Heroen Verbruggen

• PhD
• Professor (Associate) at University of Melbourne

Molecular sequence data have become a ubiquitous tool for delimiting species and are particularly important in organisms where morphological traits are not informative about species boundaries. A range of statistical methods have been developed to derive species limits from molecular data, for example, by quantifying changes in branching patterns i...

The transition from interbreeding populations to species continues to represent difficult terrain for phylogenetic investigations. Genotyping entire genomes holds promise for enhancing insights into the process of speciation and evolutionary relationships among recently speciated taxa. Northeast Pacific ribbon kelp was once recognized as four speci...

The pelagophytes are a morphologically diverse class of marine heterokont algae defined by deoxyribonucleic acid (DNA) gene sequences, the presence of a multilayered, perforated theca (PT), and the novel role of the Golgi apparatus in the formation and secretion of the PT, as well as materials for the synthesis of the outer extracellular layers (e....

The coral skeleton is home to a highly diverse microeukaryotic and prokaryotic community, including algae from the genus Ostreobium: siphonous green algae living inside the calcium carbonate coral skeleton and visible as conspicuous green bands beneath the coral tissue. This alga’s broader potential functional role is a contemporary area of focus i...

Ochrophyta is a vast and morphologically diverse group of algae with complex plastids, including familiar taxa with fundamental ecological importance (diatoms or kelp) and a wealth of lesser-known and obscure organisms. The sheer diversity of ochrophytes poses a challenge for reconstructing their phylogeny, with major gaps in sampling and an unsett...

Global decline of coral reefs due to climate change calls for effective, nature-based strategies to protect these crucial ecosystems. Developing such strategies requires a thorough understanding of the complex roles and interactions of key inhabitants within coral holobionts. Using a metatranscriptomics approach, we investigated the transcriptional...

Premise Seaweeds are gaining substantial research interest, particularly for genomic applications, where high‐quality DNA is a prerequisite. Extracting DNA from these organisms presents challenges due to high levels of biomacromolecules resulting from their diverse cell structures. Existing protocols often lack versatility, leading to inconsistent...

Microbial plankton play fundamental roles in biogeochemical cycles, driving nutrient cycling that influences the global climate and supports life on Earth. Picoplankton are the smallest and most abundant planktonic organisms. The distribution and ecology of these organisms is determined by environmental factors and their biogeography is largely sha...

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...

Genome-scale metabolic models (GEMs) of microbial communities offer valuable insights into the functional capabilities of their members and facilitate the exploration of microbial interactions. These models are generated using different automated reconstruction tools, each relying on different biochemical databases that may affect the conclusions d...

Phylogenomics has enriched our understanding that the Tree of Life can have network-like or reticulate structures among some taxa and genes. Non-vertical modes of evolution—such as hybridization/introgression and horizontal gene transfer—deviate from a strictly bifurcating tree model, causing non-treelike patterns. Here, we present a brief overview...

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 Interco...

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...

Genome-scale metabolic models (GEMs) of microbial communities offer valuable insights into the functional capabilities of their members and facilitate the exploration of microbial interactions. These models are generated using different automated reconstruction tools, each relying on different biochemical databases that may affect the conclusions d...

Species trees, which depict the evolutionary relationships among organisms, underlie many evolutionary studies. Phylogenomics, the use of genome-scale datasets for phylogenetic inference, is the current gold standard for species tree inference. The development, maintenance, and execution of phylogenomic workflows is challenging, requiring programmi...

Species trees, which depict the evolutionary relationships among organisms, underlie many evolutionary studies. Phylogenomics, the use of genome-scale datasets for phylogenetic inference, is the current gold standard for species tree inference. The development, maintenance, and execution of phylogenomic workflows is challenging, requiring programmi...

Cryptic diversity is common among marine macroalgae, with molecular tools leading to the discovery of many new species. To assign names to these morphologically similar species, the type and synonyms have to be examined , and if appropriate, new species must be described. The turf-forming red alga Polysiphonia scopulorum was originally described fr...

Genome-scale metabolic models (GEMs) of microbial communities offer valuable insights into the functional capabilities of their members and facilitate the exploration of microbial interactions. These models are generated using different automated reconstruction tools, each relying on different biochemical databases that may affect the conclusions d...

Parasitic red algae are an interesting system for investigating the genetic changes that occur in parasites. These parasites have evolved independently multiple times within the red algae. The functional loss of plastid genomes can be investigated in these multiple independent examples, and fine-scale patterns may be discerned. The only plastid gen...

Introduced seaweeds and undescribed species often remain undetected because marine regional floras are as yet poorly understood. DNA sequencing facilitates their detection, but databases are incomplete, so their improvement will continue to lead the discovery of these species. Here we aim to clarify the taxonomy of two turf-forming red algal Austra...

Ostreobium, the major algal symbiont of the coral skeleton, remains understudied despite extensive research on the coral holobiont. The enclosed nature of the coral skeleton might reduce the dispersal and exposure of residing bacteria to the outside environment, allowing stronger associations with the algae. Here, we describe the bacterial communit...

The coral skeleton harbours a diverse community of bacteria and microeukaryotes exposed to light, O2 and pH gradients, but how such physicochemical gradients affect the coral skeleton microbiome remains unclear. In this study, we employed chemical imaging of O2 and pH, hyperspectral reflectance imaging and spatially resolved taxonomic and inferred...

Interactions between microalgae and bacteria can directly influence the global biogeochemical cycles but the majority of such interactions remain unknown. 16S rRNA gene-based co-occurrence networks have potential to help identify microalgal-bacterial interactions. Here, we used data from 10 Earth microbiome projects to identify potential microalgal...

At present, our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed toward the millimeter-thin coral tissue, leaving the diverse coral skeleton microbiome underexplored. Here, we present a genome-centric view of the skeleton of the reef-building corals Porites lutea and Isopora palifera, through a compendium of ∼40...

Recent advances in bioinformatics and high-throughput sequencing have enabled the large-scale recovery of genomes from metagenomes. This has the potential to bring important insights as researchers can bypass cultivation and analyze genomes sourced directly from environmental samples. There are, however, technical challenges associated with this pr...

Ostreobium, the major algal symbiont of the coral skeleton, remains understudied despite extensive research on the coral holobiont. The enclosed nature of the coral skeleton might reduce the dispersal and exposure of residing bacteria to the outside environment, allowing stronger associations with the algae. Here, we describe the bacterial communit...

Molecular analyses, in combination with morphological studies, provide invaluable tools for delineating red algal taxa. However, molecular datasets are incomplete and taxonomic revisions are often required once additional species or populations are sequenced. The small red alga Conferva parasitica was described from the British Isles in 1762 and th...

Abstract The pelagophytes, a morphologically diverse class of marine heterokont algae, have been historically united only by DNA sequences. Recently we described a novel perforated theca (PT) encasing cells from the Pelagophyceae and hypothesized it may be the first morphological feature to define the class (Wetherbee et al. 2021). Here we consolid...

Coastal refugia during the Last Glacial Maximum (~21,000 years ago) have been hypothesized at high latitudes in the North Atlantic, suggesting marine populations persisted through cycles of glaciation and are potentially adapted to local environments. Here, whole‐genome sequencing was used to test whether North Atlantic marine coastal populations o...

MetaGenePipe (MGP) is an efficient, flexible, portable, and scalable metagenomics pipeline that uses performant bioinformatics software suites and genomic databases to create an accurate taxonomic and functional characterization of the prokaryotic fraction of sequenced microbiomes. Written in the Workflow Definition Language (WDL), MGP produces out...

At present our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed towards the millimetre-thin coral tissue, leaving the diverse coral skeleton microbiome underexplored. Here, we present a genome-centric view of the skeleton of the reef-building corals' Porites lutea and Isopora palifera , through a compendium of ~...

The coral skeleton harbours a diverse community of bacteria and microeukaryotes exposed to gradients of light, O 2 and pH, but how such physicochemical gradients affect the coral skeleton microbiome remains unclear. We employed chemical imaging of O 2 and pH, hyperspectral reflectance imaging and spatially explicit taxonomic and functional microbio...

Ostreobium is a genus of siphonous green algae that lives as an endolith in carbonate substrates under extremely limited light conditions and has recently been gaining attention due to its roles in reef carbonate budgets and its association with reef corals. Knowledge about this genus remains fairly limited due to the scarcity of strains available...

Ostreobium is a siphonous green alga in the Bryopsidales (Chlorophyta) that burrows into calcium carbonate (CaCO3) substrates. In this habitat, it lives under environmental conditions unusual for an alga (i.e., low light and low oxygen) and it is a major agent of carbonate reef bioerosion. In coral skeletons, Ostreobium can form conspicuous green b...

The Arctic is among the fastest‐warming areas of the globe. Understanding the impact of climate change on foundational Arctic marine species is needed to provide insight on ecological resilience at high latitudes. Marine forests, the underwater seascapes formed by seaweeds, are predicted to expand their ranges further north in the Arctic in a warme...

The success of tropical scleractinian corals depends on their ability to establish symbioses with microbial partners. Host phylogeny and traits are known to shape the coral microbiome, but to what extent they affect its composition remains unclear. Here, by using 12 coral species representing the complex and robust clades, we explored the influence...

The genomic diversity underpinning high ecological and species diversity in the green algae (Chlorophyta) remains little known. Here, we aimed to track genome evolution in the Chlorophyta, focusing on loss and gain of homologous genes, and lineage‐specific innovations of the core Chlorophyta. We generated a high‐quality nuclear genome for pedinophy...

Microalgae and bacteria have a wide spectrum of associations in aquatic environments. Since their interactions can directly influence global carbon and nutrient cycling, understanding these associations help us evaluate their influence on ecosystem productivity. Algal biodiversity is large, and bacterial associations have been characterised for a s...

A positive relationship between cell size and chloroplast genome size within chloroplast-bearing protists has been hypothesized in the past and shown in some case studies, but other factors influencing chloroplast genome size during the evolution of chlorophyte algae have been less studied. We study chloroplast genome size and GC content as a funct...

Cephaleuros is often known as an algal pathogen with 19 taxonomically valid species, some of which are responsible for red rust and algal spot diseases in vascular plants. No chloroplast genomes have yet been reported in this genus, and the limited genetic information is an obstacle to understanding the evolution of this genus. In this study, we se...

Endosymbiosis, the establishment of a former free-living prokaryotic or eukaryotic cell as an organelle inside a host cell, can dramatically alter the genomic architecture of the endosymbiont. Plastids or chloroplasts, the light-harvesting organelle of photosynthetic eukaryotes, are excellent models to study this phenomenon because plastid origin h...

The genomic diversity underpinning high ecological and species diversity in the green algae (Chlorophyta) remains little known. Here, we aimed to track genome evolution in the Chlorophyta, focusing on loss and gain of homologous genes, and lineage-specific innovations of the Core Chlorophyta. We generated a high-quality nuclear genome for pedinophy...

The genomic era continues to revolutionize our understanding about the evolution of biodiversity. In phycology, emphasis remains on assembling nuclear and organellar genomes, leaving the full potential of genomic datasets to answer long standing questions about the evolution of biodiversity largely unexplored. Here, we used Whole Genome Sequencing...

Ostreobium is a genus of siphonous green algae that lives as an endolith in carbonate substrates under extremely limited light conditions and has recently been gaining attention due to its roles in reef carbonate budgets and its association with reef corals. Knowledge about this genus remains fairly limited due to the scarcity of strains available...

The success of tropical scleractinian corals depends on their ability to establish symbioses with microbial partners. Host traits and evolution are known to shape the coral microbiome, but to what extent they affect its composition remains unclear. Here, by using twelve coral species representing the complex and robust clades, we show that function...

Endosymbiosis, the establishment of a former free–living prokaryotic or eukaryotic cell as an organelle inside a host cell, can dramatically alter the genomic architecture of the endosymbiont. Plastids, the light harvesting organelles of photosynthetic eukaryotes, are excellent models to study this phenomenon because plastid origin has occurred mul...

Background Chloroplasts are important semi-autonomous organelles in plants and algae. Unlike higher plants, the chloroplast genomes of green algal linage have distinct features both in organization and expression. Despite the architecture of chloroplast genome having been extensively studied in higher plants and several model species of algae, litt...

Whole genome sequencing datasets present the opportunity to not only study evolution in the target organism, but also the associated holobiont. The capacity to study epi-endobiotic kelp associations is improving substantially with the increased availability of high-throughput sequencing datasets. The goal of this study was to determine if shotgun s...

The advent of high‐throughput‐sequencing (HTS) has allowed for the use of large numbers of coding regions to produce robust phylogenies. These phylogenies have been used to highlight relationships at ancient diversifications (subphyla, class), and highlight the evolution of plastid genome structure. The Erythropeltales are an order in the Compsopog...

The limestone skeleton of Scleractinian corals is a complex and intricate environment consisting of an array of ecological microniches, which harbour a vast microbial community. In addition, recent studies have demonstrated that endolithic microbes play a variety of important ecological roles. Here, we use a combination of metabarcoding of the smal...

The green alga Ostreobium is an important coral holobiont member, playing key roles in skeletal decalcification and providing photosynthate to bleached corals that have lost their dinoflagellate endosymbionts. Ostreobium lives in the coral’s skeleton, a low-light environment with variable pH and O2 availability. We present the Ostreobium nuclear ge...

The classification of Cystoclonium obtusangulum has been questioned since the species was first described by Hooker and Harvey as Gracilaria? obtusangula. The objective of this study was to provide the first comprehensive taxonomic analysis of Cystoclonium obtusangulum, based on DNA sequences coupled with morphological observations made on syntype...

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 a...

The relationships among the Aurearenophyceae, Phaeothamniophyceae, Phaeophyceae and Xanthophyceae lineages of the Heterokontophyta SI clade are not well known. By adding previously unexamined taxa related to these classes in a five gene phylogeny (SSU rRNA, atpB, psaA, psaB, rbcL), we recovered an assemblage of taxa previously unrecognized. We prop...

Background: Chloroplasts are important semi-autonomous organelles in plants and algae. Unlike higher plants, the chloroplast genomes of green algal linage have distinct features both in organization and expression. Despite the architecture of chloroplast genome have been extensively studied in higher plants and several model species of algae, littl...

Our knowledge of the diversity and evolution of the virosphere will likely increase dramatically with the study of microbial eukaryotes, including the microalgae within which few RNA viruses have been documented. By combining total RNA sequencing with sequence and structural-based homology detection, we identified 18 novel RNA viruses in cultured s...

Pelagophytes (Heterokonta) are a morphologically diverse class of marine algae historically united only by DNA sequences. We established clonal cultures of sand-dwelling pelagophytes collected from intertidal pools around Australia. Phylogenetic trees based on nuclear 18S rDNA and plastid rbcL, psaA, psaB, psbA and psbC sequences revealed two new g...

The Ulvophyceae (Chlorophyta) of eastern Sorsogon, Philippines, including Halimeda magnicuneata sp. nov. (Bryopsidales) Abstract: The marine algal flora of eastern Sorsogon has been intensively collected and is generally considered as the richest in the Philippines. A trend of species records in the area has been dominated by rhodophytes (red algae...

Significance Our work challenges the existing paradigm that marine Arctic ecosystems are depauperate extensions of southerly (temperate) communities established in the wake of recent glaciation, fundamentally changing how these systems should be viewed and interpreted. We forward hypotheses regarding the history of Arctic marine systems, particular...

Red algae are frequently dominant components of the non-native biotas in coastal areas. They often remain undetected because of morphological similarity between native and introduced species and cryptic diversity. Routine use of DNA barcodes can aid in setting baseline tabulations of native species and for detecting introduced species. We performed...

The brown algae (Phaeophyceae) are a group of multicellular heterokonts that are ubiquitous in today’s oceans. Large brown algae from multiple orders are the foundation to temperate coastal ecosystems globally, a role that extends into arctic and tropical regions, providing services indirectly through increased coastal productivity and habitat prov...

The green alga Ostreobium is an important coral holobiont member, playing key roles in skeletal decalcification and providing photosynthate to bleached corals that have lost their dinoflagellate endosymbionts. Ostreobium lives in the coral's skeleton, a low-light environment with variable pH and O₂ availability. We present the Ostreobium nuclear ge...

Our knowledge of seaweed diversity and biogeography still largely relies on information derived from morphological identifications, but the use of molecular tools is revealing that cryptic diversity is common among algae. Polysiphonia scopulorum is a turf-forming red alga widely reported in tropical and temperate coasts worldwide. The only study ba...

Our knowledge of the diversity and evolution of the virosphere will likely increase dramatically with the study of microbial eukaryotes, including the microalgae in few RNA viruses have been documented to date. By combining meta-transcriptomic approaches with sequence and structural-based homology detection, followed by PCR confirmation, we identif...

Populations of many Mediterranean marine species show a strong phylogeographic structure, but the knowledge available for native seaweeds is limited. We investigated the genetic diversity of the green alga Halimeda tuna based on two plastid markers (tufA gene and a newly developed amplicon spanning 5 ribosomal protein genes and intergenic spacers,...

The Arctic is experiencing a rapid shift towards warmer regimes, calling for a need to understand levels of biodiversity and ecosystem responses to climate cycles. This study examines marine refugial locations during the Last Glacial Maximum in order to link recolonization pathways to patterns of genetic diversity in Arctic marine forests. We prese...

Comparative organelle genome studies of parasites can highlight genetic changes that occur during the transition from a free‐living to a parasitic state. Our study focuses on a poorly studied group of red algal parasites, which are often closely related to their red algal hosts and from which they presumably evolved. Most of these parasites are pig...

Corals live in close association with a diverse community of eukaryotes, bacteria, archaea and viruses that, together with the coral host, form the coral holobiont. Fungi are an important component of the coral holobiont; however, knowledge about their taxonomic diversity and the ecological functions these organisms play in reef corals is still sca...

The Neoproterozoic Era records the transition from a largely bacterial to a predominantly eukaryotic phototrophic world, creating the foundation for the complex benthic ecosystems that have sustained Metazoa from the Ediacaran Period onward. This study focuses on the evolutionary origins of green seaweeds, which play an important ecological role in...

Within the siphonous green algal order Bryopsidales, the size and gene arrangement of chloroplast genomes has been examined extensively, while mitochondrial genomes have been mostly overlooked. The recently published mitochondrial genome of Caulerpa lentillifera is large with expanded noncoding DNA, but it remains unclear if this is characteristic...

Coral microbial ecology is a burgeoning field, driven by the urgency of understanding coral health and slowing reef loss due to climate change. Coral resilience depends on its microbiota, and both the tissue and the underlying skeleton are home to a rich biodiversity of eukaryotic, bacterial and archaeal species that form an integral part of the co...

Cryptic diversity is common in the red algae and is often discovered when comparing specimens from distant locations or different morphotypes of species with high phenotypic plasticity. The genus Lophurella includes seven species from the cold-temperate coasts of the southern hemisphere. L. periclados is the only species reported from Australia whe...

Tydemania Weber-van Bosse is a genus belonging to the family Udoteaceae (Bryopsidales, Chlorophyta) and currently thought to be monospecific throughout its distribution range in the Indo-Pacific. We tested the assumption that Tydemania is a single species using species delimitation methods, morphological observations and phylogenetic reconstruction...

Prasinophytes (Chlorophyta) are a diverse, paraphyletic group of planktonic microalgae for which benthic species are largely unknown. Here, we report a sand‐dwelling, marine prasinophyte with several novel features observed in clonal cultures established from numerous locations around Australia. The new genus and species, which we name Microrhizoid...

When DNA sequences from Bermuda plants described as Codium isthmocladum ssp. clavatum and a recent collection from Florida originally thought to be C. decorticatum were analyzed, they were found to be a genetic match to the Pacific Mexican species C. simulans. Historical voucher collections assigned to C. isthmocladum ssp. clavatum show that this P...

The Neoproterozoic Era records the transition from a largely bacterial to a predominantly eukaryotic phototrophic world, creating the foundation for the complex benthic ecosystems that have sustained Metazoa from the Ediacaran Period onward. This study focusses on the evolutionary origins of green seaweeds, which play an important ecological role i...

Aim Biogeographic barriers emerged in the tropical oceans as continental masses moved with plate tectonics, and as the tropics contracted to lower latitudes from the late Eocene. These barriers have shaped tropical marine biodiversity. We characterize large‐scale diversity patterns for tropical brittle stars and investigate the effect of biogeograp...

Coral microbial ecology is a burgeoning field, driven by the urgency of understanding coral health and slowing reef loss due to climate change. Coral resilience depends on its microbiota, and both the tissue and the underlying skeleton are home to a rich biodiversity of eukaryotic, bacterial and archaeal species that form an integral part of the co...

Caves are a useful system for testing evolutionary and biogeographic hypotheses, as they are isolated, and their environmental conditions have resulted in adaptive selection across different taxa. Although in recent years many more cave species have been discovered, cave-dwelling members of the class Ophiuroidea (brittle stars) remain scarce. Out o...

The order Ceramiales contains about one third of red algal diversity and it was classically classified into four families according to morphology. The first phylogenies based on one or two molecular markers were poorly supported and failed to resolve these families as monophyletic. Nine families are currently recognized, but relationships within an...