Marco Thines

Goethe-Universität Frankfurt am Main · Institute of Ecology, Evolution and Diversity

Even though the microevolution of plant hosts and pathogens has been intensely studied, knowledge regarding macro-evolutionary patterns is limited. Having the highest species diversity and host-specificity among Oomycetes, downy mildews are a useful a model for investigating long-term host-pathogen coevolution. We show that phylogenies of Bremia an...

Root endophytic fungi are found in a great variety of plants and ecosystems, but the ecological drivers of their biogeographic distribution are poorly understood. Here, we investigate the occurrence of root endophytes in the non-mycorrhizal plant genus Microthlaspi, and the effect of environmental factors and geographic distance in structuring thei...

Background The European Beech is arguably the most important climax broad-leaved tree species in Central Europe, widely planted for its valuable wood. Here we report the 542 Mb draft genome sequence of an up to 300-year-old individual (Bhaga) from an undisturbed stand in the Kellerwald-Edersee National Park in central Germany. Findings Using a hyb...

Plant-pathogenic fungi hijack their hosts by secreting effector proteins. Effectors serve to suppress plant immune responses and modulate the host metabolism to benefit the pathogen. Smut fungi are biotrophic pathogens that also parasitize important cereals, including maize¹. Symptom development is usually restricted to the plant inflorescences. Us...

Host jumping is a process by which pathogens settle in new host groups. It is a cornerstone in the evolution of pathogens, as it leads to pathogen diversification. It is unsurprising that host jumping is observed in facultative pathogens, as they can reproduce even if they kill their hosts. However, host jumps were thought to be rare in obligate bi...

Oomycetes classified in the genera Phytophthora and Nothophytophthora encompass a wide range of lifestyles, from saprotrophic and water-borne to destructive soil-borne or wind-dispersed plant pathogens. To clarify the evolutionary and genomic basis of these transitions, genome sequences for a wide range of species are necessary. However, the amount...

Fungi are one of the most diverse groups of organisms with an estimated number of species in the range of 2–3 million. The higher-level ranking of fungi has been discussed in the framework of molecular phylogenetics since Hibbett et al., and the definition and the higher ranks (e.g., phyla) of the ‘true fungi’ have been revised in several subsequen...

Downy mildews are cosmopolitan obligate biotrophic parasites of flowering plants. They are fungus-like eukaryotes of the kingdom Straminipila, and most species are highly specialised, often parasitising only a single host species. Due to the prevalence of a broad species concept before the advent of molecular phylogenetics and the paucity of differ...

Nanopore sequencing technology has enabled the rapid, on-site taxonomic identification of samples from anything and anywhere. However, sequencing errors, inadequate databases, as well as the need for bioinformatic expertise and powerful computing resources, have hampered the widespread use of the technology for pathogen identification in the agricu...

Peronospora is the largest genus of obligate biotrophic oomycetes, causing downy mildew disease on various cultivated and ornamental plants worldwide. Despite the known high host specificity in Peronospora, many host–pathogen combinations have not been thoroughly investigated with respect to their phylogenetic relationships. This is especially the...

The debates over the requirement of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) for a viable specimen to represent the name-bearing type material for a species or infraspecific taxon have a long history. Taxonomy of fungi commonly studied as living cultures exemplified by yeasts and moulds, strongly depend on viable...

The global diversity of fungi has been estimated between 2 to 11 million species, of which only about 155 000 have been named. Most fungi are invisible to the unaided eye, but they represent a major component of biodiversity on our planet, and play essential ecological roles, supporting life as we know it. Although approximately 20 000 fungal gener...

The genus Peronospora is the largest genus of the oomycetes, fungus-like members of the kingdom Straminipila that also contains amoeboid (e.g., Leukarachnion) and plant-like (e.g., Laminaria) lifeforms. Peronospora species are obligate biotrophic plant pathogens, causing high economic losses in various crops and ornamentals, including Plantago spec...

Phytophthora infestans (Peronosporaceae, Oomycota) is the causal agent of late blight of potato (Solanum tuberosum) and a native to Central America. When introduced to Europe, it rapidly spread in 1845, triggering the Irish Potato Famine, which claimed millions of lives and led to an exodus of Europeans to North America. The spread of the species w...

Saprolegniaceae s.l. is a species-rich family of the monophyletic order Saprolegniales (Oomycota, Straminipila). Members of this family are primarily saprotrophs on cellulosic, chitinous, and proteinaceous materials in both aquatic and terrestrial ecosystems. This family also includes pathogens infecting various hosts, such as plants, crustaceans,...

Human induced land-cover change within the past decades has resulted in severe biodiversity loss, adversely affecting ecosystems and their contributions to human societies 1,2 . Addressing the biodiversity crisis requires the development of monitoring frameworks that can reliably detect biodiversity change and inform conservation actions 3,4,5 . Sa...

There is increasing evidence that holocarpic oomycetes, i.e., those converting their entire vegetative thallus into zoospores upon maturation, are a phylogenetically diverse group in both freshwater and marine ecosystems. Most of the known holocarpic oomycete species diverge before the main split of Peronosporomycetes and Saprolegniomycetes and are...

Bremia species cause downy mildew disease of Asteraceae, in particular in the subfamilies Cichorioideae and Carduoideae. The most notorious species is B. lactucae, which causes lettuce downy mildew. Previously, it was often assumed that this species causes disease on dozens of different host genera, but recent phylogenetic and morphological studies...

Societal Impact Statement Native medicinal plants contribute essential health benefits to populations globally, constituting a major natural resource that human societies rely on. Being an integral part of terrestrial biodiversity, medicinal plants are detrimentally affected by ongoing climate and land‐use change, yet comprehensive studies on the r...

Novel species of fungi described in this study include those from various countries as follows: Argentina, Neocamarosporium halophilum in leaf spots of Atriplex undulata. Australia, Aschersonia merianiae on scale insect (Coccoidea), Curvularia huamulaniae isolated from air, Hevansia mainiae on dead spider, Ophiocordyceps poecilometigena on Poecilom...

Novel species of fungi described in this study include those from various countries as follows: Argentina, Neocamarosporium halophilum in leaf spots of Atriplex undulata. Australia, Aschersonia merianiae on scale insect (Coccoidea), Curvularia huamulaniae isolated from air, Hevansia mainiae on dead spider, Ophiocordyceps poecilometigena on Poecilom...

The Global Consortium for the Classification of Fungi and fungus-like taxa is an international initiative of more than 550 mycologists to develop an electronic structure for the classification of these organisms. The members of the Consortium originate from 55 countries/regions worldwide, from a wide range of disciplines, and include senior, mid-ca...

Aim Spreading infectious diseases associated with introduced pathogens can have devastating effects on native biota and human livelihoods. We analyse the global distribution of 100 major alien fungal and oomycete pathogens with substantial socio‐economic and environmental impacts and examine their taxonomy, ecological characteristics, temporal accu...

The genus Ducellieria (Ducellieriaceae) contains three species (D. chodatii, D. tricuspidata, D. corcontica), and a single variety (D. chodatii var. armata) of obligate endobiotic pollen parasites. These organisms have been first assigned to the green alga genus Coelastrum, as they form very similar spherical structures, but the observation of hete...

Phylogenetic inference is done regularly in many biological studies not focussed on the phylogeny itself, but which use phylogeny as a tool to infer hypotheses for the interpretation of laboratory experiments. However, phylogenetic inference is often performed at low standards in these studies, which can result in wrong interpretations. Using high-...

Downy mildews are the most species-rich group of oomycetes, with more than 700 known species. The relationships within the main downy mildew lineages (i.e. the downy mildews with pyriform haustoria, the downy mildews with coloured conidia, and the brassicolous downy mildews) are increasingly well resolved, and 20 well-characterised monophyletic gen...

Holocarpic oomycetes, which had fallen into relative scientific obscurity for quite some time, recently regained scientific interest. Among these organisms, some stand out for infecting commercially valuable red algae, such as the nori algae of the genus Pyropia, rendering them economically significant. After having observed simple holocarpic patho...

In the summer, symptoms of fruit rot and necrosis were observed in peach (Prunus persica var. platycarpa) orchards of Hamedan, Iran. Samples of infected fruits were collected and investigated for the possible causing agent. Small fragments from the border area of healthy and infected tissues were cultured on PDA at 25 °C in darkness. For identifica...

While it is increasingly well understood how plants and animals spread around the world, and how they diversify and occupy new niches, such knowledge is fairly limited for fungi and oomycetes. As is true for animals and plants, many plant pathogenic fungi have been spread anthropogenically, but, in contrast to them, only rarely as a deliberate intr...

Oomycetes, a large group of fungus-like organisms, include some destructive plant pathogens causing enormous economic damage. Phylogenetically, oomycetes belong to the kingdom Straminipila and have diverse lifestyles, including saprotrophs and both general and specialized pathogens of various eukaryotic supergroups. A rapid increase in genomic stud...

Oomycetes are a group of fungus-like organisms, which phylogenetically comprise early diverging lineages that are mostly holocarpic, and two crown classes, the Peronosporomycetes and Saprolegniomycetes, including many well-investigated pathogens of plants and animals. However, there is a poorly studied group, the Rhipidiales, which placement amongs...

Phytophthora plurivora can affect a range of ecologically and silviculturally important tree species, including European beech ( Fagus sylvatica), a common late successional tree species native to Europe. Here, we report on the high-quality genome of P. plurivora strain TJ71 (CBS 124093). We sequenced it using Oxford Nanopore MinION and PacBio Sequ...

The wild relatives of modern tomato crops are native to South America. These plants occur in habitats as different as the Andes and the Atacama Desert and are, to some degree, all susceptible to fungal pathogens of the genus Alternaria. Alternaria is a large genus. On tomatoes, several species cause early blight, leaf spots and other diseases. We c...

Downy mildew disease of sunflower, caused by the obligate biotrophic oomycete Plasmopara halstedii, can have significant economic impact on sunflower cultivation. Using high-throughput whole transcriptome sequencing, four developmental phases in 16 time-points of Pl. halstedii infecting Helianthus annuus were investigated. With the aim of identifyi...

The access to molecular collections worldwide greatly improves the quality of scientific research by making a growing number of data available for investigation. The efforts on digitisation also aim at facilitating the exchange of material between institutions and researchers that must follow regulations in place and respect best practice. The hand...

Medicinal plants and their bioactive molecules are integral components of nature and have supported the health of human societies for millennia. However, the prevailing view of medicinal biodiversity solely as an ecosystem-decoupled natural resource of commercial value prevents people from fully benefiting from the capacity of nature to provide med...

Downy mildew is a serious threat to corn (maize) production in the tropics and subtropics. Corn is native to Central America, and was introduced into South-East Asia by the Spanish colonisers in the 1700s. Corn is evolutionarily naïve to downy mildews of the genus Peronosclerospora . Consequently, corn monocultures are particularly susceptible to a...

Plasmopara halstedii (Farl.) Berl. et de Toni, is a biotrophic parasite of sunflower (Helianthus annuus). We genetically analysed 162 P. halstedii samples collected in the years 1982 to 2018, representing a 3,500 km west‐east transect across Europe, from France to the Krasnodar region in Southern Russia. To assess the population genetic structure a...

Oomycetes, a large group of fungi-like organisms, include some destructive plant pathogens causing enormous economic damage. Phylogenetically, oomycetes belong to the kingdom Straminipila and have diverse lifestyles, including saprotrophs and both general and specialized pathogens of various eukaryotic supergroups. A rapid increase in genomic studi...

The access to molecular collections worldwide greatly improves the quality of scientific research by making a growing number of data available for investigation. The efforts on digitization also aim at facilitating the exchange of material between institutions and researchers that must follow regulations in place and respect best practice. The hand...

The wild relatives of modern tomato crops are native to South America. These plants occur in habitats as different as the Andes and the Atacama Desert and are to some degree all susceptible to fungal pathogens of the genus Alternaria. Alternaria is a large genus. On tomato, several species cause early blight, leaf spot, and other diseases. We colle...

Tilletia caries and T. laevis , which are the causal agents of common bunt, as well as T. controversa, which causes dwarf bunt of wheat, threaten especially organic wheat farming. The three closely related fungal species differ in their teliospore morphology and partially in their physiology and infection biology. The gene content as well as intras...

The genus Miracula represents an early-diverging lineage of diatom-parasitic Oomycota, straminipilous eukaryotes that have evolved fungal features independent from the opisthokont Fungi. Recent studies have revealed that diatom parasitoids are much more species-rich than previously thought and may play an important role in limnic and marine ecosyst...

Bloom-forming phytoplankton are key players in aquatic ecosystems, fixing carbon dioxide and forming the base of the marine food web. Diverse stresses, such as nutrient depletion, temperature increase, and pathogen emergence can influence the health and dynamics of algal populations. While population responses to these stressors are well-documented...

Holocarpic oomycetes have been neglected over several decades, until interest in these organisms has recently resurged. One of the most widespread genera of holocarpic oomycetes is Pontisma, parasitic to red seaweeds throughout all oceans. Recently, the genus Sirolpidium (parasitic to green algae) was found to be congeneric with Pontisma. This hint...

Genomic alteration can be generated through various means, in which transposable elements (TEs) can play a pivotal role. Their mobility causes mutagenesis in itself and can disrupt the function of the sequences they insert into.

Lagena has so far only been known from the scarcely reported but widespread species Lagena radicicola, which is a parasite of root epidermal cells. While it was mostly reported from a wide range of cereals and other grasses, it has been shown to affect some dicot species under, e.g. tobacco and sugar beet. Due to the wide host spectrum under labora...

Downy mildew species in the genus Plasmopara are obligate biotrophic pathogens responsible for destructive diseases of economically important cultivated and ornamental plants. During September 2020 and 2021, a downy mildew was observed on porcelain berry (Ampelopsis grandulosa var. brevipedunculata) in different locations in MD, USA. A total of thi...

Seven Fusarium species complexes are treated, namely F. aywerte species complex (FASC) (two species), F. buharicum species complex (FBSC) (five species), F. burgessii species complex (FBURSC) (three species), F. camptoceras species complex (FCAMSC) (three species), F. chlamydosporum species complex (FCSC) (eight species), F. citricola species compl...

Nonmycorrhizal root-colonizing fungi are key determinants of plant growth, driving processes ranging from pathogenesis to stress alleviation. Evidence suggests that they might also facilitate host access to soil nutrients in a mycorrhiza-like manner, but the extent of their direct contribution to plant nutrition is unknown. To study how widespread...

Downy mildew pathogens of graminicolous hosts (Poaceae) are members of eight morphologically and phylogenetically distinct genera in the Peronosporaceae (Oomycota, Peronosporales). Graminicolous downy mildews (GDMs) cause severe losses in crops such as maize, millets, sorghum, and sugarcane in many parts of the world, especially in tropical climate...

Oomycetes, fungus-like protists of the kingdom Straminipila that also includes diatoms and sea-weeds, were collected in July 2021 from various natural environments of Iceland. Substrates included plant debris, meadow and forest soil, pond water, and lake sediments. From this, 200 isolates were acquired. Based on morphological features and phylogene...

Kálmán Vánky (15 th of June 1930-18 th of October 2021) was arguably the most prolific researcher of smut fungi so far. He published more than 1000 taxonomic novelties, and crowned his outstanding oeuvre with the most comprehensive monograph of the smut fungi (Smut Fungi of the World) written to date.

Eleven new downy mildew species on grasses are described from Australia based on morphology and DNA sequence analysis of the mitochondrial cox2 and/or ribosomal large subunit genes. Peronosclerospora aristidae is proposed to accommodate a downy mildew on the indigenous Australian tropical grass Aristida hygrometrica. Baobabopsis marneyi occurs on E...

Transformation of Pythium oligandrum using CRISPR/Cas9

Asexually reproducing fungi play a significant role in essential processes in managed and wild ecosystems such as nutrients cycling and multitrophic interactions. A large number of such taxa are among the most notorious plant and animal pathogens. In addition, they have a key role in food production, biotechnology and medicine. Taxa without or rare...

This paper provides an updated classification of the Kingdom Fungi (including fossil fungi) and fungus-like taxa. Five-hundred and twenty-three (535) notes are provided for newly introduced taxa and for changes that have been made since the previous outline. In the discussion, the latest taxonomic changes in Basidiomycota are provided and the class...

The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here, we present a chromosome-level assembly of the more...

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics,...

Transposable elements (TEs) play a pivotal role in shaping diversity in eukaryotic genomes. The covered smut pathogen on barley, Ustilago hordei , encountered a recent genome expansion. Using long reads, we assembled genomes of 6 U. hordei strains and 3 sister species, to study this genome expansion. We found that larger genome sizes can mainly be...

A Correction to this paper has been published: https://doi.org/10.1007/s10658-021-02338-0

Quaternary climatic fluctuations changed the floristic composition of large areas and forced biota to repeated movements following gradients of their ecological tolerance. Different and contrasting patterns of responses were reported for various species. In this study we focused on Adenophora liliifolia, a perennial herbaceous species representing...

Holocarpic oomycetes infecting freshwater diatoms are obligate endobiotic parasites reported from a wide range of habitats. So far, the taxonomy of and phylogeny of most species remains unresolved, since most have not been reported throughout the past decades and sequence data are available for only the four species, Aphanomycopsis bacillariacearum...

Oomycete flora of ornamental trees in Iran

Plants have evolved a variety of defences to reduce losses to herbivores and pathogens. The benefits of these may, however, be modified by resistance evolution in antagonists, changes in antagonist fauna, context-dependent “costs of defence”, and by interactions between antagonists. In Barbarea vulgaris (Brassicaceae), the so-called “G-type” produc...

Biotrophic plant parasites cause economically important diseases, e.g. downy mildew of grape, powdery mildew of legumes, wheat stripe rust, and wheat bunt. But also in natural ecosystems, these organisms are abundant and diverse, and for many hosts more than one specialised biotrophic pathogen is known. However, only a fraction of their diversity i...

Species delimitation is one of the most fundamental processes in biology. Biodiversity undertakings, for instance, require explicit species concepts and criteria for species delimitation in order to be relevant and translatable. However, a perfect species concept does not exist for Fungi. Here, we review the species concepts commonly used in Basidi...

Growing amounts of genomic data and more efficient assembly tools advance organelle genomics at an unprecedented scale. Genomic resources are increasingly used for phylogenetic analyses of many plant species, but are less frequently used to investigate within-species variability and phylogeography. In this study, we investigated genetic diversity o...