Trends in yeast diversity discovery

Yeasts, usually defined as unicellular fungi, occur in various fungal lineages. Hence, they are not a taxonomic unit, but rather represent a fungal lifestyle shared by several unrelated lineages. Although the discovery of new yeast species occurs at an increasing speed, at the current rate it will likely take hundreds of years, if ever, before they will all be documented. Many parts of the earth, including many threatened habitats, remain unsampled for yeasts and many others are only superficially studied. Cold habitats, such as glaciers, are home to a specific community of cold-adapted yeasts, and, hence, there is some urgency to study such environments at locations where they might disappear soon due to anthropogenic climate change. The same is true for yeast communities in various natural forests that are impacted by deforestation and forest conversion. Many countries of the so-called Global South have not been sampled for yeasts, despite their economic promise. However, extensive research activity in Asia, especially China, has yielded many taxonomic novelties. Comparative genomics studies have demonstrated the presence of yeast species with a hybrid origin, many of them isolated from clinical or industrial environments. DNA-metabarcoding studies have demonstrated the prevalence, and in some cases dominance, of yeast species in soils and marine waters worldwide, including some surprising distributions, such as the unexpected and likely common presence of Malassezia yeasts in marine habitats.TG acknowledges support from the Spanish Ministry of Science and Innovation for grant PGC2018-099921-B-I00, cofounded by European Regional Development Fund (ERDF); from the Catalan Research Agency (AGAUR) SGR423; from the European Union’s Horizon 2020 research and innovation program (ERC-2016–724173); from the Gordon and Betty Moore Foundation (Grant # GBMF9742). JG acknowledges support from the Lendület Program (award no. 96049) of the Hungarian Academy of Sciences and the Eötvös Lóránd Research Network. Q-MW was supported by grants No. 31961133020 and No. 31770018 from the National Natural Science Foundation of China (NSFC). ASA and FEB were supported by grant 9343 from the Gordon and Betty Moore Foundation: https://doi.org/10.37807/GBMF9343."Article signat per 12 autors/es: Teun Boekhout, Anthony S. Amend, Fouad El Baidouri, Toni Gabaldón, József Geml, Moritz Mittelbach, Vincent Robert, Chen Shuhui Tan, Benedetta Turchetti, Duong Vu, Qi-Ming Wang & Andrey Yurkov "Postprint (published version

Genetic structure and evolution of the Leishmania genus in Africa and Eurasia: what does MLSA tell us

Leishmaniasis is a complex parasitic disease from a taxonomic, clinical and epidemiological point of view. The role of genetic exchanges has been questioned for over twenty years and their recent experimental demonstration along with the identification of interspecific hybrids in natura has revived this debate. After arguing that genetic exchanges were exceptional and did not contribute to Leishmania evolution, it is currently proposed that interspecific exchanges could be a major driving force for rapid adaptation to new reservoirs and vectors, expansion into new parasitic cycles and adaptation to new life conditions. To assess the existence of gene flows between species during evolution we used MLSA-based (MultiLocus Sequence Analysis) approach to analyze 222 Leishmania strains from Africa and Eurasia to accurately represent the genetic diversity of this genus. We observed a remarkable congruence of the phylogenetic signal and identified seven genetic clusters that include mainly independent lineages which are accumulating divergences without any sign of recent interspecific recombination. From a taxonomic point of view, the strong genetic structuration of the different species does not question the current classification, except for species that cause visceral forms of leishmaniasis (L. donovani, L. infantum and L. archibaldi). Although these taxa cause specific clinical forms of the disease and are maintained through different parasitic cycles, they are not clearly distinct and form a continuum, in line with the concept of species complex already suggested for this group thirty years ago. These results should have practical consequences concerning the molecular identification of parasites and the subsequent therapeutic management of the disease

Evolutionary history of Leishmania killicki (synonymous Leishmania tropica) and taxonomic implications

Background: Leishmania (L.) killicki is responsible for the chronic cutaneous leishmaniasis. The taxonomic status of this parasite is still not well defined. It was suggested on one hand to include this taxon within L. tropica complex but also on the other hand to consider it as a distinct phylogenetic complex. The present work represents the more detailed study on the evolutionary history of L. killicki relative to L. tropica and the taxonomic implications. Methods: Thirty five L. killicki and 25 L. tropica strains isolated from humans and from several countries were characterized using the MultiLocus Enzyme Electrophoresis (MLEE) and the MultiLocus Sequence Typing (MLST) approaches. Results: The genetic and phylogenetic analyses strongly support that L. killicki belongs to L. tropica complex. The study suggests the emergence of L. killicki by a funder effect followed by an independent evolution from L. tropica, but does not validate the species status of this taxon. In this context, we suggest to call this taxon L. killicki (synonymous L. tropica) until further epidemiological and phylogenetic studies justify the L. killicki denomination. Conclusions: These findings provided taxonomic and phylogenetic informations on L. killicki and helped to better know the evolutionary history of this taxon

Geographical distribution and epidemiological features of Old World Leishmania infantum and Leishmania donovani foci, based on the isoenzyme analysis of 2277 strains

A series of 2277 Leishmania strains from Old World visceral leishmaniasis foci, isolated between 1973 and 2008, were studied by isoenzyme analysis. The strains were obtained from humans, domestic and wild carnivores, rodents and phlebotomine sandflies, and came from 36 countries. In all, 60 different zymodemes were identified and clustered by a phenetic analysis into 3 different groups corresponding to the typically visceralizing species L. donovani (20 zymodemes, 169 strains), L. archibaldi (3 zymodemes, 46 strains) and L. infantum (37 zymodemes, 2,062 strains). The taxonomic position of these isoenzymatic groups is discussed in view of contradictory results obtained from recent molecular studie

The Leishmania donovani species complex: A new insight into taxonomy.

Among the 20 or so Leishmania spp. described as pathogenic for humans, those of the Leishmania donovani complex are the exclusive causative agents of systemic and fatal visceral leishmaniasis. Although well studied, the complex is taxonomically controversial, which hampers clinical and epidemiological research. In this work, we analysed 56 Leishmania strains previously identified as L. donovani, Leishmania archibaldi or Leishmania infantum, isolated from humans, dogs and sandfly vectors throughout their distribution area. The strains were submitted to biochemical and genetic analyses and the resulting data were compared for congruence. Our results show: i) a partial concordance between biochemical and genetic-based data, ii) very limited genetic variability within the L. donovani complex, iii) footprints of frequent genetic exchange along an east-west gradient, marked by a widespread diffusion of alleles across the geographical range, and iv) a large-scale geographical spreading of a few genotypes. From a taxonomic point of view, considering the absence of relevant terminology in existing classes, the L. donovani complex could be treated as a single entit

Outbreak of Leishmania braziliensis cutaneous leishmaniasis, Saül, French Guiana [letter]

New World cutaneous leishmaniasis (CL), a zoonotic disease, is increasingly seen among travelers returning from Latin American countries, particularly from Bolivia, Belize, and French Guiana (1). The epidemiology of CL in the Americas is heterogeneous and has complex variations in transmission cycles, reservoir hosts, and sandfly vectors. Changing human activities that affect these factors may have resulted in the emergence of species with distinct pathogenic potentials and responses to therapy. In the Guianan ecoregion complex, leishmaniasis is endemic, and 5 coexisting Leishmania parasite species are known to infect humans: L. guyanensis, L. braziliensis, L. amazonensis, L. naiffi, and L. lainsoni. Among these species, L. guyanensis accounts for ≈85% of CL cases (2). We report an outbreak of 7 cases of L. braziliensis CL that occurred among 24 scientists who participated in a field mission at Limonade Creek in Saül, French Guiana, during October 10–25, 2013. Saül is an isolated village in the Amazonian rainforest (3°55′18′′N, 53°18′02′′W)

Genetic, serological and biochemical characterization of Leishmania tropica from foci in northern Palestine and discovery of zymodeme MON-307

Background Many cases of cutaneous leishmaniasis (CL) have been recorded in the Jenin District based on their clinical appearance. Here, their parasites have been characterized in depth. Methods Leishmanial parasites isolated from 12 human cases of CL from the Jenin District were cultured as promastigotes, whose DNA was extracted. The ITS1 sequence and the 7SL RNA gene were analysed as was the kinetoplast minicircle DNA (kDNA) sequence. Excreted factor (EF) serotyping and multilocus enzyme electrophoresis (MLEE) were also applied. Results This extensive characterization identified the strains as Leishmania tropica of two very distinct sub-types that parallel the two sub-groups discerned by multilocus microsatellite typing (MLMT) done previously. A high degree of congruity was displayed among the results generated by the different analytical methods that had examined various cellular components and exposed intra-specific heterogeneity among the 12 strains. Three of the ten strains subjected to MLEE constituted a new zymodeme, zymodeme MON-307, and seven belonged to the known zymodeme MON-137. Ten of the 15 enzymes in the profile of zymodeme MON-307 displayed different electrophoretic mobilities compared with the enzyme profile of the zymodeme MON-137. The closest profile to that of zymodeme MON-307 was that of the zymodeme MON-76 known from Syria. Strains of the zymodeme MON-307 were EF sub-serotype A2 and those of the zymodeme MON-137 were either A9 or A9B4. The sub-serotype B4 component appears, so far, to be unique to some strains of L. tropica of zymodeme MON-137. Strains of the zymodeme MON-137 displayed a distinctive fragment of 417 bp that was absent in those of zymodeme MON-307 when their kDNA was digested with the endonuclease RsaI. kDNA-RFLP after digestion with the endonuclease MboI facilitated a further level of differentiation that partially coincided with the geographical distribution of the human cases from which the strains came. Conclusions The Palestinian strains that were assigned to different genetic groups differed in their MLEE profiles and their EF types. A new zymodeme, zymodeme MON-307 was discovered that seems to be unique to the northern part of the Palestinian West Bank. What seemed to be a straight forward classical situation of L. tropica causing anthroponotic CL in the Jenin District might be a more complex situation, owing to the presence of two separate sub-types of L. tropica that, possibly, indicates two separate transmission cycles involving two separate types of phlebotomine sand fly vector

The Leishmania genus : genetic structure and evolutionary mechanisms

Les protozoaires parasites du genre Leishmania infectent de très nombreuses espèces de mammifères à travers le Monde. Transmis par des insectes vecteurs, ces pathogènes sont endémiques dans une centaine de pays et chez l'Homme l'incidence de la maladie est estimée à environ 2 millions de nouveaux cas chaque année. Les questions qui se posent aujourd'hui sur les modalités de reproduction et d'échanges génétiques chez ces protozoaires sont multiples. Elles ont des prolongements sur l'évolution, l'adaptation à de nouveaux cycles, la virulence, l'identification spécifique, la taxonomie ou la prise en charge thérapeutique.Au cours de ce travail, nous avons d'abord eu pour objectif d'aborder ces questions par une analyse génétique globale de toutes les espèces de Leishmania d'Eurasie et d'Afrique par une approche de type MLSA (MultiLocus Sequence Analysis) à partir d'un jeu de plus de 220 souches provenant de 43 pays. Nous avons ensuite essayé de comprendre en participant à l'analyse de données isoenzymatiques de plus de 2200 souches de Leishmania viscérotropes quelle pouvait être la structuration de ce groupe controversé. Enfin, à partir de données sur un foyer très restreint de l'espèce anthoponotique Leishmania tropica, nous avons contribué à l'analyse des données de caractérisation isoenzymatique de cette population et à l'étude des possibles cycles de transmission.Nos résultats mettent en évidence un certain nombre de points importants. Ils montrent d'abord que les différentes espèces de Leishmania présentes en Afrique et en Eurasie se répartissent en sept groupes distincts, recouvrant partiellement les dix espèces définies jusqu'ici sur des critères essentiellement biochimiques. Le système multilocus que nous avons développé s'avère plus résolutif que celui basé sur les isoenzymes. La mise en place d'un schéma MLST pour l'identification des souches pourrait être une contribution significative à la prise en charge thérapeutique des Leishmanioses de l'Ancien Monde. D'un point de vue taxonomique et épidémiologique, les trois espèces viscérotropes séparées jusqu'ici (L. infantum, L. donovani et L. archibaldi) apparaissent former un continuum génétique (complexe d'espèces). Nos analyses des données isoenzymatiques élargie à 2200 souches vont dans le même sens.Nos résultats montrent également que les sept loci génomiques étudiés par MLSA présentent une congruence phylogénétique remarquable. Ceci est en défaveur d'éventuels échanges génétiques et de recombinaisons entre les différentes espèces, contrairement à ce qui était supposé jusqu'ici. Potentiellement fréquente, l'hybridation inter-spécifique ne contribuerait pourtant pas à l'évolution des génotypes et serait un évènement transitoire, instable, incapable de se fixer dans les génomes. Il sera cependant sans doute indispensable d'explorer de façon exhaustive différents modèles avant d'en tirer des conclusions définitives.Enfin l'étude des corrélations entre structuration génétique et distance géographique révèle à la fois la focalisation de très nombreux génotypes mais également une dispersion très forte de certains autres, sans qu'on puisse proposer pour l'instant d'hypothèse robuste pour rendre compte de ces différences. Dans le même sens, notre analyse de données isoenzymatiques de souches de L. tropica provenant du même micro-foyer palestinien semble montrer une hétérogénéité intra-spécifique qui pourrait reposer malgré la proximité géographique sur des cycles parasitaires différenciés.Parasitic protozoa of the Leishmania genus infect many mammal species throughout the world. Transmitted by insect vectors, these pathogens are endemic in a hundred countries. In humans, the incidence of the disease is estimated at about 2 million new cases each year. Today, multiple issues arise on the modes of reproduction and genetic exchanges among these protozoa. They have implications on evolution, adaptation to new cycles, virulence, specific identification, taxonomy or therapeutic management.In this work, we first aimed at addressing these issues through a comprehensive genetic analysis of all Leishmania species from Eurasia and Africa, using a MLSA (MultiLocus Sequence Analysis)-based approach, from a dataset of more than 220 strains from 43 countries. We then tried to understand the structuration of this controversial group by participating in the isozyme data analysis of more than 2200 strains of viscerotropic Leishmania. Finally, using data from a very small focus of the anthoponotic species Leishmania tropica, we contributed to the analysis of isozyme characterization of this population and to the study of possible transmission cycles.Our results highlight a number of important points. They first show that the different Leishmania species found in Africa and Eurasia are divided into seven distinct groups, partially overlapping the ten species identified so far mainly on biochemical criteria. The multilocus system we developed is more resolutive than that based on isozymes. Implementing a MLST scheme for strain identification could contribute significantly to the therapeutic management of leishmaniases in the Old World. From taxonomic and epidemiological points of view, three viscerotropic species which were separated so far (L. infantum, L. archibaldi, L. donovani) appear to form a genetic continuum (species complex). Our analyzes of isozyme data extended to 2200 strains are in line with this conclusion. Our results also show a remarkable phylogenetic congruence of the seven genomic loci studied by MLSA. This does not support potential genetic exchanges and recombinations between different species, contrary to what was assumed so far. Potentially frequent, inter-specific hybridization would not contribute to the evolution of genotypes and would be a transient and unstable event, unable to settle in genomes. However, it will probably be necessary to explore different models exhaustively before drawing definitive conclusions.Finally, the study of correlations between geographic distance and genetic structuration revealed the focus of many genotypes but also a very high dispersion of some others, even if no convincing hypothesis can be made to explain such differences. In the same way, our analysis of isozyme data of L. tropica strains from the same Palestinian micro-focus seems to show an intra-specific heterogeneity which could be due to differentiated parasitic cycles, despite the geographical proximity

Plankton microecology, or how physics rules the life of microorganisms

La física que experimenten els microorganismes ens és contraintuïtiva. Aspectes sense importància a escales grans, com ara la viscositat, la difusió molecular, el moviment brownià i la reversibilitat cinemàtica, afecten moltes facetes de la vida dels organismes del plàncton, des de la dinàmica de nutrients fins a les interaccions entre individus. Les conseqüències per a la seva ecologia i evolució són, doncs, transcendentals. En aquest article repassem breument les particularitats de la física de nombres de Reynolds i de com afecten la motilitat dels microorganismes i la captació de nutrients, i ho il·lustrem amb exemples concrets de la nostra recerca sobre la funció de la morfologia cel·lular. La incorporació d’aquests conceptes a l’ecologia planctònica, en conjunció amb el desenvolupament de models numèrics i de tecnologies per a l’anàlisi i experimentació individual, ens està portant a un salt qualitatiu en la nostra comprensió mecanicista de com el comportament dels microorganismes afecta el sistema planctònic.Paraules clau: plàncton, nombre de Reynolds, viscositat, morfologia bacteriana.The physics experienced by microorganisms is non-intuitive to us. Aspects that bear no importance at large scales, such as viscosity, molecular diffusion, Brownian movement and kinematic reversibility, have a profound impact in all aspects of planktonic life, from nutrient dynamics to individual interactions. The consequences for the ecology and evolution of microorganisms are transcending. Here we briefly review the peculiarities of low Reynolds numbers physics and their implications to nutrient uptake and motility, and illustrate them with examples from our own research on the function of microbial shape. The incorporation of these concepts, along with new developments in numerical modelling, microfluidics and single-cell analyses, are leading us to a qualitative leap in our mechanistic understanding of how individual behaviouraffects the entire planktonic system.Keywords: plankton, Reynolds number, viscosity, bacterial morphology

Autochthonous disseminated dermal and visceral leishmaniasis in an AIDS patient, southern Thailand, caused by Leishmania siamensis

We report the first establishment of in vitro cultivation and genotypic characterization of Leishmania siamensis isolated from an autochthonous disseminated dermal and visceral leishmaniasis in a Thai acquired immunodeficiency syndrome (AIDS) patient. The molecular identification has shown that the parasite was identical to L. siamensis, a recently described Leishmania species reported in the southern provinces of Thailand. The phylogenetic analysis has confirmed L. siamensis as closely related to the zoonotic Leishmania species L. enrietti