Revisiting Salisapiliaceae

Adding a missing piece to the puzzle of oomycete phylogeny: the placement of Rhipidium interruptum (Rhipidiaceae)

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 amongst the crown oomycetes is ambiguous. It accommodates several taxa with a sophisticated vegetative and reproductive cycle, as well as structural organisation, that is arguably the most complex in the oomycete lineage. Despite the remarkable morphological complexity and their notable perseverance in the face of faster-growing saprotrophic oomycetes and fungi, the knowledge on Rhipidiales is limited to date, as the most complex members are not easily cultured, even by targeted approaches. This also leads to inadequate sequence data for the order, which was sourced from only the two least complex out of seven introduced genera, i.e. Sapromyces and Salispina. In the present study, ex-situ baiting was done using various fruit substrates, and naturally-shed twigs or fruits acquired from water bodies were examined. As a result of these efforts, the species Rhipidium interruptum was obtained and gross cultivation was accomplished using poplar (Populus nigra) twigs as substrate, which allowed further documentation of both asexual and sexual reproduction. This enabled phylogenetic and detailed morphological study, as well as an epitypification of the species. Phylogenetic analyses based on cox2 and nrLSU sequences revealed Rhipidium as the sister genus of Sapromyces. The morphological studies done support a conspecificity of R. interruptum and R. continuum, which might in turn be conspecific with R. americanum. Though several further studies will be required to fit the scattered missing pieces of knowledge on Rhipidiales together revealing a more complete picture of oomycete evolution, we hope that the current study can serve as a cornerstone for future investigations in the group. Citation: Tsai I, Thines M (2023). Adding a missing piece to the puzzle of oomycete phylogeny: the placement of Rhipidium interruptum (Rhipidiaceae). Fungal Systematics and Evolution 11: 95-108. doi: 10.3114/fuse.2023.11.08.

Unravelling the Lipids Content and the Fatty Acid Profiles of Eight Recently Described Halophytophthora Species and H. avicennae from the South Coast of Portugal

In this study, mycelia of eight recently described species of Halophytophthora and H. avicennae collected in Southern Portugal were analysed for lipids and fatty acids (FA) content to evaluate their possible use as alternative sources of FAs and understand how each species FAs profile relates to their phylogenetic position. All species had a low lipid percentage (0.06% in H. avicennae to 0.28% in H. frigida). Subclade 6b species contained more lipids. All species produced monounsaturated (MUFA), polyunsaturated (PUFA) and saturated (SFA) FAs, the latter being most abundant in all species. H. avicennae had the highest FA variety and was the only producer of γ-linolenic acid, while H. brevisporangia produced the lowest number of FAs. The best producer of arachidonic acid (ARA) and eicosapentaenoic acid (EPA) was H. thermoambigua with 3.89% and 9.09% of total FAs, respectively. In all species, palmitic acid (SFA) was most abundant and among the MUFAs produced oleic acid had the highest relative percentage. Principal component analysis (PCA) showed partial segregation of species by phylogenetic clade and subclade based on their FA profile. H. avicennae (Clade 4) differed from all other Clade 6 species due to the production of γ-linolenic and lauric acids. Our results disclosed interesting FA profiles in the tested species, adequate for energy (biodiesel), pharmaceutical and food industries (bioactive FAs). Despite the low amounts of lipids produced, this can be boosted by manipulating culture growth conditions. The observed interspecific variations in FA production provide preliminary insights into an evolutionary background of its production.

Lagena—an overlooked oomycete genus with a wide range of hosts

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 laboratory conditions, there were no attempts to subdivide the genus into several species, even though some morphological differentiation was reported and the species had been found in several continents. During a survey of diatoms, we came across some parasitoids that would have previously been assumed to be members of the genus Lagenidium. The species exhibited rather narrow host specificity in nature. One species was brought into dual culture with host diatoms of the genus Ulnaria, but could not be transferred to other host genera. Surprisingly, phylogenetic analyses revealed that Lagena radicicola was in a sister clade to that formed by the diatom parasitoids, suggesting a versatile pathogenicity of the genus. Interestingly, several phylogenetic lineages only known from environmental sequencing were clustered with the species found in this study, hinting an undiscovered diversity in the genus Lagena.

Current Insight into Traditional and Modern Methods in Fungal Diversity Estimates

Fungi are an important and diverse component in various ecosystems. The methods to identify different fungi are an important step in any mycological study. Classical methods of fungal identification, which rely mainly on morphological characteristics and modern use of DNA based molecular techniques, have proven to be very helpful to explore their taxonomic identity. In the present compilation, we provide detailed information on estimates of fungi provided by different mycologistsover time. Along with this, a comprehensive analysis of the importance of classical and molecular methods is also presented. In orderto understand the utility of genus and species specific markers in fungal identification, a polyphasic approach to investigate various fungi is also presented in this paper. An account of the study of various fungi based on culture-based and cultureindependent methods is also provided here to understand the development and significance of both approaches. The available information on classical and modern methods compiled in this study revealed that the DNA based molecular studies are still scant, and more studies are required to achieve the accurate estimation of fungi present on earth.

Neofunctionalization of Glycolytic Enzymes: An Evolutionary Route to Plant Parasitism in the Oomycete Phytophthora nicotianae

Oomycetes, of the genus Phytophthora, comprise of some of the most devastating plant pathogens. Parasitism of Phytophthora results from evolution from an autotrophic ancestor and adaptation to a wide range of environments, involving metabolic adaptation. Sequence mining showed that Phytophthora spp. display an unusual repertoire of glycolytic enzymes, made of multigene families and enzyme replacements. To investigate the impact of these gene duplications on the biology of Phytophthora and, eventually, identify novel functions associated to gene expansion, we focused our study on the first glycolytic step on P. nicotianae, a broad host range pathogen. We reveal that this step is committed by a set of three glucokinase types that differ by their structure, enzymatic properties, and evolutionary histories. In addition, they are expressed differentially during the P. nicotianae life cycle, including plant infection. Last, we show that there is a strong association between the expression of a glucokinase member in planta and extent of plant infection. Together, these results suggest that metabolic adaptation is a component of the processes underlying evolution of parasitism in Phytophthora, which may possibly involve the neofunctionalization of metabolic enzymes.

Comparative analyses of saprotrophy in Salisapilia sapeloensis and diverse plant pathogenic oomycetes reveal lifestyle-specific gene expression

Oomycetes include many devastating plant pathogens. Across oomycete diversity, plant-infecting lineages are interspersed by non-pathogenic ones. Unfortunately, our understanding of the evolution of lifestyle switches is hampered by a scarcity of data on the molecular biology of saprotrophic oomycetes, ecologically important primary colonizers of dead tissue that can serve as informative reference points for understanding the evolution of pathogens. Here, we established Salisapilia sapeloensis as a tractable system for the study of saprotrophic oomycetes. We generated multiple transcriptomes from S. sapeloensis and compared them with (i) 22 oomycete genomes and (ii) the transcriptomes of eight pathogenic oomycetes grown under 13 conditions. We obtained a global perspective on gene expression signatures of oomycete lifestyles. Our data reveal that oomycete saprotrophs and pathogens use similar molecular mechanisms for colonization but exhibit distinct expression patterns. We identify a S. sapeloensis-specific array and expression of carbohydrate-active enzymes and putative regulatory differences, highlighted by distinct expression levels of transcription factors. Salisapilia sapeloensis expresses only a small repertoire of candidates for virulence-associated genes. Our analyses suggest lifestyle-specific gene regulatory signatures and that, in addition to variation in gene content, shifts in gene regulatory networks underpin the evolution of oomycete lifestyles.

Cox2 community barcoding at Prince Edward Island reveals long-distance dispersal of a downy mildew species and potentially marine members of the Saprolegniaceae

Marine oomycetes are highly diverse, globally distributed, and play key roles in marine food webs as decomposers, food source, and parasites. Despite their potential importance in global ocean ecosystems, marine oomycetes are comparatively little studied. Here, we tested if the primer pair cox2F_Hud and cox2-RC4, which is already well-established for phylogenetic investigations of terrestrial oomycetes, can also be used for high-throughput community barcoding. Community barcoding of a plankton sample from Brudenell River (Prince Edward Island, Canada), revealed six distinct oomycete OTU clusters. Two of these clusters corresponded to members of the Peronosporaceae—one could be assigned to Peronospora verna, an obligate biotrophic pathogen of the terrestrial plant Veronica serpyllifolia and related species, the other was closely related to Globisporangium rostratum. While the detection of the former in the sample is likely due to long-distance dispersal from the island, the latter might be a bona fide marine species, as several cultivable species of the Peronosporaceae are known to withstand high salt concentrations. Two OTU lineages could be assigned to the Saprolegniaceae. While these might represent marine species of the otherwise terrestrial genus, it is also conceivable that they were introduced on detritus from the island. Two additional OTU clusters were grouped with the early-diverging oomycete lineages but could not be assigned to a specific family. This reflects the current underrepresentation of cox2 sequence data which will hopefully improve with the increasing interest in marine oomycetes.

A Global Survey of Carbohydrate Esterase Families 1 and 10 in Oomycetes

Carbohydrate-active enzymes (CAZymes) are a cornerstone in the phytopathogenicity of filamentous microbes. CAZymes are required for every step of a successful infection cycle-from penetration, to nutrient acquisition (during colonization), to exit and dispersal. Yet, CAZymes are not a unique feature of filamentous pathogens. They are found across eukaryotic genomes and including, for example, saprotrophic relatives of major pathogens. Comparative genomics and functional analyses revealed that CAZyme content is shaped by a multitude of factors, including utilized substrate, lifestyle, and host preference. Yet, family size alone says little about usage. Indeed, in a previous study, we found that genes putatively coding for the CAZyme families of carbohydrate esterase (CE)1 and CE10, while not specifically enriched in number, were suggested to have lifestyle-specific gene expression patterns. Here, we used comparative genomics and a clustering approach to understand how the repertoire of the CE1- and CE10-encoding gene families is shaped across oomycete evolution. These data are combined with comparative transcriptomic analyses across homologous clusters within the gene families. We find that CE1 and CE10 have been reduced in number in biotrophic oomycetes independent of the phylogenetic relationship of the biotrophs to each other. The reduction in CE1 is different from that observed for CE10: While in CE10 specific clusters of homologous sequences show convergent reduction, CE1 reduction is caused by species-specific losses. Comparative transcriptomics revealed that some clusters of CE1 or CE10 sequences have a higher expression than others, independent of the species composition within them. Further, we find that CE1- and CE10-encoding genes are mainly induced in plant pathogens and that some homologous genes show lifestyle-specific gene expression levels during infection, with hemibiotrophs showing the highest expression levels.

Marine Oomycetes of the Genus Halophytophthora Harbor Viruses Related to Bunyaviruses

We investigated the incidence of RNA viruses in a collection of Halophytophthora spp. from estuarine ecosystems in southern Portugal. The first approach to detect the presence of viruses was based on the occurrence of dsRNA, typically considered as a viral molecule in plants and fungi. Two dsRNA-banding patterns (∼7 and 9 kb) were observed in seven of 73 Halophytophthora isolates tested (9.6%). Consequently, two dsRNA-hosting isolates were chosen to perform stranded RNA sequencing for de novo virus sequence assembly. A total of eight putative novel virus species with genomic affinities to members of the order Bunyavirales were detected and their full-length RdRp gene characterized by RACE. Based on the direct partial amplification of their RdRp gene by RT-PCR multiple viral infections occur in both isolates selected. Likewise, the screening of those viruses in the whole collection of Halophytophthora isolates showed that their occurrence is limited to one single Halophytophthora species. To our knowledge, this is the first report demonstrating the presence of negative (−) ssRNA viruses in marine oomycetes.