Marinobacter) can be beneficial to Nannochloropsis, a commercially important micro-algal species; it can block the adverse activity of contaminating bacteria (Alteromonas). This leads us to believe that Nannochloropsis cultivation may benefit from having the 'right' type of bacteria present. This work showed that Marinobacter were a promising candidate bacterial taxa for this role. This genus is frequently found associated with algae, including Nannochloropsis, where it has been shown to be beneficial to the algal host.

This project is focussing on the specific contribution Marinobacter make to their algal host growth and survival, and will characterise the proteins Marinobacter secrete and other functions that are believed to play a role in these interactions. More...

In addition to conducting a multidisciplinary research project, the sudents will be enrolled on a specialised postgraduate training programme, which is provided by their respective university.

The programme will also provide six exciting and rewarding network-wide courses organised by leading experts in their respective areas. These courses will bring all students together in a supportive and collaborative environment. They will also help the students to develop transferrable and high-level multidisciplinary research skills. They will also broaden thier knowledge of future employment opportunities in the academic, government and private sectors. The courses will cover specialized and high relevant areas such as algal culturing, systems biology and bioinformatics, regulatory water quality monitoring, and the study of symbiotic interactions with metabolomics.

- See more at:

In addition to conducting a multidisciplinary research project, the sudents will be enrolled on a specialised postgraduate training programme, which is provided by their respective university.

The programme will also provide six exciting and rewarding network-wide courses organised by leading experts in their respective areas. These courses will bring all students together in a supportive and collaborative environment. They will also help the students to develop transferrable and high-level multidisciplinary research skills. They will also broaden thier knowledge of future employment opportunities in the academic, government and private sectors. The courses will cover specialized and high relevant areas such as algal culturing, systems biology and bioinformatics, regulatory water quality monitoring, and the study of symbiotic interactions with metabolomics.

- See more at:

Johannes Schicker (based at Applied Maths, Belgium): Innovative bioinformatic tools for metagenomics, functional and evolutionary analysis of bacterial endophytic communities

This industry-based project is focussed on developing software which will be able to: 1) report on sequences that lack suffcient match with known, publicly available sequences; and 2) store and analyze multidimensional metagenomics data (gathered from spatially and temporally-resolved, ecological gradients). We are also aiming for the software to be capable of developing and/or linking different software tools in a comparaitve way to form an easy to use data analysis pipeline that can interpret changes and functionalities across complex metagenomics and metatranscriptomic datasets in light of observed changes in functionality of the ecosystem. More...

(based at VIB, Belgium): Development of an online algal system biology platform that integrates diverse omics data

No video exists for this project yet as the student was not appointed when video production took place.

This project aims to build on advances made in the generation of large datasets which have drastically improved the way we now conduct biological research. It is crucial that these data resources are integrated as tightly and efficiently as possible in order to allow researchers to use them to their full potential. The ORCAE portal is a well-established online resource enabling communities to conduct manual curation of automatically generated genome annotations55. It currently contains more than 25 genomes including the brown seaweed model Ectocarpus siliculosus. ORCAE attracts several thousand visitors per month, and currently the main focus of the resource is the curation of structural and functional annotations of genes. However, in its current form, ORCAE should be suitable for upgrading to a central integration point for various 'omic' information. More...

Srilakshmy L Harikrishnan (based at VIB, Belgium): Genome-wide gene analysis in Eurychasma (oomycete) and Ectocarpus (brown alga) to decipher algal host-pathogen interaction

This project aims to apply tools for genome/transcriptome-wide variant identification and subsequent analysis of gene evolution (e.g. positive selection) across orthologues, whilst using them to address questions on pathogen perception and the evolution of pathogenicity on a model algal-pathogen interaction. Transcriptomics is currently the chosen approach for analysing species without available genomes, as is often the case for algae. Beyond functionally oriented gene-expression analysis, the increasingly common investigation of multiple, closely related genomes (or transcriptomics) unveils precious but hitherto under-exploited information on gene variants and gene evolution. More...

Our aims

Purpose and objectives

Why are we studying algae and their relationship with microbes?

Globally, algal aquaculture is developing rapidly and is a multi-billion dollar industry employing millions of people. As any friend of Asian cuisine knows, algae are an important and healthy source of food that is growing in popularity, but we use algae also in many other industries. In the chemical and pharmaceutical industries algae serve as fertilizers, soil conditioners and for wastewater treatment. The energy industry has been developing biofuels from both microalgae and seaweeds and scientists from the University of Konstanz now even suggest their use as a crude oil substitute. Algae are also popular ingredients in the cosmetics industry too. 

But like all farmed crops, it is important to know what algae need to flourish, and to understand and control their diseases and pests. The single biggest biological challenge to further develop algal aquaculture is to first understand and then control both beneficial and harmful microbes – the microbial flora or algal microbiome. Some bacteria control the development of algae, others are indispensable for their survival while pathogens may cause devastating diseases, the impact of which worsens with the intensification of aquaculture practices. This is why we must study algae and their microbiome.

The main aims of ALFF research are to...

  1. identify, classify and utilise naturally occurring algal symbionts and pathogens
  2. tackle inter- and intra-species signalling and chemical ecology in aquaculture, the natural environment and simplified systems
  3. harness state of the art genomics, molecular and biochemical techniques to characterise these interactions

Our research aims to support the development of superior mass algal cultivation and bio-control strategies.

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April 2016
  • Miriam Bernard is visiting SAMS as part of a 4-week secondment from her home institution at Roscoff. She will be working with Dr Claire Gachon and her lab team.
  • Javier Giraldo delivered a poster presentation at the Young Algaeneers Symposium 2016 - for more information click here
  • We are preparing an outreach display on ALFF for the Festival of the Sea which will take place from 26 to 29 May. More information on this event will be available soon.
March 2016
  • Javier Giraldo, ALFF student based at Proviron, has his first paper published online - Congratulations! Based on his MSc thesis, Javier's papers focusses on 'Understanding the salinity effect on cationic polymers in inducing flocculation of the microalga Neochloris oleoabundans'. More information can be found here
February 2016
  • Congratulations to Frederike Stock, ALFF student based at the University of Ghent, who won a prize for Best Pitch Presentation at the VLIZ Marine Scientist Day held at Bruges. More information can be found here
  • ALFF student Emilio Cirri publishes the first ALFF paper, only six months into his PhD project: A solid phase extraction based non-disruptive sampling technique to investigate the surface chemistry of macroalgae. Congratulations on this fine achievement!
  • Our 2nd ALFF network-wide course is to be held in Portugal - the key theme of this event is "Commercial Algal Culturing: Technologies, Markets and Business Skills", where students and staff focus on the role of private companies in microalgae biotechnology development and cultivation. For more information, please see our Events section.


January 2016
  • Students of the Karel de Grote Hogeschool have produced 66 animated video clips explaining the concepts of parasitism, symbiosis, biofilms and endosymbiosis between bacteria and algae. You are invited to watch these videos here and for more information, please see our Outreach section.
  • Andrea Garvetto presents his research poster, "Chararacterising Novel Oomycete and Protist Pathogens in the context of Harmful Algal Blooms", at the EMBL Symposium in Heidelberg, entitled "A New Age of Discovery for Aquatic Microeukaryotes."
  • Noreen Hiegle arrives for a 6-month secondment at SAMS. She will work with Dr Claire Gachon and her lab team here at SAMS.


December 2015
  • Our first outreach event covering the ALFF project is prepared by Miriam Bernard at Roscoff, France 
September 2015
  • The first network-wide training course for ALFF students takes place in Roscoff (see 'events'). Organised by Dr Catherine Leblanc, from CNRS, and Dr Akira Peters of Bezhin Rosko, this event focusses on Algal Culturing - from the field to the lab. 
August 2015
  • Our first ALFF workshop takes place at the 6th European Phycological Congress in London and brings together for the first time the students and supervisors of the various projects comprising ALFF. The students deliver a short presentation on their background, specialisms and research.  
July  - Setember 2015
  • Our new ALFF students are recruited!





19 - 23 September 2016 at Friedrich Schiller University Jena (organised by Thomas Wichard and Georg Pohnert)

Deciphering Symbiotic Interactions with Metabolomics

The first 2 days of this course are available only to ALFF students. However, we then offer the final 3 days to non-ALFF participants. if you are interested in attending, please send enquiries to 


22-26 Feb 2016, Hotel Fenix, Lisbon, organised by ALFF partner A4F

Commercial Algal Culturing: technologies, markets and business skills 

This course, which focussed on the role of private companies in microalgae cultivation, brought together our 15 PhD students, and staff and associates from the universities and research institutes leading the ALFF project. Representatives from industry delivered presentations on cutting-edge research in the fields of microalgae biotechnology development and production. The course was led by Dr Helena Vieira, a lecturer from the University of Lisboa and the Executive Director of BLUEBIO ALLIANCE - Portugal's network comprising all sub-sectors of the marine bio-resources value chain. Portugese and European Patent Attorney Dr Anabela Carvalho introduced the students to patents and trade secrets, with workshops focussing on case studies of algal biotechnology companies based in Portugal, Belgium and Ireland.

Two site visits - one to A4F Pilot Plant unit and the other to AlgaPlus facilities - completed the week-long programme. The main outcome of the event were student presentations using a 'Dragon's Den' style and format.





7-11 Sep 2015, Station Biologique de Roscoff, co-organised by Catherine Leblanc of CNRS, Roscoff and Akira Peters of Bezhin Rosko

Algal Culturing: from the field to the lab


This was the first network-wide training course for our PhD students, with the main ojective of bringing together all 15 students from across Europe and begin building a cohesive team. The course aimed to encourage students to develop the necessary field and lab skills for algal (macro- and micro-) culturing and production, and bacterial, fungal isolation.


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The ALFF Consortium

ALFF is a consortium of ten institutions from across the EU that collaborate to train 15 doctoral students from 2015 to 2018.
ALFF consortium logo banner

The lead scientist for the programme is Dr Claire Gachon who is based at SAMS (The Scottish Association for Marine Science). SAMS is a partner of the University of the Highlands and Islands and is the coordinating partner for ALFF. More about SAMS...

Below is information about all ALFF institutions and collaborating partners.

University of Jena (Germany)

University of Constance (Germany)

University of Ostrava (Czech Republic)

A4F-AlgaFuel (Portugal)

VIB (Belgium)

University of Ghent (Belgium)

CNRS-Station Biologique de Roscoff (France)

Proviron (Belgium)

Applied Maths (Belgium)


The programme also has 17 partners who will help deliver the research and training programmes:




ALFF delivers a range of outreach and public engagement activities aimed at informing the general public, businesses, educators and policy makers about the purpose and main concepts of this programme.

With the help of organisations such as the Marine Flanders Institute (VLIZ) and the Ocean Explorer Centre at SAMS, and also film-makers, early career researchers and scientists will be able to communicate their research through various media including art, films, photography and exhibitions.

Science and multimedia student collaboration

VLIZ is renowned for its communication programmes for scientists, teachers, entrepreneurs and journalist. To this end, the Institute has been working with first year multimedia technology students at the the Karel de Grote Hogeschool in recent months to make short animation videos relating to ALFF. These videos explained the concepts of parasitism, symbiosis, biofilms and endosymbiosis between bacteria and algae. Each video provided an explanation of these four concepts followed by short stories illustrating these concepts and storyboards. All 66 videos were showcased one evening in January 2016 at UGC cinemas in Antwerp, with around 150 people attending the event. The videos were evaluated by a jury comprising staff from VLIZ and the high school, and also multimedia and illustration experts. Ivan Waumans from Karel de Grote Hogeschool, who coordinated the event, has ranked the Top-20 animation videos on a website – you are invited to watch these animations here.


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VLIZ is currently exploring the possibility of Karel de Grote students working with a group of ALFF researchers to develop more activities, including in-depth projects that will investigate the gap between scientists and the public  and help communicate the work of ALFF.

Mobile display unit

The SAMS communications team is working on a range of display materials that can be taken to festivals, events and tradeshows and is accessible for general audiences, schools and business.


Events: ALFF at the Festival of the Sea in Oban 

We are preparing an outreach display on ALFF for the Festival of the Sea which will take place from 26 to 29 May. More information on this event will be available soon. - See more at:
We are preparing an outreach display on ALFF for the Festival of the Sea which will take place from 26 to 29 May. More information on this event will be available soon. - See more at:

The ALFF students based at SAMS, Andrea Garvetto and Frederik De Boever, are working with the communications team on an outreach talk and workshop for the Festival of the Sea in Oban on Saturday 28th May. More information on this event is available here

Contact ALFF

ALFF coordination team
T: +44 (0) 1631 559 000
F: +44 (0) 1631 559 001
SAMS, Scottish Marine Institute
Oban, Argyll PA37 1QA, UK

Funding provider

Marie Curie logo

EU funder logo

This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 642575.


The information provided is correct to the best of our knowledge, but not contractual. SAMS does not accept any liability for any mistake or omission.