Olivier De Clerck

Ghent University | UGhent · Department of Biology

Third-generation sequencing platforms, such as Oxford Nanopore Technology (ONT), have made it possible to characterize communities through the sequencing of long amplicons. While this theoretically allows for an increased taxonomic resolution compared to short-read sequencing platforms such as Illumina, the high error rate remains problematic for a...

The green seaweed Ulva compressa is a promising model for functional biology. In addition to historical research on growth and development, -omics data and molecular tools for stable transformation are available. However, more efficient tools are needed to study gene function. Here, we expand the molecular toolkit for Ulva. We screened the survival...

Photosynthetic organisms have an enormous influence on our environment through their effects on the development of other life on Earth and the way they alter the planet's geology and geochemistry. This book takes a unique approach by examining the evolutionary history of the major groups of aquatic photoautotrophs in the context of the ecophysiolog...

Genome merging is a common phenomenon causing a wide range of consequences on phenotype, adaptation, and gene expression, yet its broader implications are not well‐understood. Two consequences of genome merging on gene expression remain particularly poorly understood: dosage effects and evolution of expression. We employed Chlamydomonas reinhardtii...

Whole genome duplications, widely observed in plant lineages, have significant evolutionary and ecological impacts. Yet, our current understanding of the direct implications of ploidy shifts on short- and long-term plant evolution remains fragmentary, necessitating further investigations across multiple ploidy levels. Chlamydomonas reinhardtii, a h...

There are many gaps in our knowledge of how life cycle variation and organismal body architecture associate with molecular evolution. Using the diverse range of green algal body architectures and life cycle types as a test case, we hypothesize that increases in cytomorphological complexity are likely to be associated with a decrease in the effectiv...

Using a DNA barcoding approach, we document an extensive number of inter-species cryptic introductions of bladed Bangiales (Pyropia) at an historic oyster aquaculture site in the Southern North Sea. We sampled the intertidal of 20 locations along the Belgian and Dutch coastline, ranging from sheltered to exposed, between February 2022 and April 202...

Genome merging is common in many organisms, causing diverse consequences on phenotype, adaptation, and gene expression, yet its broader implications are not well understood. Two consequences of genome merging on gene expression remain poorly understood: dosage effects and evolution of expression. We employed Chlamydomonas reinhardtii as a model to...

The role of maternal tissue in embryogenesis remains enigmatic in many complex organisms. Here, we investigate the contribution of maternal tissue to apical–basal patterning in the kelp embryo. Focussing on Undaria pinnatifida, we studied the effects of detachment from the maternal tissue using microsurgery, staining of cell wall modifications, mor...

Third-generation sequencing platforms, such as Oxford Nanopore Technology (ONT), have made it possible to characterise communities through the sequencing of long amplicons. Whilst this theoretically allows for an increased taxonomic resolution compared to short-read sequencing platforms such as Illumina, the high error rate remains problematic to a...

The green seaweed Ulva depends on its associated bacteria for morphogenesis and is an important model to study algal-bacterial interactions. Ulva-associated bacteria exhibit high turnover across environmental gradients, leading to the hypothesis that bacteria contribute to the acclimation potential of the host. Yet little is known about the variati...

The southern coast of Africa is one of the few places in the world where water temperatures are predicted to cool in the future. This endemism-rich coastline is home to two sister species of kelps of the genus Ecklonia maxima and Ecklonia radiata, each associated with specific thermal niches, and occuring primarily on opposite sides of the southern...

The role of maternal tissue in the control of embryogenesis remains enigmatic in many complex organisms. Here, we investigate the contribution of maternal tissue to apical-basal patterning in the kelp embryo. Using a modified kelp fertilisation protocol which yields synchronously developing kelp embryos, we show that detachment from maternal tissue...

Motivation: Impacts of climate change on marine biodiversity are often projected with species distribution modelling using standardized data layers representing physical, chemical and biological conditions of the global ocean. Yet, the available data layers (1) have not been updated to incorporate data of the Sixth Phase of the Coupled Model Interc...

Brown seaweeds are keystone species of coastal ecosystems, often forming extensive underwater forests, that are under considerable threat from climate change. Despite their ecological and evolutionary importance, this phylogenetic group, which is very distantly related to animals and land plants, is still poorly characterised at the genome level. H...

Effective monitoring of non-indigenous seaweeds and combatting their effects relies on a solid confirmation of the non-indigenous status of the respective species. We critically analysed the status of presumed non-indigenous seaweed species reported from the Mediterranean Sea, the Northeast Atlantic Ocean and Macaronesia, resulting in a list of 140...

Ocean Census is a new Large-Scale Strategic Science Mission aimed at accelerating the discovery and description of marine species. This mission addresses the knowledge gap of the diversity and distribution of marine life whereby of an estimated 1 million to 2 million species of marine life between 75% to 90% remain undescribed to date. Without impr...

Marine macroalgae (seaweeds) are important primary producers and foundation species in coastal ecosystems around the world. Seaweeds currently contribute to an estimated 51% of the global mariculture production, with a long-term growth rate of 6% per year, and an estimated market value of more than US$11.3 billion. Viral infections could have a sub...

Marine heatwaves (MHWs) are becoming increasingly common, with devastating ecosystem impacts. However, MHW understanding has almost exclusively relied on sea surface temperature with limited knowledge about their subsurface characteristics. Here we estimate global MHWs from the surface to 2,000 m depth, covering the period 1993–2019, and explore bi...

The Viridiplantae comprise two main clades, the Chlorophyta (including a diverse array of marine and freshwater green algae) and the Streptophyta (consisting of the freshwater charophytes and the land plants). Lineages sister to core Chlorophyta, informally refer to as prasinophytes, form a grade of mainly planktonic green algae. Recently, one of t...

Located in the heart of the South Pacific Ocean, the French Polynesian islands represent a remarkable setting for biological colonization and diversification, because of their isolation. Our knowledge of this region’s biodiversity is nevertheless still incomplete for many groups of organisms. In the late 1990s and 2000s, a series of publications pr...

The analysis of biological and ecological traits has a long history in evolutionary and ecological research. However, trait data are often scattered and standardised terminology that transcends taxonomic and biogeographical context are generally missing. As part of the development of a global trait database of marine species, we collated trait info...

In this study we explore the introduction of the brown alga Dictyota acutiloba in the Mediterranean Sea and provide a substantive update on the geographic distribution of this species, which was long thought to be confined to the Pacific Ocean. A critical assessment of published distribution records and additional identifications based on cox1, psb...

Effective monitoring and combatting the effect of non-indigenous seaweeds relies on a solid confirmation of the non-indigenous status of the species. We critically analysed the status of presumed non-indigenous seaweed species reported from the Mediterranean Sea, the Northeast Atlantic Ocean and Macaronesia, resulting in a list of 140 species whose...

Green seaweeds exhibit a wide range of morphologies and occupy various ecological niches, spanning from freshwater to marine and terrestrial habitats. These organisms, which predominantly belong to the class Ulvophyceae, showcase a remarkable instance of parallel evolution toward complex multicellularity and macroscopic thalli in the Viridiplantae...

While microbiome alterations are increasingly proposed as a rapid mechanism to buffer organisms under changing environmental conditions, studies of these processes in the marine realm are lagging far behind their terrestrial counterparts. Here, we used a controlled laboratory experiment to examine whether the thermal tolerance of the brown seaweed...

Warming and nutrient enrichment are key pervasive drivers of ecological shifts in both aquatic and terrestrial ecosystems, impairing the physiology and survival of a wide range of foundation species. But the underlying mechanisms often remain unclear, and experiments have overlooked the potential effects mediated by changes in the microbial communi...

In this chapter, we present the use of Chlamydomonas reinhardtii in experiments designed to study the evolutionary impacts of whole genome duplication. We shortly introduce the algal species and depict why it is an excellent model for experimental evolution. Subsequently, we discuss the most relevant steps and methods in the design of a ploidy-rela...

Aim Global warming is affecting the distribution of species worldwide, but the level of adaptation of edge populations to warmer temperatures remains an open question. Here, we assess the thermal tolerance of populations of two habitat‐forming seaweeds along their latitudinal range, using thermal niche unfilling to assess their resilience to global...

The immediate effects of plant polyploidization are well characterized and it is generally accepted that these morphological, physiological, developmental, and phenological changes contribute to polyploid establishment. Studies on the environmental dependence of the immediate effects of whole-genome duplication (WGD) are, however, scarce but sugges...

Species diversity of Ulva in Vietnam was investigated using three commonly used genetic markers, the nuclear encoded rDNA ITS region and the plastid encoded rbcL and tufA genes. Single locus species delimitation methods, complemented with morphological and ecological information resulted in the delimitation of 19 species. This diversity is largely...

The role that seaweeds play as primary producers and ecosystems engineers in marine coastal ecosystems is widely acknowledged. Seaweeds, however, are also important drivers in the development of the blue bioeconomy due to their vast diversity of unique chemicals with a broad range of industrial and biotechnological applications. In tropical regions...

The analysis of biological and ecological traits has a long history in evolutionary and ecological research. However, trait data are often scattered and standardised terminology that transcends taxonomic and biogeographical context are generally missing. As part of the development of a global trait database of marine species, we collated trait info...

The green seaweed Ulva is important from ecological and economic perspectives, but the identification of species is often problematic. Here we assessed and discussed different perspectives to establish a stable taxonomic framework for Ulva, which will benefit both ecological and applied research. We evaluated (1) the performance of commonly used DN...

We re-evaluated the diversity of Lobophora using an integrative taxonomic approach based on a broad sampling across French Polynesian archipelagos. Our results show that French Polynesia supports at least 37 Lobophora species of which ~57% (21) are endemic. This level of endemicity is comparable to that presently known in the Caribbean and the west...

We provide an account of two newly recorded non-indigenous tropical seaweed species, Siphonocladus tropicus (Cladophorales, Chlorophyta) and Caulerpa integerrima (Caulerpaceae, Chlorophyta), from the northern and central Levantine Mediterranean shores of Israel. Reports are supported by morphological and molecular evidence. The new record of C. int...

We investigated the globally distributed red algal genus Pterocladiella, comprising 24 described species, many of which are economically important sources of agar and agarose. We used DNA-based species delimitation approaches, phylogenetic, and historical biogeographical analyses to uncover cryptic diversity and infer the drivers of biogeographic p...

The calcified encrusting brown algal genus Newhousia is reported from three new archipelagos in the Pacific: (1) Society Islands, French Polynesia; (2) Guam, Mariana Islands; and (3) Vanuatu. Newhousia presents a simple morphology consisting of small, rounded, two-layered calcified blades with limited interspecific variability in morphological feat...

The green seaweed Ulva is a model system to study seaweed‐bacteria interactions, but the impact of environmental drivers on the dynamics of these interactions is little understood. In this study, we investigated the stability and variability of the seaweed‐associated bacteria across the Atlantic‐Baltic Sea salinity gradient. We characterised the ba...

Kelp forests are declining in many regions globally with climatic perturbations causing shifts to alternate communities and significant ecological and economic loss. Range edge populations are often at most risk and are often only sustained through localised areas of upwelling or on deeper reefs. Here we document the loss of kelp forests (Ecklonia...

The Ulvophyceae, a major group of green algae, is of particular evolutionary interest because of its remarkable morphological and ecological diversity. Its phylogenetic relationships and diversification timeline, however, are still not fully resolved. In this study, using an extensive nuclear gene dataset, we apply coalescent- and concatenation-bas...

Brown algae are a group of multicellular, heterokont algae that have convergently evolved developmental complexity that rivals that of embryophytes, animals or fungi. Early in development, brown algal zygotes establish a basal and an apical pole, which will become respectively the basal system (holdfast) and the apical system (thallus) of the adult...

Aim Marine forests of brown macroalgae create essential habitats for coastal species and support invaluable ecological services. Here, we provide the first global analysis of species richness and endemicity of both the kelp and fucoid biomes. Location Global. Time period Contemporary. Major taxa studied Marine forests of brown macroalgae, fo...

Background The molecular mechanism underlying sexual reproduction in land plants is well understood in model plants and is a target for crop improvement. However, unlike land plants, the genetic basis involved in triggering reproduction and gamete formation remains elusive in most seaweeds, which are increasingly viewed as an alternative source of...

The taxonomy of the genera Grateloupia, Phyllymenia and Prionitis has been revised several times but remains controversial. The female reproductive structure in combination with phylogenetic reconstructions are mostly used to define the genera. However, the architecture and behavior of the auxiliary cell ampullae before and after diploidization are...

The brown algal genus Lobophora (Dictyotales, Phaeophyceae) is an important ecological component of tropical marine systems. Although still scantily sampled, 35 species of Lobophora were discovered previously from the western Indian Ocean. This study updates previous diversity estimates by incorporating recent collections from Madagascar, Mozambiqu...

Considered as holobiont systems, marine macroalgae and their microbiota constitute functional units displaying a large diversity of interactions. Main factors driving the assembly of epiphytic microbiota, and subsequent interactions with the host, are often associated to environmental differences but also to host taxonomy displaying specific chemic...

Microbes are vitally important for seaweed growth, functioning and reproduction, and are likely to have a big impact on aquaculture. Algae-associated bacteria, however, remain mostly unmonitored in aquaculture. Here, we studied the microbiomes of Ulva australis and Ulva lacinulata, three natural populations and an aquaculture set-up, based on full-...

Marine biodiversity underpins ecosystem health and societal well-being. Preservation of biodiversity hotspots is a global challenge. Molecular tools, like DNA barcoding and metabarcoding, hold great potential for biodiversity monitoring, possibly outperforming more traditional taxonomic methods. However, metabarcoding-based biodiversity assessments...

Many western countries show an increased interest in using algae in several sectors such as human food and animal feed, nutraceuticals, cosmetics and pharmaceuticals, agriculture, or bioenergy. Biomass of marine origin, and especially seaweed, is a key element for blue growth and is expected to contribute to the development of the growing European...

Algal associated bacteria are fundamental to the ecological success of green macroalgae such as Caulerpa. The resistance and resilience of algal-associated microbiota to environmental stress can promote algal health and genetic adaptation to changing environments. The composition of bacterial communities has been shown to be unique to algal morphol...

Algal-associated bacteria are fundamental to the ecological success of marine green macroalgae such as Caulerpa. The resistance and resilience of algal-associated mi-crobiota to environmental stress can promote algal health and genetic adaptation to changing environments. The composition of bacterial communities has been shown to be unique to algal...

Auxin is a key regulator of many developmental processes in land plants and plays a strikingly similar role in the phylogenetically distant brown seaweeds. Emerging evidence shows that the PIN and PIN-like (PILS) auxin transporter families have preceded the evolution of the canonical auxin response pathway. A wide conservation of PILS-mediated auxi...

Background The molecular mechanism underlying sexual reproduction in land plants is well understood in model plants and is a target for crop improvement. However, unlike land plants, the genetic basis involved in triggering reproduction and gamete formation remains elusive in most seaweeds, which are increasingly viewed as an alternative source of...

The molecular mechanism underlying sexual reproduction in land plants is well understood in model plants and is a target for crop improvement. However, unlike land plants, the genetic basis involved in triggering reproduction and gamete formation remains elusive in most seaweeds, which are increasingly viewed as an alternative source of functional...

The green seaweed Ulva is an ecologically-important marine primary producer as well as a promising cash crop cultivated for multiple uses. Despite its importance, several molecular tools are still needed to better understand seaweed biology. Here, we report the development of a flexible and modular molecular cloning toolkit for the green seaweed Ul...

A floristic survey of the marine algal biodiversity of Antsiranana Bay, northern Madagascar, was conducted during November 2018. This represents the first inventory encompassing the three major macroalgal classes (Phaeophyceae, Florideophyceae and Ulvophyceae) for the little-known Malagasy marine flora. Combining morphological and DNA-based approac...

The Mediterranean Sea is a hotspot for introduced marine species, including seaweeds. Among red algae, Grateloupia, with no less than eight introduced species, occupies a prominent position. Here, we report a large foliose Grateloupia species collected in Eastern Harbour, Alexandria, Egypt, which had previously been reported as G. acuminata and G....

Aim: Historical processes that shaped current diversity patterns of seaweeds remain poorly understood. Using Dictyotales, a globally distributed order of brown seaweeds as a model, we test if historical biogeographical and diversification patterns are comparable across clades. Dictyotales contain some 22 genera, three of which, Dictyota, Lobophora...

The Mediterranean Sea is a hotspot for introduced marine species, including seaweeds. Among red algae, Grateloupia, with no less than eight introduced species, occupies a prominent position. Here, we report a large foliose Grateloupia species collected in Eastern Harbour, Alexandria, Egypt, which had previously been reported as G. acuminata and G....

The green seaweed Ulva is an ecologically-important marine primary producer as well as a promising cash crop cultivated for multiple uses. Despite its importance, several molecular tools are still needed to better understand seaweed biology. Here, we report the development of a flexible and modular molecular cloning toolkit for the green seaweed Ul...

Stress-induced reductions in the world's coral populations are, in many locations, giving way to an increase in macroalgae, for example the common brown macroalgal genus Lobophora. While many ecological studies report a single species (Lobo-phora variegata), DNA-based identification methods have recently shown that Lobophora is a highly diverse gen...