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Members of the genus Lysinibacillus attract attention for their mosquitocidal, bioremediation, and plant growth-promoting abilities. Despite this interest, comprehensive studies focusing on genomic traits governing plant growth and stress resilience in this genus using whole-genome sequencing are still scarce. Therefore, we sequenced and compared the genomes of three endophytic Lysinibacillus irui strains isolated from Canary Island date palms with the ex-type strain IRB4-01. Overall, the genomes of these strains consist of a circular chromosome with an average size of 4.6 Mb and a GC content of 37.2%. Comparative analysis identified conserved gene clusters within the core genome involved in iron acquisition, phosphate solubilization, indole-3-acetic acid biosynthesis, and volatile compounds. In addition, genome analysis revealed the presence of genes encoding carbohydrate-active enzymes, and proteins that confer resistance to oxidative, osmotic, and salinity stresses. Furthermore, pathways of putative novel bacteriocins were identified in all genomes. This illustrates possible common plant growth-promoting traits shared among all strains of L. irui. Our findings highlight a rich repertoire of genes associated with plant lifestyles, suggesting significant potential for developing inoculants to enhance plant growth and resilience. This study is the first to provide insights into the overall genomic signatures and mechanisms of plant growth promotion and biocontrol in the genus Lysinibacillus. KEY POINTS: • Pioneer study in elucidating plant growth promoting in L. irui through comparative genomics. • Genome mining identified biosynthetic pathways of putative novel bacteriocins. • Future research directions to develop L. irui-based biofertilizers for sustainable agriculture., (© 2024. The Author(s).)

Lasiodiplodia hormozganensis, initially recognized as a fungal plant pathogen, is recognized now acknowledged as a potential threat to humans. However, our understanding of the pathogenesis mechanisms of Lasiodiplodia species remains limited, and the impact of temperature on its pathogenicity is unclear. This study aims to elucidate the effects of temperature on the biology of L. hormozganensis, focusing on the expression of pathogenesis-related molecules and its ability to function as a cross-kingdom pathogen. We conducted experiments at two different temperatures, 25 and 37 °C, analyzing the proteome and transcriptome of L. hormozganensis. Using strain CBS339.90, initially identified as L. theobromae but confirmed through ITS and tef1-α sequence analysis to be L. hormozganensis, we aimed to understand the fungus's protein expression under varying temperature conditions. Results from the functional analysis of the secretome at 25 °C showed a noteworthy presence of proteins related to carbohydrate metabolism, catabolism, plant cell wall degradation, and pathogenesis. However, when grown at 37 °C, the fungus exhibited an increased production of stress response and pathogenesis-related proteins. Our findings identified various pathways crucial for pathogenesis in both plants and humans, suggesting that L. hormozganensis possesses the genetic foundation to infect both hosts. Specific pathogenesis-related proteins, including the phytotoxin snodprot1, aspartic protease aspergillopepsin, and virulence protein SSD1, were also identified. Concluding, we propose a possible mechanism of how L. hormozganensis adapts to different temperatures. The shift in temperature results in the expression of genes that favor human related pathogenesis molecules., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Due to cryptic diversification, phenotypic plasticity and host associations, multilocus phylogenetic analyses have become the most important tool in accurately identifying and circumscribing species in the Diaporthe genus. However, the application of the genealogical concordance criterion has often been overlooked, ultimately leading to an exponential increase in novel Diaporthe spp. Due to the large number of species, many lineages remain poorly understood under the so-called species complexes. For this reason, a robust delimitation of the species boundaries in Diaporthe is still an ongoing challenge. Therefore, the present study aimed to resolve the species boundaries of the Diaporthe arecae species complex (DASC) by implementing an integrative taxonomic approach. The Genealogical Phylogenetic Species Recognition (GCPSR) principle revealed incongruences between the individual gene genealogies. Moreover, the Poisson Tree Processes' (PTPs) coalescent-based species delimitation models identified three well-delimited subclades represented by the species D. arecae , D. chiangmaiensis and D. smilacicola . These results evidence that all species previously described in the D. arecae subclade are conspecific, which is coherent with the morphological indistinctiveness observed and the absence of reproductive isolation and barriers to gene flow. Thus, 52 Diaporthe spp. are reduced to synonymy under D. arecae . Recent population expansion and the possibility of incomplete lineage sorting suggested that the D. arecae subclade may be considered as ongoing evolving lineages under active divergence and speciation. Hence, the genetic diversity and intraspecific variability of D. arecae in the context of current global climate change and the role of D. arecae as a pathogen on palm trees and other hosts are also discussed. This study illustrates that species in Diaporthe are highly overestimated, and highlights the relevance of applying an integrative taxonomic approach to accurately circumscribe the species boundaries in the genus Diaporthe .

The recent multi-country outbreak of Mpox (Monkeypox disease) constituted a public health emergency. Although animal-to-human transmission is known to be the primary way of transmission, an increasing number of cases transmitted by person-to-person contact have been reported. During the recent Mpox outbreak sexual or intimate contact has been considered the most important way of transmission. However, other routes of transmission must not be ignored. The knowledge of how the Monkeypox Virus (MPXV) spreads is crucial to implement adequate measures to contain the spread of the disease. Therefore, this systematic review aimed to collect scientific data published concerning other implicated sources of infection beyond sexual interaction, such as the involvement of respiratory particles, contact with contaminated surfaces and skin-to-skin contact. The current study was performed using the guidelines of Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). Publications analyzing contacts of Mpox index cases and their outcome after contact were included. A total of 7319 person-to-person contacts were surveyed and 273 of them became positive cases. Positive secondary transmission of MPXV was verified after contact with people cohabiting in the same household, with family members, with healthcare workers, or within healthcare facilities, and sexual contact or contact with contaminated surfaces. Using the same cup, sharing the same dishes, and sleeping in the same room or bed were also positively associated with transmission. Five studies showed no evidence of transmission despite contact with surfaces, skin-to-skin contact, or through airway particles within healthcare facilities where containment measures were taken. These records support the case for person-to-person transmission and suggest that other types of contact beyond sexual contact pose a significant risk of acquiring the infection. Further investigation is crucial to elucidate MPXV transmission dynamics, and to implement adequate measures to contain the spread of the infection.

Zalerion maritima is a marine fungus that has been studied for the biodegradation of (micro)plastics. Here, we report the draft genome sequence of strain ATCC 34329, which was shown to have a size of 58.4 Mb, a GC content of 44.39%, and 10,802 predicted genes.

Prostate cancer (PCa) is the most common malignant neoplasm with the highest worldwide incidence in men aged 50 years and older. Emerging evidence suggests that the microbial dysbiosis may promote chronic inflammation linked to the development of PCa. Therefore, this study aims to compare the microbiota composition and diversity in urine, glans swabs, and prostate biopsies between men with PCa and non-PCa men. Microbial communities profiling was assessed through 16S rRNA sequencing. The results indicated that α-diversity (number and abundance of genera) was lower in prostate and glans, and higher in urine from patients with PCa, compared to non-PCa patients. The different genera of the bacterial community found in urine was significantly different in PCa patients compared to non-PCa patients, but they did not differ in glans and prostate. Moreover, comparing the bacterial communities present in the three different samples, urine and glans show a similar genus composition. Linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed significantly higher levels of the genera Streptococcus , Prevotella , Peptoniphilus , Negativicoccus , Actinomyces , Propionimicrobium , and Facklamia in urine of PCa patients, whereas Methylobacterium / Methylorubrum , Faecalibacterium , and Blautia were more abundant in the non-PCa patients. In glans, the genus Stenotrophomonas was enriched in PCa subjects, while Peptococcus was more abundant in non-PCa subjects. In prostate, Alishewanella , Paracoccus , Klebsiella , and Rothia were the overrepresented genera in the PCa group, while Actinomyces , Parabacteroides , Muribaculaceae sp., and Prevotella were overrepresented in the non-PCa group. These findings provide a strong background for the development of potential biomarkers with clinical interest.

The human upper respiratory tract comprises the nasal cavity, pharynx and larynx regions and offers distinct microbial communities. However, an imbalance and alterations in the nasal mucosa microbiome enhance the risk of chronic respiratory conditions in patients with allergic respiratory diseases. This is particularly important in children and adolescents once allergic rhinitis (AR) is an inflammatory disorder of the nasal mucosa, often associated with an increase in pulmonary allergic inflammation. Therefore, this systematic review aimed to collect scientific data published concerning the microbial community alterations in nasal mucosa of children and adolescents suffering from AR or in association with adenotonsillar hypertrophy (AH) and allergic rhinoconjunctivitis (ARC). The current study was performed using the guidelines of Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). Publications related to microbiome alterations in the nasal mucosa in pediatric age, studies including next-generation sequencing platforms, and studies exclusively written in the English language were some of the inclusion criteria. In total, five articles were included. Despite the scarcity of the published data in this research field and the lack of prospective studies, the genera Acinetobacter , Corynebacterium , Dolosigranulum , Haemophilus , Moraxella , Staphylococcus and Streptococcus dominate the nares and nasopharyngeal microbiome of the pediatric population regardless of their age. However, an imbalance in the resident bacterial community in the nasal mucosa was observed. The genera Acinetobacter , and Pseudomonas were more abundant in the nasal cavity of AR and AH children, while Streptococcus and Moraxella were predominant in the hypopharyngeal region of AR infants. An abundance of Staphylococcus spp. was also reported in the anterior nares and hypopharyngeal region of children and adolescents suffering from AR passive smoke exposure and ARC. These records suggest that different nasal structures, ageing, smoke exposure and the presence of other chronic disorders shape the nasal mucosa microbiome. Therefore, the establishment of adequate criteria for sampling would be established for a deeper understanding and a trustworthy comparison of the microbiome alterations in pediatric age.

Plant pathogens are responsible for causing economic and production losses in several crops worldwide, thus reducing the quality and quantity of agricultural supplies. To reduce the usage of chemically synthesized pesticides, strategies and approaches using microorganisms are being used in plant disease management. Most of the studies concerning plant-growth promotion and biological agents to control plant diseases are mainly focused on bacteria. In addition, a great portion of registered and commercialized biopesticides are bacterial-based products. Despite fungal endophytes having been identified as promising candidates for their use in biological control, it is of the utmost importance to develop and improve the existing knowledge on this research field. The genus Diaporthe , encompasses plant pathogens, saprobes and endophytes that have been screened for secondary metabolite, mainly due to their production of polyketides and a variety of unique bioactive metabolites with agronomic importance. Some of these metabolites exhibit antifungal and antibacterial activity for controlling plant pathogens, and phytotoxic activity for the development of potential mycoherbicides. Moreover, species of Diaporthe are reported as promising agents in the development of biofertilizers. For this reason, in this review we summarize the potential of Diaporthe species to produce natural products with application in agriculture and describe the benefits of these fungi to promote their host plant's growth.

The human body represents a complex and diverse reservoir of microorganisms. Although the human microbiome remains poorly characterized and understood, it should not be underestimated, since recent studies have highlighted its importance in health. This is especially evident when considering microbiota in the male reproductive system, responsible for men’s fertility and sexual behavior. Therefore, the aim of this systematic review is to provide an overview of the microbial communities of the healthy male genital mucosa and its role in disease. This study was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The search was limited to the English language and studies published until August 2022 that included culture-independent techniques for microbiome characterization in male genital mucosa. Ten articles were included. The bacterial composition of the male genital mucosa consists of several genera including Prevotella, Finegoldia, Peptoniphilus, Staphylococcus, Corynebacterium, and Anaerococcus, suggesting that the male genital microbiome composition shows similarities with the adjacent anatomical sites and is related with sexual intercourse. Moreover, male circumcision appears to influence the penile microbiome. Despite the lack of knowledge on the male genital mucosa microbiome in disease, it was reported that Staphylococcus warneri and Prevotella bivia were associated with balanoposthitis, whereas Enterobacteriaceae, Prevotella, and Fusobacterium were more abundant in male genital lichen sclerosus. The limited data and paucity of prospective controlled studies highlight the need for additional studies and established criteria for sampling methods and the microbiome assay procedure. Such a consensus would foster the knowledge about the composition of the genital microbiome of healthy males and its role in disease.

The genus Diaporthe includes pathogenic species distributed worldwide and affecting a wide variety of hosts. Diaporthe amygdali and Diaporthe eres have been found to cause cankers, dieback, or twig blights on economically important crops such as soybean, almond, grapevine, and blueberry. Despite their importance as plant pathogens, the strategies of species of Diaporthe to infect host plants are poorly explored. To provide a genomic basis of pathogenicity, the genomes of D. amygdali CAA958 and D. eres CBS 160.32 were sequenced and analyzed. Cellular transporters involved in the transport of toxins, ions, sugars, effectors, and genes implicated in pathogenicity were detected in both genomes. Hydrolases and oxidoreductases were the most prevalent carbohydrate-active enzymes (CAZymes). However, analyses of the secreted proteins revealed that the secretome of D. eres CBS 160.32 is represented by 5.4% of CAZymes, whereas the secreted CAZymes repertoire of D. amygdali CAA958 represents 29.1% of all secretomes. Biosynthetic gene clusters (BGCs) encoding compounds related to phytotoxins and mycotoxins were detected in D. eres and D. amygdali genomes. The core gene clusters of the phytotoxin Fusicoccin A in D. amygdali are reported here through a genome-scale assembly. Comparative analyses of the genomes from 11 Diaporthe species revealed an average of 874 CAZymes, 101 secondary metabolite BGCs, 1640 secreted proteins per species, and genome sizes ranging from 51.5 to 63.6 Mbp. This study offers insights into the overall features and characteristics of Diaporthe genomes. Our findings enrich the knowledge about D. eres and D. amygdali , which will facilitate further research into the pathogenicity mechanisms of these species.

The genus Emericellopsis is found in terrestrial, but mainly in marine, environments with a worldwide distribution. Although Emericellopsis has been recognized as an important source of bioactive compounds, the range of metabolites expressed by the species of this genus, as well as the genes involved in their production are still poorly known. Untargeted metabolomics, using UPLC- QToF-MS/MS, and genome sequencing (Illumina HiSeq) was performed to unlock E . cladophorae MUM 19.33 chemical diversity. The genome of E . cladophorae is 26.9 Mb and encodes 8572 genes. A large set of genes encoding carbohydrate-active enzymes (CAZymes), secreted proteins, transporters, and secondary metabolite biosynthetic gene clusters were identified. Our analysis also revealed genomic signatures that may reflect a certain fungal adaptability to the marine environment, such as genes encoding for (1) the high-osmolarity glycerol pathway; (2) osmolytes' biosynthetic processes; (3) ion transport systems, and (4) CAZymes classes allowing the utilization of marine polysaccharides. The fungal crude extract library constructed revealed a promising source of antifungal (e.g., 9,12,13-Trihydroxyoctadec-10-enoic acid, hymeglusin), antibacterial (e.g., NovobiocinA), anticancer (e.g., daunomycinone, isoreserpin, flavopiridol), and anti-inflammatory (e.g., 2'-O-Galloylhyperin) metabolites. We also detected unknown compounds with no structural match in the databases used. The metabolites' profiles of E . cladophorae MUM 19.33 fermentations were salt dependent. The results of this study contribute to unravel aspects of the biology and ecology of this marine fungus. The genome and metabolome data are relevant for future biotechnological exploitation of the species.

Aspergillus section Circumdati encompasses several species that express both beneficial (e.g., biochemical transformation of steroids and alkaloids, enzymes and metabolites) and harmful compounds (e.g., production of ochratoxin A (OTA)). Given their relevance, it is important to analyze the genetic and metabolic diversity of the species of this section. We sequenced the genome of Aspergillus affinis CMG 70, isolated from sea water, and compared it with the genomes of species from section Circumdati , including A. affinis 's strain type. The A. affinis genome was characterized considering secondary metabolites biosynthetic gene clusters (BGCs), carbohydrate-active enzymes (CAZymes), and transporters. To uncover the biosynthetic potential of A. affinis CMG 70, an untargeted metabolomics (LC-MS/MS) approach was used. Cultivating the fungus in the presence and absence of sea salt showed that A. affinis CMG 70 metabolite profiles are salt dependent. Analyses of the methanolic crude extract revealed the presence of both unknown and well-known Aspergillus compounds, such as ochratoxin A, anti-viral (e.g., 3,5-Di-tert-butyl-4-hydroxybenzoic acid and epigallocatechin), anti-bacterial (e.g., 3-Hydroxybenzyl alcohol, l-pyroglutamic acid, lecanoric acid), antifungal (e.g., lpyroglutamic acid, 9,12,13-Trihydroxyoctadec-10-enoic acid, hydroxyferulic acid), and chemotherapeutic (e.g., daunomycinone, mitoxantrone) related metabolites. Comparative analysis of 17 genomes from 16 Aspergillus species revealed abundant CAZymes (568 per species), secondary metabolite BGCs (73 per species), and transporters (1359 per species). Some BGCs are highly conserved in this section (e.g., pyranonigrin E and UNII-YC2Q1O94PT (ACR toxin I)), while others are incomplete or completely lost among species (e.g., bikaverin and chaetoglobosins were found exclusively in series Sclerotiorum , while asperlactone seemed completely lost). The results of this study, including genome analysis and metabolome characterization, emphasize the molecular diversity of A. affinis CMG 70, as well as of other species in the section Circumdati .

DNA sequence analysis has been of the utmost importance to delimit species boundaries in the genus Diaporthe . However, the common practice of combining multiple genes, without applying the genealogical concordance criterion has complicated the robust delimitation of species, given that phylogenetic incongruence between loci has been disregarded. Despite the several attempts to delineate the species boundaries in the D. eres complex, the phylogenetic limits within this complex remain unclear. In order to bridge this gap, we employed the Genealogical Phylogenetic Species Recognition principle (GCPSR) and the coalescent-based model Poisson Tree Processes (PTPs) and evaluated the presence of recombination within the D. eres complex. Based on the GCPSR principle, presence of incongruence between individual gene genealogies, i.e., conflicting nodes and branches lacking phylogenetic support, was evident. Moreover, the results of the coalescent model identified D. eres complex as a single species, which was not consistent with the current large number of species within the complex recognized in phylogenetic analyses. The absence of reproductive isolation and barriers to gene flow as well as the high haplotype and low nucleotide diversity indices within the above-mentioned complex suggest that D. eres constitutes a population rather than different lineages. Therefore, we argue that a cohesive approach comprising genealogical concordance criteria and methods to detect recombination must be implemented in future studies to circumscribe species in the genus Diaporthe .

Lignicolous marine fungi are a particular group of microorganisms that are typically found in mangroves, salt marshes, and estuaries, normally associated with driftwood or submerged wood. During investigations of lignicolous fungi occurring in the estuary Ria de Aveiro, Portugal, wood baits were submerged in a marina for 1 year. Seventeen distinct marine fungal species were identified, with the most abundant taxa belonging to the family Lulworthiaceae. Through single- and multilocus phylogenies based on sequences of the internal transcribed spacer (ITS) region and large subunit (28S) and small subunit (18S) of the ribosomal RNA gene cluster in combination with morphological and physiological data, we describe Remispora submersa , sp. nov., and Zalerion pseudomaritima , sp. nov., as novel species. Additionally, we propose that Papulaspora halima , a species whose taxonomic placement has been somehow confusing, be transferred to the genus Paralulworthia as Paralulworthia halima .

Fungal communities associated with macroalgae remain largely unexplored. To characterize algicolous fungal communities using culture dependent methods, macroalgae were collected from different sampling sites in the Ria de Aveiro estuary, Portugal. From a collection of 486 isolates that were obtained, 213 representative isolates were selected through microsatellite-primed PCR (MSP-PCR) fingerprinting analysis. The collection yielded 33 different genera, which were identified using the ITS region of the rDNA. The results revealed that the most abundant taxa in all collections were Acremonium -like species: Alternaria , Cladosporium , Leptobacillium and Penicillium . The fungal community composition varied with macroalgae species. Through multilocus phylogenetic analyses based on ITS, tub2 , tef1-α and actA sequences, in addition to detailed morphological data, we propose Cladosporium rubrum sp. nov. (type strain=CMG 28=MUM 19.39) and Hypoxylon aveirense sp. nov. (type strain=CMG 29=MUM 19.40) as novel species.

Fungi are ubiquitous organisms with a wide distribution in almost all ecosystems, including marine environments. Coastal and estuarine ecosystems remain poorly unexplored as fungal habitats, potentially harbouring a hidden diversity with important ecological roles. During an extensive survey of marine fungi in coastal and estuarine Portuguese environments, a collection of 612 isolates was obtained from water, algae, sponges and driftwood. From these, 282 representative isolates were selected through microsatellite-primed PCR (MSP-PCR) fingerprinting analysis, which were identified based on DNA sequence data. The collection yielded 117 taxa from 38 distinct genera, which were identified using DNA sequence analysis. Overall, fungal community composition varied with host/substrate, but the most abundant taxa in the collection were Cladosporium cladosporioides , Penicillium terrigenum , Penicillium brevicompactum and Fusarium equiseti / incarnatum complex. The occurrence of a high fungal diversity harbouring novel species was disclosed. Through a multilocus phylogeny based on ITS, tub2 and tef1-α sequences, in conjunction with morphological and physiological data, we propose Neoascochyta fuci sp. nov. and Paraconiothyrium salinum sp. nov.

A collection of fungal isolates obtained from crop plants, specifically grapevine and blueberry, in Peru were characterised through morphological and DNA sequence analyses of the nuclear ribosomal internal transcribed spacer (ITS), beta-tubulin ( tub2 ) and translation elongation factor 1-alpha ( tef-1 α) regions. Isolates produced monomorphic and dimorphic conidiophores typical of members of the genus Clonostachys . Single- and multi-locus gene phylogenies confirmed the isolates as representing members of the genus Clonostachys , more closely related to species in the subgenus Bionectria . In phylogenetic analyses the isolates grouped in two separate clades, one corresponding to the species Clonostachys pseudochroleuca and the other one distinct from all known species of the genus Clonostachys . These isolates are recognized as representing a novel species species for which the name Clonostachys viticola is proposed.

Novel species of fungi described in this study include those from various countries as follows: Antarctica , Cladosporium arenosum from marine sediment sand. Argentina , Kosmimatamyces alatophylus (incl. Kosmimatamyces gen. nov.) from soil. Australia , Aspergillus banksianus , Aspergillus kumbius , Aspergillus luteorubrus , Aspergillus malvicolor and Aspergillus nanangensis from soil, Erysiphe medicaginis from leaves of Medicago polymorpha , Hymenotorrendiella communis on leaf litter of Eucalyptus bicostata , Lactifluus albopicri and Lactifluus austropiperatus on soil, Macalpinomyces collinsiae on Eriachne benthamii , Marasmius vagus on soil, Microdochium dawsoniorum from leaves of Sporobolus natalensis , Neopestalotiopsis nebuloides from leaves of Sporobolus elongatus , Pestalotiopsis etonensis from leaves of Sporobolus jacquemontii , Phytophthora personensis from soil associated with dying Grevillea mccutcheonii. Brazil , Aspergillus oxumiae from soil, Calvatia baixaverdensis on soil, Geastrum calycicoriaceum on leaf litter, Greeneria kielmeyerae on leaf spots of Kielmeyera coriacea . Chile , Phytophthora aysenensis on collar rot and stem of Aristotelia chilensis. Croatia , Mollisia gibbospora on fallen branch of Fagus sylvatica. Czech Republic , Neosetophoma hnaniceana from Buxus sempervirens. Ecuador , Exophiala frigidotolerans from soil. Estonia , Elaphomyces bucholtzii in soil. France , Venturia paralias from leaves of Euphorbia paralias. India , Cortinarius balteatoindicus and Cortinarius ulkhagarhiensis on leaf litter. Indonesia , Hymenotorrendiella indonesiana on Eucalyptus urophylla leaf litter. Italy , Penicillium taurinense from indoor chestnut mill. Malaysia , Hemileucoglossum kelabitense on soil, Satchmopsis pini on dead needles of Pinus tecunumanii. Poland , Lecanicillium praecognitum on insects' frass. Portugal , Neodevriesia aestuarina from saline water. Republic of Korea , Gongronella namwonensis from freshwater. Russia , Candida pellucida from Exomias pellucidus , Heterocephalacria septentrionalis as endophyte from Cladonia rangiferina , Vishniacozyma phoenicis from dates fruit, Volvariella paludosa from swamp. Slovenia , Mallocybe crassivelata on soil. South Africa , Beltraniella podocarpi , Hamatocanthoscypha podocarpi , Coleophoma podocarpi and Nothoseiridium podocarpi (incl. Nothoseiridium gen. nov.) from leaves of Podocarpus latifolius , Gyrothrix encephalarti from leaves of Encephalartos sp., Paraphyton cutaneum from skin of human patient, Phacidiella alsophilae from leaves of Alsophila capensis , and Satchmopsis metrosideri on leaf litter of Metrosideros excelsa. Spain , Cladophialophora cabanerensis from soil, Cortinarius paezii on soil, Cylindrium magnoliae from leaves of Magnolia grandiflora , Trichophoma cylindrospora (incl. Trichophoma gen. nov.) from plant debris, Tuber alcaracense in calcareus soil, Tuber buendiae in calcareus soil. Thailand , Annulohypoxylon spougei on corticated wood, Poaceascoma filiforme from leaves of unknown Poaceae. UK , Dendrostoma luteum on branch lesions of Castanea sativa , Ypsilina buttingtonensis from heartwood of Quercus sp. Ukraine , Myrmecridium phragmiticola from leaves of Phragmites australis. USA , Absidia pararepens from air, Juncomyces californiensis (incl. Juncomyces gen. nov.) from leaves of Juncus effusus , Montagnula cylindrospora from a human skin sample, Muriphila oklahomaensis (incl. Muriphila gen. nov.) on outside wall of alcohol distillery, Neofabraea eucalyptorum from leaves of Eucalyptus macrandra , Diabolocovidia claustri (incl. Diabolocovidia gen. nov.) from leaves of Serenoa repens , Paecilomyces penicilliformis from air, Pseudopezicula betulae from leaves of leaf spots of Populus tremuloides . Vietnam , Diaporthe durionigena on branches of Durio zibethinus and Roridomyces pseudoirritans on rotten wood. Morphological and culture characteristics are supported by DNA barcodes., (© 2020 Naturalis Biodiversity Center & Westerdijk Fungal Biodiversity Institute.)

Blueberry, an increasingly cultivated fruit crop in Portugal, is known to be susceptible to twig blight and dieback caused by species of Diaporthe . The diversity of Diaporthe species associated with symptomatic and asymptomatic Vaccinium corymbosum plants in Portugal was assessed. A multilocus sequence analysis of the rDNA internal transcribed spacer (ITS) region and the translation elongation factor 1-alpha ( tef1-α ), β-tubulin ( tub2 ), calmodulin ( cal ), and histone 3 ( his3 ) genes revealed the presence of Diaporthe foeniculina, Diaporthe rudis , and four new species, which are described as Diaporthe crousii, Diaporthe phillipsii, Diaporthe rossmaniae , and Diaporthe vacuae . These new species were characterized in terms of their morphology, mating strategies, and temperature growth requirements. In artificial inoculation trials of V. corymbosum cv. Bluecrop plants, all Diaporthe species caused minor symptoms. Further, no differences in aggressiveness were apparent between species. This study provides the first survey of Diaporthe species associated with blueberry twig blight and dieback in Portugal. It disclosed the occurrence of a diverse assemblage of Diaporthe species, whose status and impact as pathogens of blueberry is not yet fully understood.

Macroalgae of the genera Fucus, Ulva , and Enteromorpha are typically abundant in estuaries. Endophytic fungi may have beneficial effects on the hosts affecting their ability to cope with stress. They are also a source of biologically active compounds. However, little is known about the endophytic fungi that colonize these macroalgae. Endophytic isolates were obtained from macroalgae from various sites in the estuary Ria de Aveiro (Portugal), as well as from saline water and sponges. Six Acremonium -like species could not be affiliated to any known species. Phylogenetic analyses based on internal transcribed spacer (ITS) region of the ribosomal DNA and β-tubulin ( tub2 ) and actin ( act1 ) genes placed these species in the genera Emericellopsis and Parasarocladium , but distinct from all currently known species. Although sharing morphological characteristics with the most closely related species, these genera differ in micromorphological and molecular characters. Thus, three novel species of Emericellopsis ( E. cladophorae , sp. nov., E. enteromorphae , sp. nov., and E. phycophila , sp. nov.) and three novel species of Parasarocladium ( P. aestuarinum , sp. nov., P. alavariense , sp. nov., and P. fusiforme , sp. nov.) are proposed.

Lasiodiplodia theobromae is one of the most aggressive agents of the grapevine trunk disease Botryosphaeria dieback. Through a dual RNA-sequencing approach, this study aimed to give a broader perspective on the infection strategy deployed by L. theobromae , while understanding grapevine response. Approximately 0.05% and 90% of the reads were mapped to the genomes of L. theobromae and Vitis vinifera , respectively. Over 2500 genes were significantly differentially expressed in infected plants after 10 dpi, many of which are involved in the inducible defense mechanisms of grapevines. Gene expression analysis showed changes in the fungal metabolism of phenolic compounds, carbohydrate metabolism, transmembrane transport, and toxin synthesis. These functions are related to the pathogenicity mechanisms involved in plant cell wall degradation and fungal defense against antimicrobial substances produced by the host. Genes encoding for the degradation of plant phenylpropanoid precursors were up-regulated, suggesting that the fungus could evade the host defense response using the phenylpropanoid pathway. The up-regulation of many distinct components of the phenylpropanoid pathway in plants supports this hypothesis. Moreover, genes related to phytoalexin biosynthesis, hormone metabolism, cell wall modification enzymes, and pathogenesis-related proteins seem to be involved in the host responses observed. This study provides additional insights into the molecular mechanisms of L. theobromae and V. vinifera interactions.

The genus Verrucoconiothyrium was erected to accommodate Coniothyrium -like species with verruculose conidia. So far, it includes only four species, which have been found in association with plants, and very little is known about their distribution and host preferences. In this study, a Coniothyrium -like fungus isolated from sea water from the north of Portugal was characterised. Phylogenetic analysis, based on sequence data of the internal transcribed spacer and beta-tubulin loci, placed this fungus within the genus Verrucoconiothyrium but clearly distinct from the other known species. A novel species Verrucoconiothyrium ambiguum sp. nov. is described and illustrated. The taxonomic affiliation of the genus Verrucoconiothyrium at the family level was addressed through individual and combined gene genealogies. Our results show that the genus Verrucoconiothyrium is a member of the family Didymellaceae .

A collection of fungi was isolated from macroalgae of the genera Gracilaria , Enteromorpha and Ulva in the estuary Ria de Aveiro in Portugal. These isolates were characterized through a multilocus phylogeny based on ITS region of the ribosomal DNA, beta-tubulin ( tub2 ) and translation elongation factor 1 alpha ( tef1-α ) sequences, in conjunction with morphological and physiological data. These analyses showed that the isolates represented an unknown fungus for which a new genus, Neptunomyces gen. nov. and a new species, Neptunomyces aureus sp. nov. are proposed. Phylogenetic analyses supported the affiliation of this new taxon to the family Didymosphaeriaceae., (Micael F. M. Gonçalves, Tânia F. L. Vicente, Ana C. Esteves, Artur Alves.)

During an extensive survey of marine fungi in coastal marine environments from Portugal, a collection of Penicillium isolates were obtained from sea water, macroalgae and driftwood. Sixteen distinct Penicillium species were identified with Penicillium terrigenum and Penicillium brevicompactum being the most frequent. A Penicillium species isolated from sea water could not be affiliated to any known species. Phylogenetic analyses based on the ITS region of the rDNA and the beta-tubulin ( benA ) gene placed it into Penicillium section Ramosa , distinct from all currently known species and with Penicillium tunisiense as its closest relative. Although having similar morphological characteristics, these species differ in micromorphological and molecular characters. Thus, Penicillium lusitanum sp. nov. is proposed as a novel species.

Lasiodiplodia theobromae (Botryosphaeriaceae, Ascomycota) is a plant pathogen and human opportunist whose pathogenicity is modulated by temperature. The molecular effects of temperature on L. theobromae are mostly unknown, so we used a multi-omics approach to understand how temperature affects the molecular mechanisms of pathogenicity. The genome of L. theobromae LA-SOL3 was sequenced (Illumina MiSeq) and annotated. Furthermore, the transcriptome (Illumina TruSeq) and proteome (Orbitrap LC-MS/MS) of LA-SOL3 grown at 25 °C and 37 °C were analysed. Proteins related to pathogenicity (plant cell wall degradation, toxin synthesis, mitogen-activated kinases pathway and proteins involved in the velvet complex) were more abundant when the fungus grew at 25 °C. At 37 °C, proteins related to pathogenicity were less abundant than at 25 °C, while proteins related to cell wall organisation were more abundant. On the other hand, virulence factors involved in human pathogenesis, such as the SSD1 virulence protein, were expressed only at 37 °C. Taken together, our results showed that this species presents a typical phytopathogenic molecular profile that is compatible with a hemibiotrophic lifestyle. We showed that L. theobromae is equipped with the pathogenesis toolbox that enables it to infect not only plants but also animals.

Novel species of fungi described in this study include those from various countries as follows: Antarctica , Apenidiella antarctica from permafrost, Cladosporium fildesense from an unidentified marine sponge. Argentina , Geastrum wrightii on humus in mixed forest. Australia , Golovinomyces glandulariae on Glandularia aristigera, Neoanungitea eucalyptorum on leaves of Eucalyptus grandis, Teratosphaeria corymbiicola on leaves of Corymbia ficifolia, Xylaria eucalypti on leaves of Eucalyptus radiata. Brazil , Bovista psammophila on soil, Fusarium awaxy on rotten stalks of Zea mays, Geastrum lanuginosum on leaf litter covered soil, Hermetothecium mikaniae-micranthae (incl. Hermetothecium gen. nov.) on Mikania micrantha, Penicillium reconvexovelosoi in soil, Stagonosporopsis vannaccii from pod of Glycine max. British Virgin Isles , Lactifluus guanensis on soil. Canada , Sorocybe oblongispora on resin of Picea rubens. Chile , Colletotrichum roseum on leaves of Lapageria rosea. China , Setophoma caverna from carbonatite in Karst cave. Colombia , Lareunionomyces eucalypticola on leaves of Eucalyptus grandis. Costa Rica , Psathyrella pivae on wood. Cyprus , Clavulina iris on calcareous substrate. France , Chromosera ambigua and Clavulina iris var. occidentalis on soil. French West Indies , Helminthosphaeria hispidissima on dead wood. Guatemala , Talaromyces guatemalensis in soil. Malaysia , Neotracylla pini (incl. Tracyllales ord. nov. and Neotracylla gen. nov.) and Vermiculariopsiella pini on needles of Pinus tecunumanii. New Zealand , Neoconiothyrium viticola on stems of Vitis vinifera, Parafenestella pittospori on Pittosporum tenuifolium, Pilidium novae-zelandiae on Phoenix sp. Pakistan , Russula quercus-floribundae on forest floor. Portugal , Trichoderma aestuarinum from saline water. Russia , Pluteus liliputianus on fallen branch of deciduous tree, Pluteus spurius on decaying deciduous wood or soil. South Africa , Alloconiothyrium encephalarti, Phyllosticta encephalarticola and Neothyrostroma encephalarti (incl. Neothyrostroma gen. nov.) on leaves of Encephalartos sp., Chalara eucalypticola on leaf spots of Eucalyptus grandis × urophylla, Clypeosphaeria oleae on leaves of Olea capensis, Cylindrocladiella postalofficium on leaf litter of Sideroxylon inerme , Cylindromonium eugeniicola (incl. Cylindromonium gen. nov.) on leaf litter of Eugenia capensis , Cyphellophora goniomatis on leaves of Gonioma kamassi , Nothodactylaria nephrolepidis (incl. Nothodactylaria gen. nov. and Nothodactylariaceae fam. nov.) on leaves of Nephrolepis exaltata , Falcocladium eucalypti and Gyrothrix eucalypti on leaves of Eucalyptus sp., Gyrothrix oleae on leaves of Olea capensis subsp. macrocarpa , Harzia metrosideri on leaf litter of Metrosideros sp., Hippo pota myces phragmitis (incl. Hippo pota myces gen. nov.) on leaves of Phragmites australis , Lectera philenopterae on Philenoptera violacea , Leptosillia mayteni on leaves of Maytenus heterophylla , Lithohypha aloicola and Neoplatysporoides aloes on leaves of Aloe sp., Millesimomyces rhoicissi (incl. Millesimomyces gen. nov.) on leaves of Rhoicissus digitata , Neodevriesia strelitziicola on leaf litter of Strelitzia nicolai , Neokirramyces syzygii (incl. Neokirramyces gen. nov.) on leaf spots of Syzygium sp., Nothoramichloridium perseae (incl. Nothoramichloridium gen. nov. and Anungitiomycetaceae fam. nov.) on leaves of Persea americana , Paramycosphaerella watsoniae on leaf spots of Watsonia sp., Penicillium cuddlyae from dog food, Podocarpomyces knysnanus (incl. Podocarpomyces gen. nov.) on leaves of Podocarpus falcatus , Pseudocercospora heteropyxidicola on leaf spots of Heteropyxis natalensis , Pseudopenidiella podocarpi, Scolecobasidium podocarpi and Ceramothyrium podocarpicola on leaves of Podocarpus latifolius , Scolecobasidium blechni on leaves of Blechnum capense , Stomiopeltis syzygii on leaves of Syzygium chordatum , Strelitziomyces knysnanus (incl. Strelitziomyces gen. nov.) on leaves of Strelitzia alba , Talaromyces clemensii from rotting wood in goldmine, Verrucocladosporium visseri on Carpobrotus edulis. Spain , Boletopsis mediterraneensis on soil, Calycina cortegadensisi on a living twig of Castanea sativa , Emmonsiellopsis tuberculata in fluvial sediments, Mollisia cortegadensis on dead attached twig of Quercus robur , Psathyrella ovispora on soil, Pseudobeltrania lauri on leaf litter of Laurus azorica , Terfezia dunensis in soil, Tuber lucentum in soil, Venturia submersa on submerged plant debris. Thailand , Cordyceps jakajanicola on cicada nymph, Cordyceps kuiburiensis on spider, Distoseptispora caricis on leaves of Carex sp., Ophiocordyceps khonkaenensis on cicada nymph. USA , Cytosporella juncicola and Davidiellomyces juncicola on culms of Juncus effusus , Monochaetia massachusettsianum from air sample, Neohelicomyces melaleucae and Periconia neobrittanica on leaves of Melaleuca styphelioides × lanceolata , Pseudocamarosporium eucalypti on leaves of Eucalyptus sp . , Pseudogymnoascus lindneri from sediment in a mine, Pseudogymnoascus turneri from sediment in a railroad tunnel, Pulchroboletus sclerotiorum on soil, Zygosporium pseudomasonii on leaf of Serenoa repens. Vietnam , Boletus candidissimus and Veloporphyrellus vulpinus on soil. Morphological and culture characteristics are supported by DNA barcodes., (© 2019 Naturalis Biodiversity Center & Westerdijk Fungal Biodiversity Institute.)

Gene expression can vary with the organisms' life stage. It is known that embryos can be more sensitive to toxicant exposure, as previously demonstrated for Enchytraeus crypticus (Oligochaeta) exposed to cadmium (Cd), known to cause embryotoxicity and hatching delay. It was shown that Ca enters embryos via the L-type Ca channels in the cocoon membrane, this being affected in Cd exposed embryos (Cd-Ca competition is well-known). In the present study, the embryotoxic mechanisms of Cd were studied via high-throughput gene expression for E. crypticus. Cocoons (1-2 days old), instead of the adult organism, were exposed in Cd spiked LUFA 2.2 soil during 1 day. Results showed that Cd affected Ca homeostasis which is implicated in several other molecular processes. Several of the major modulators of Cd toxicity (e.g., impaired gene expression, cell cycle arrest, DNA and mitochondrial damage) were identified in the embryos showing its relevancy as a model in ecotoxicogenomics. The draft Adverse Outcome Pathway was improved. Previously was hypothesized that gene regulation mechanisms were activated to synthesize more Ca channel proteins - this was confirmed here. Further, novel evidences were that, besides the extracellular competition, Cd competes intracellularly which causes a reduction in Ca efflux, and potentiates Cd embryotoxicity., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Toxicity tests that last the all life duration of the organisms are not common, instead, long-term tests usually include one reproductive cycle. In the present study we optimized and propose a lifespan (all life) term test using Enchytraeus crypticus (Oligochaeta). The effect of copper oxide nanoparticles (CuO-NPs) was assessed in this lifespan test and compared to copper salt (CuCl 2 ), using the same effect concentrations on reproduction (EC 50 ). Monitored endpoints included survival and reproduction over-time (202 days). Results from survival showed that CuO-NPs caused shorter life of the adults compared to CuCl 2 (control LT 50 : 218 days > CuCl 2 LT 50 : 175 days > CuO-NPs LT 50 : 145 days). The effect was even more amplified in terms of reproduction (control ET 50 : 158 days > CuCl 2 ET 50 : 138 days > CuO-NPs ET 50 : 92 days). Results suggest that CuO-NPs may cause a higher Cu effect via a trojan horse mechanism. The use of lifespan tests brings a novel concept in soil ecotoxicity, the longevity. This is a particularly important aspect when the subject is nanomaterials toxicity, where longer term exposure time is expected to reveal unpredicted effects via the current short/long-term tests. The present study confirms this higher effect for CuO-NPs.

Organisms' density can influence physiological processes related with fitness. In the present study we assessed the influence of organisms' density on the life-history parameters in two consecutive generations in Enchytraeus crypticus (Oligochaeta), a standard model in soil ecotoxicology. The densities tested were 1 (N1) and 20 (N20) organisms per replicate and 10 vs. 20 g of soil (for the 2nd generation test only). Results showed that reproductive output was affected by density, with organisms in N1 producing three times more juveniles per adult than when at N20. Organisms' length was affected by both density and space, i.e., organisms were smaller when less space available. Further, the density of parental generation (F0) had no influence on the endpoints reproduction and length assessed in F1, hence there was no transference of effects. These findings have potential implications in the standard Enchytraeid Reproduction Test, i.e. early mortality of the adults during toxicant exposure can affect the number and size of the offspring and the final results will also reflect the density related changes in reproduction.