Enhancement of soil aggregation and physical properties through fungal amendments under varying moisture conditions

Soil structure and aggregation are crucial for soil functionality, particularly under drought conditions. Saprobic soil fungi, known for their resilience in low moisture conditions, are recognized for their influence on soil aggregate dynamics. In this study, we explored the potential of fungal amendments to enhance soil aggregation and hydrological properties across different moisture regimes. We used a selection of 29 fungal isolates, recovered from soils treated under drought conditions and varying in colony density and growth rate, for single-strain inoculation into sterilized soil microcosms under either low or high moisture (≤-0.96 and -0.03 MPa, respectively). After 8 weeks, we assessed soil aggregate formation and stability, along with soil properties such as soil water content, water hydrophobicity, sorptivity, total fungal biomass and water potential. Our findings indicate that fungal inoculation altered soil hydrological properties and improved soil aggregation, with effects varying based on the fungal strains and soil moisture levels. We found a positive correlation between fungal biomass and enhanced soil aggregate formation and stabilization, achieved by connecting soil particles via hyphae and modifying soil aggregate sorptivity. The improvement in soil water potential was observed only when the initial moisture level was not critical for fungal activity. Overall, our results highlight the potential of using fungal inoculation to improve the structure of agricultural soil under drought conditions, thereby introducing new possibilities for soil management in the context of climate change.

The pleiotropic phenotype of FlbA of Aspergillus niger is explained in part by the activity of seven of its downstream-regulated transcription factors

Inactivation of flbA in Aspergillus niger results in thinner cell walls, increased cell lysis, abolished sporulation, and an increased secretome complexity. A total of 36 transcription factor (TF) genes are differentially expressed in ΔflbA. Here, seven of these genes (abaA, aslA, aslB, azf1, htfA, nosA, and srbA) were inactivated. Inactivation of each of these genes affected sporulation and, with the exception of abaA, cell wall integrity and protein secretion. The impact on secretion was strongest in the case of ΔaslA and ΔaslB that showed increased pepsin, cellulase, and amylase activity. Biomass was reduced of agar cultures of ΔabaA, ΔaslA, ΔnosA, and ΔsrbA, while biomass was higher in liquid shaken cultures of ΔaslA and ΔaslB. The ΔaslA and ΔhtfA strains showed increased resistance to H2O2, while ΔaslB was more sensitive to this reactive oxygen species. Together, inactivation of the seven TF genes impacted biomass formation, sporulation, protein secretion, and stress resistance, and thereby these genes explain at least part of the pleiotropic phenotype of ΔflbA of A. niger.

Compatible solutes determine the heat resistance of conidia

BACKGROUND

Asexually developed fungal spores (conidia) are key for the massive proliferation and dispersal of filamentous fungi. Germination of conidia and subsequent formation of a mycelium network give rise to many societal problems related to human and animal fungal diseases, post-harvest food spoilage, loss of harvest caused by plant-pathogenic fungi and moulding of buildings. Conidia are highly stress resistant compared to the vegetative mycelium and therefore even more difficult to tackle.

RESULTS

In this study, complementary approaches are used to show that accumulation of mannitol and trehalose as the main compatible solutes during spore maturation is a key factor for heat resistance of conidia. Compatible solute concentrations increase during conidia maturation, correlating with increased heat resistance of mature conidia. This maturation only occurs when conidia are attached to the conidiophore. Moreover, conidia of a mutant Aspergillus niger strain, constructed by deleting genes involved in mannitol and trehalose synthesis and consequently containing low concentrations of these compatible solutes, exhibit a sixteen orders of magnitude more sensitive heat shock phenotype compared to wild-type conidia. Cultivation at elevated temperature results in adaptation of conidia with increased heat resistance. Transcriptomic and proteomic analyses revealed two putative heat shock proteins to be upregulated under these conditions. However, conidia of knock-out strains lacking these putative heat shock proteins did not show a reduced heat resistance.

CONCLUSIONS

Heat stress resistance of fungal conidia is mainly determined by the compatible solute composition established during conidia maturation. To prevent heat resistant fungal spore contaminants, food processing protocols should consider environmental conditions stimulating compatible solute accumulation and potentially use compatible solute biosynthesis as a novel food preservation target.

The C2H2 transcription factor SltA is required for germination and hyphal development in Aspergillus fumigatus

Germination of inhaled Aspergillus fumigatus conidia is a necessary sequitur for infection. Germination of conidia starts with the breaking of dormancy, which is initiated by an increase of the cellular perimeter in a process termed isotropic growth. This swelling phase is followed by polarized growth, resulting in the formation of a germ tube. The multinucleate tubular cells exhibit tip growth from the hyphae, after which lateral branches emerge to form the mycelial network. The regulatory mechanisms governing conidial germination are not well defined. In this study, we identified a novel role for the transcription factor SltA in the orchestration of germination and hyphal development. Conidia lacking sltA fail to appropriately regulate isotropic growth and begin to swell earlier and subsequently switch to polarized growth faster. Additionally, hyphal development is distorted in a ∆sltA isolate as hyphae are hyper-branching and wider, and show branching at the apical tip. ∆sltA conidia are more tolerant to cell wall stressors on minimal medium compared to the wild-type (WT) strain. A transcriptome analysis of different stages of early growth was carried out to assess the regulatory role of SltA. Null mutants generated for three of the most dysregulated genes showed rapid germ tube emergence. Distinct from the phenotype observed for ∆sltA, conidia from these strains lacked defects in isotropic growth, but switched to polarized growth faster. Here, we characterize and describe several genes in the regulon of SltA, highlighting the complex nature of germination.IMPORTANCEAspergillus fumigatus is the main human fungal pathogen causing aspergillosis. For this fungus, azoles are the most commonly used antifungal drugs for treatment of aspergillosis. However, the prevalence of azole resistance is alarmingly increasing and linked with elevated mortality. Germination of conidia is crucial within its asexual life cycle and plays a critical role during the infection in the human host. Precluding germination could be a promising strategy considering the role of germination in Aspergillus spp. pathogenicity. Here, we identify a novel role for SltA in appropriate maintenance of dormancy, germination, and hyphal development. Three genes in the regulon of SltA were also essential for appropriate germination of conidia. With an expanding knowledge of germination and its different morphotypes, more advances can be made toward potential anti-germination targets for therapy.

Endosymbionts: Bacterial hijacking of fungi?

Bacteria inside fungal hyphae allow the fungus Rhizopus microsporus to form spores and operate via effectors in 'stealth' mode. When the functionality of one effector is taken away, bacteria are captured in septated cells and die.

Fungal Planet description sheets: 1550-1613

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 Poecilometis sp. Bolivia, Lecanora menthoides on sandstone, in open semi-desert montane areas, Sticta monlueckiorum corticolous in a forest, Trichonectria epimegalosporae on apothecia of corticolous Megalospora sulphurata var. sulphurata, Trichonectria puncteliae on the thallus of Punctelia borreri. Brazil, Catenomargarita pseudocercosporicola (incl. Catenomargarita gen. nov.) hyperparasitic on Pseudocercospora fijiensis on leaves of Musa acuminata, Tulasnella restingae on protocorms and roots of Epidendrum fulgens. Bulgaria, Anthracoidea umbrosae on Carex spp. Croatia, Hymenoscyphus radicis from surface-sterilised, asymptomatic roots of Microthlaspi erraticum, Orbilia multiserpentina on wood of decorticated branches of Quercus pubescens. France, Calosporella punctatispora on dead corticated twigs of Aceropalus. French West Indies (Martinique), Eutypella lechatii on dead corticated palm stem. Germany, Arrhenia alcalinophila on loamy soil. Iceland, Cistella blauvikensis on dead grass (Poaceae). India, Fulvifomes maritimus on living Peltophorum pterocarpum, Fulvifomes natarajanii on dead wood of Prosopis juliflora, Fulvifomes subazonatus on trunk of Azadirachta indica, Macrolepiota bharadwajii on moist soil near the forest, Narcissea delicata on decaying elephant dung, Paramyrothecium indicum on living leaves of Hibiscus hispidissimus, Trichoglossum syamviswanathii on moist soil near the base of a bamboo plantation. Iran, Vacuiphoma astragalicola from stem canker of Astragalus sarcocolla. Malaysia, Neoeriomycopsis fissistigmae (incl. Neoeriomycopsidaceae fam. nov.) on leaf spots on flower Fissistigma sp. Namibia, Exophiala lichenicola lichenicolous on Acarospora cf. luederitzensis. Netherlands, Entoloma occultatum on soil, Extremus caricis on dead leaves of Carex sp., Inocybe pseudomytiliodora on loamy soil. Norway, Inocybe guldeniae on calcareous soil, Inocybe rupestroides on gravelly soil. Pakistan, Hymenagaricus brunneodiscus on soil. Philippines, Ophiocordyceps philippinensis parasitic on Asilus sp. Poland, Hawksworthiomyces ciconiae isolated from Ciconia ciconia nest, Plectosphaerella vigrensis from leaf spots on Impatiens noli-tangere, Xenoramularia epitaxicola from sooty mould community on Taxus baccata. Portugal, Inocybe dagamae on clay soil. Saudi Arabia, Diaporthe jazanensis on branches of Coffea arabica. South Africa, Alternaria moraeae on dead leaves of Moraea sp., Bonitomyces buffels-kloofinus (incl. Bonitomyces gen. nov.) on dead twigs of unknown tree, Constrictochalara koukolii on living leaves of Itea rhamnoides colonised by a Meliola sp., Cylindromonium lichenophilum on Parmelina tiliacea, Gamszarella buffelskloofina (incl. Gamszarella gen. nov.) on dead insect, Isthmosporiella africana (incl. Isthmosporiella gen. nov.) on dead twigs of unknown tree, Nothoeucasphaeria buffelskloofina (incl. Nothoeucasphaeria gen. nov.), on dead twigs of unknown tree, Nothomicrothyrium beaucarneae (incl. Nothomicrothyrium gen. nov.) on dead leaves of Beaucarnea stricta, Paramycosphaerella proteae on living leaves of Protea caffra, Querciphoma foliicola on leaf litter, Rachicladosporium conostomii on dead twigs of Conostomium natalense var. glabrum, Rhamphoriopsis synnematosa on dead twig of unknown tree, Waltergamsia mpumalanga on dead leaves of unknown tree. Spain, Amanita fulvogrisea on limestone soil, in mixed forest, Amanita herculis in open Quercus forest, Vuilleminia beltraniae on Cistus symphytifolius. Sweden, Pachyella pulchella on decaying wood on sand-silt riverbank. Thailand, Deniquelata cassiae on dead stem of Cassia fistula, Stomiopeltis thailandica on dead twigs of Magnolia champaca. Ukraine, Circinaria podoliana on natural limestone outcrops, Neonematogonum carpinicola (incl. Neonematogonum gen. nov.) on dead branches of Carpinus betulus. USA, Exophiala wilsonii water from cooling tower, Hygrophorus aesculeticola on soil in mixed forest, and Neocelosporium aereum from air in a house attic. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Costa MM, Kandemir H, et al. 2023. Fungal Planet description sheets: 1550-1613. Persoonia 51: 280-417. doi: 10.3767/persoonia.2023.51.08.

Da Vinci's yeast: Blastobotrys davincii f.a., sp. nov

A new species of the yeast genus Blastobotrys was discovered during a worldwide survey of culturable xerophilic fungi in house dust. Several culture-dependent and independent studies from around the world detected the same species from a wide range of substrates including indoor air, cave wall paintings, bats, mummies, and the iconic self-portrait of Leonardo da Vinci from ca 1512. However, none of these studies identified their strains, clones, or OTUs as Blastobotrys. We introduce the new species as Blastobotrys davincii f.a., sp. nov. (holotype CBS H-24879) and delineate it from other species using morphological, phylogenetic, and physiological characters. The new species of asexually (anamorphic) budding yeast is classified in Trichomonascaceae and forms a clade along with its associated sexual state genus Trichomonascus. Despite the decade-old requirement to use a single generic name for fungi, both names are still used. Selection of the preferred name awaits a formal nomenclatural proposal. We present arguments for adopting Blastobotrys over Trichomonascus and introduce four new combinations as Blastobotrys allociferrii (≡ Candida allociferrii), B. fungorum (≡ Sporothrix fungorum), B. mucifer (≡ Candida mucifera), and Blastobotrys vanleenenianus (≡ Trichomonascus vanleenenianus). We provide a nomenclatural review and an accepted species list for the 37 accepted species in the Blastobotrys/Trichomonascus clade. Finally, we discuss the identity of the DNA clones detected on the da Vinci portrait, and the importance of using appropriate media to isolate xerophilic or halophilic fungi.

New and Interesting Fungi. 5

Nine new genera, 17 new species, nine new combinations, seven epitypes, three lectotypes, one neotype, and 14 interesting new host and / or geographical records are introduced in this study. New genera: Neobarrmaelia (based on Neobarrmaelia hyphaenes), Neobryochiton (based on Neobryochiton narthecii), Neocamarographium (based on Neocamarographium carpini), Nothocladosporium (based on Nothocladosporium syzygii), Nothopseudocercospora (based on Nothopseudocercospora dictamni), Paracamarographium (based on Paracamarographium koreanum), Pseudohormonema (based on Pseudohormonema sordidus), Quasiphoma (based on Quasiphoma hyphaenes), Rapidomyces (based on Rapidomyces narthecii). New species: Ascocorticium sorbicola (on leaves of Sorbus aucuparia, Belgium), Dactylaria retrophylli (on leaves of Retrophyllum rospigliosii, Colombia), Dactylellina miltoniae (on twigs of Miltonia clowesii, Colombia), Exophiala eucalyptigena (on dead leaves of Eucalyptus viminalis subsp. viminalis supporting Idolothrips spectrum, Australia), Idriellomyces syzygii (on leaves of Syzygium chordatum, South Africa), Microcera lichenicola (on Parmelia sulcata, Netherlands), Neobarrmaelia hyphaenes (on leaves of Hyphaene sp., South Africa), Neobryochiton narthecii (on dead leaves of Narthecium ossifragum, Netherlands), Niesslia pseudoexilis (on dead leaf of Quercus petraea, Serbia), Nothocladosporium syzygii (on leaves of Syzygium chordatum, South Africa), Nothotrimmatostroma corymbiae (on leaves of Corymbia henryi, South Africa), Phaeosphaeria hyphaenes (on leaves of Hyphaene sp., South Africa), Pseudohormonema sordidus (on a from human pacemaker, USA), Quasiphoma hyphaenes (on leaves of Hyphaene sp., South Africa), Rapidomyces narthecii (on dead leaves of Narthecium ossifragum, Netherlands), Reticulascus parahennebertii (on dead culm of Juncus inflexus, Netherlands), Scytalidium philadelphianum (from compressed air in a factory, USA). New combinations: Neobarrmaelia serenoae, Nothopseudocercospora dictamni, Dothiora viticola, Floricola sulcata, Neocamarographium carpini, Paracamarographium koreanum, Rhexocercosporidium bellocense, Russula lilacina. Epitypes: Elsinoe corni (on leaves of Cornus florida, USA), Leptopeltis litigiosa (on dead leaf fronds of Pteridium aquilinum, Netherlands), Nothopseudocercospora dictamni (on living leaves of Dictamnus albus, Russia), Ramularia arvensis (on leaves of Potentilla reptans, Netherlands), Rhexocercosporidium bellocense (on leaves of Verbascum sp., Germany), Rhopographus filicinus (on dead leaf fronds of Pteridium aquilinum, Netherlands), Septoria robiniae (on leaves of Robinia pseudoacacia, Belgium). Lectotypes: Leptopeltis litigiosa (on Pteridium aquilinum, France), Rhopographus filicinus (on dead leaf fronds of Pteridium aquilinum, Netherlands), Septoria robiniae (on leaves of Robinia pseudoacacia, Belgium). Neotype: Camarographium stephensii (on dead leaf fronds of Pteridium aquilinum, Netherlands). Citation: Crous PW, Begoude BAD, Boers J, Braun U, Declercq B, Dijksterhuis J, Elliott TF, Garay-Rodriguez GA, Jurjević Ž, Kruse J, Linde CC, Loyd A, Mound L, Osieck ER, Rivera-Vargas LI, Quimbita AM, Rodas CA, Roux J, Schumacher RK, Starink-Willemse M, Thangavel R, Trappe JM, van Iperen AL, Van Steenwinkel C, Wells A, Wingfield MJ, Yilmaz N, Groenewald JZ (2022) New and Interesting Fungi. 5. Fungal Systematics and Evolution 10: 19-90. doi: 10.3114/fuse.2022.10.02.

S5.3b Fungal spores: Initiators of colonization and infection

S5.3 Cellular pleomorphism and fungal virulence, September 22, 2022, 3:00 PM - 4:30 PM

Fungi produce asexual and sexual spores for reproduction and distribution, which can be both in space and time. Distribution in space occurs, by air movement, but also, by water or other vectors such as living organisms. Filamentous fungi from the division Ascomycota that belong to the order Eurotiales produce asexual spores called conidia. Conidia are moderately stress-tolerant cells and are able to survive unfavorable conditions such as thermal stress, dehydration, osmotic pressure, oxidative stress, variations in pH, and UV. For example, conidia of the fungus Penicillium chrysogenum are isolated worldwide and must be regarded as cosmopolitan. In many cases, conidia might ‘land’ closely to the location of production, but still many spores making into the higher air layers. There is indirect evidence that spores may be able to travel large distances through the air. For example, Aspergillus sydowii conidia have been suggested to travel over thousands of kilometers from the Sahara Desert to the Caribbean reefs.

 

Distribution in time is occurring as stress-resistant cells remain dormant at one location for an extended period, awaiting conditions that are more favorable for growth. Some ascospores (sexual spores) are extremely stress-resistant and dormant for very long periods. Other species show extended dormancy in a dried state. As microbial species are inherently variable, stress resistance varies between strains from the same species. For example, conidial heat resistance (D60) of various strains of the fungus Paecilomyces variotii ranged between 3.5 to 27.6 min. This intraspecific variation could have profound consequences on diagnostics, virulence, and antifungal treatment in clinical settings.

 

For conidial germination in most filamentous fungi, the presence of nutrients such as inorganic salts, sugars, and amino acids is required. The swelling phase of conidia is also called isotropic growth. Swollen conidia direct the growth to one side of the cell to grow in a polarized fashion, which leads to the formation of a germ tube (polarized growth). There is a notable drop in stress resistance during isotropic and polarized growth and genes expressed during these stages might represent novel targets for fungal infection.

Multiple Hybridization Events Punctuate the Evolutionary Trajectory of Malassezia furfur

Malassezia species are important fungal skin commensals and are part of the normal microbiota of humans and other animals. However, under certain circumstances these fungi can also display a pathogenic behavior. For example, Malassezia furfur is a common commensal of human skin and yet is often responsible for skin disorders but also systemic infections. Comparative genomics analysis of M. furfur revealed that some isolates have a hybrid origin, similar to several other recently described hybrid fungal pathogens. Because hybrid species exhibit genomic plasticity that can impact phenotypes, we sought to elucidate the genomic evolution and phenotypic characteristics of M. furfur hybrids in comparison to their parental lineages. To this end, we performed a comparative genomics analysis between hybrid strains and their presumptive parental lineages and assessed phenotypic characteristics. Our results provide evidence that at least two distinct hybridization events occurred between the same parental lineages and that the parental strains may have originally been hybrids themselves. Analysis of the mating-type locus reveals that M. furfur has a pseudobipolar mating system and provides evidence that after sexual liaisons of mating compatible cells, hybridization involved cell-cell fusion leading to a diploid/aneuploid state. This study provides new insights into the evolutionary trajectory of M. furfur and contributes with valuable genomic resources for future pathogenicity studies. IMPORTANCEMalassezia furfur is a common commensal member of human/animal microbiota that is also associated with several pathogenic states. Recent studies report involvement of Malassezia species in Crohn's disease, a type of inflammatory bowel disease, pancreatic cancer progression, and exacerbation of cystic fibrosis. A recent genomics analysis of M. furfur revealed the existence of hybrid isolates and identified their putative parental lineages. In this study, we explored the genomic and phenotypic features of these hybrids in comparison to their putative parental lineages. Our results revealed the existence of a pseudobipolar mating system in this species and showed evidence for the occurrence of multiple hybridization events in the evolutionary trajectory of M. furfur. These findings significantly advance our understanding of the evolution of this commensal microbe and are relevant for future studies exploring the role of hybridization in the adaptation to new niches or environments, including the emergence of pathogenicity.

New and Interesting Fungi. 4

An order, family and genus are validated, seven new genera, 35 new species, two new combinations, two epitypes, two lectotypes, and 17 interesting new host and / or geographical records are introduced in this study. Validated order, family and genus: Superstratomycetales and Superstratomycetaceae (based on Superstratomyces ). New genera: Haudseptoria (based on Haudseptoria typhae); Hogelandia (based on Hogelandia lambearum); Neoscirrhia (based on Neoscirrhia osmundae); Nothoanungitopsis (based on Nothoanungitopsis urophyllae); Nothomicrosphaeropsis (based on Nothomicrosphaeropsis welwitschiae); Populomyces (based on Populomyces zwinianus); Pseudoacrospermum (based on Pseudoacrospermum goniomae). New species: Apiospora sasae on dead culms of Sasa veitchii (Netherlands); Apiospora stipae on dead culms of Stipa gigantea (Spain); Bagadiella eucalyptorum on leaves of Eucalyptus sp. (Australia); Calonectria singaporensis from submerged leaf litter (Singapore); Castanediella neomalaysiana on leaves of Eucalyptus sp. (Malaysia); Colletotrichum pleopeltidis on leaves of Pleopeltis sp. (South Africa); Coniochaeta deborreae from soil (Netherlands); Diaporthe durionigena on branches of Durio zibethinus (Vietnam); Floricola juncicola on dead culm of Juncus sp. (France); Haudseptoria typhae on leaf sheath of Typha sp. (Germany); Hogelandia lambearum from soil (Netherlands); Lomentospora valparaisensis from soil (Chile); Neofusicoccum mystacidii on dead stems of Mystacidium capense (South Africa); Neomycosphaerella guibourtiae on leaves of Guibourtia sp. (Angola); Niesslia neoexosporioides on dead leaves of Carex paniculata (Germany); Nothoanungitopsis urophyllae on seed capsules of Eucalyptus urophylla (South Africa); Nothomicrosphaeropsis welwitschiae on dead leaves of Welwitschia mirabilis (Namibia); Paracremonium bendijkiorum from soil (Netherlands); Paraphoma ledniceana on dead wood of Buxus sempervirens (Czech Republic); Paraphoma salicis on leaves of Salix cf. alba (Ukraine); Parasarocladium wereldwijsianum from soil (Netherlands); Peziza ligni on masonry and plastering (France); Phyllosticta phoenicis on leaves of Phoenix reclinata (South Africa); Plectosphaerella slobbergiarum from soil (Netherlands); Populomyces zwinianus from soil (Netherlands); Pseudoacrospermum goniomae on leaves of Gonioma kamassi (South Africa); Pseudopyricularia festucae on leaves of Festuca californica (USA); Sarocladium sasijaorum from soil (Netherlands); Sporothrix hypoxyli in sporocarp of Hypoxylon petriniae on Fraxinus wood (Netherlands); Superstratomyces albomucosus on Pycnanthus angolensis (Netherlands); Superstratomyces atroviridis on Pinus sylvestris (Netherlands); Superstratomyces flavomucosus on leaf of Hakea multilinearis (Australia); Superstratomyces tardicrescens from human eye specimen (USA); Taeniolella platani on twig of Platanus hispanica (Germany), and Tympanis pini on twigs of Pinus sylvestris (Spain). Citation: Crous PW, Hernández-Restrepo M, Schumacher RK, Cowan DA, Maggs-Kölling G, Marais E, Wingfield MJ, Yilmaz N, Adan OCG, Akulov A, Álvarez Duarte E, Berraf-Tebbal A, Bulgakov TS, Carnegie AJ, de Beer ZW, Decock C, Dijksterhuis J, Duong TA, Eichmeier A, Hien LT, Houbraken JAMP, Khanh TN, Liem NV, Lombard L, Lutzoni FM, Miadlikowska JM, Nel WJ, Pascoe IG, Roets F, Roux J, Samson RA, Shen M, Spetik M, Thangavel R, Thanh HM, Thao LD, van Nieuwenhuijzen EJ, Zhang JQ, Zhang Y, Zhao LL, Groenewald JZ (2021). New and Interesting Fungi. 4. Fungal Systematics and Evolution 7: 255-343. doi: 10.3114/fuse.2021.07.13.

Preservation stress resistance of melanin deficient conidia from Paecilomyces variotii and Penicillium roqueforti mutants generated via CRISPR/Cas9 genome editing

Background

The filamentous fungi Paecilomyces variotii and Penicillium roqueforti are prevalent food spoilers and are of interest as potential future cell factories. A functional CRISPR/Cas9 genome editing system would be beneficial for biotechnological advances as well as future (genetic) research in P. variotii and P. roqueforti.

Results

Here we describe the successful implementation of an efficient AMA1-based CRISPR/Cas9 genome editing system developed for Aspergillus niger in P. variotii and P. roqueforti in order to create melanin deficient strains. Additionally, kusA⁻ mutant strains with a disrupted non-homologous end-joining repair mechanism were created to further optimize and facilitate efficient genome editing in these species. The effect of melanin on the resistance of conidia against the food preservation stressors heat and UV-C radiation was assessed by comparing wild-type and melanin deficient mutant conidia.

Conclusions

Our findings show the successful use of CRISPR/Cas9 genome editing and its high efficiency in P. variotii and P. roqueforti in both wild-type strains as well as kusA⁻ mutant background strains. Additionally, we observed that melanin deficient conidia of three food spoiling fungi were not altered in their heat resistance. However, melanin deficient conidia had increased sensitivity towards UV-C radiation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40694-021-00111-w.

Identifying Conserved Generic Aspergillus spp. Co-Expressed Gene Modules Associated with Germination Using Cross-Platform and Cross-Species Transcriptomics

Aspergillus spp. is an opportunistic human pathogen that may cause a spectrum of pulmonary diseases. In order to establish infection, inhaled conidia must germinate, whereby they break dormancy, start to swell, and initiate a highly polarized growth process. To identify critical biological processes during germination, we performed a cross-platform, cross-species comparative analysis of germinating A. fumigatus and A. niger conidia using transcriptional data from published RNA-Seq and Affymetrix studies. A consensus co-expression network analysis identified four gene modules associated with stages of germination. These modules showed numerous shared biological processes between A. niger and A. fumigatus during conidial germination. Specifically, the turquoise module was enriched with secondary metabolism, the black module was highly enriched with protein synthesis, the darkgreen module was enriched with protein fate, and the blue module was highly enriched with polarized growth. More specifically, enriched functional categories identified in the blue module were vesicle formation, vesicular transport, tubulin dependent transport, actin-dependent transport, exocytosis, and endocytosis. Genes important for these biological processes showed similar expression patterns in A. fumigatus and A. niger, therefore, they could be potential antifungal targets. Through cross-platform, cross-species comparative analysis, we were able to identify biologically meaningful modules shared by A. fumigatus and A. niger, which underscores the potential of this approach.

Cathelicidin-inspired antimicrobial peptides as novel antifungal compounds

Fungal infections in humans are increasing worldwide and are currently mostly treated with a relative limited set of antifungals. Resistance to antifungals is increasing, for example, in Aspergillus fumigatus and Candida auris, and expected to increase for many medically relevant fungal species in the near future. We have developed and patented a set of cathelicidin-inspired antimicrobial peptides termed 'PepBiotics'. These peptides were initially selected for their bactericidal activity against clinically relevant Pseudomonas aeruginosa and Staphylococcus aureus isolates derived from patients with cystic fibrosis and are active against a wide range of bacteria (ESKAPE pathogens). We now report results from studies that were designed to investigate the antifungal activity of PepBiotics against a set of medically relevant species encompassing species of Aspergillus, Candida, Cryptococcus, Fusarium, Malassezia, and Talaromyces. We characterized a subset of PepBiotics and show that these peptides strongly affected metabolic activity and/or growth of a set of medically relevant fungal species, including azole-resistant A. fumigatus isolates. PepBiotics showed a strong inhibitory activity against a large variety of filamentous fungi and yeasts species at low concentrations (≤1 μM) and were fungicidal for at least a subset of these fungal species. Interestingly, the concentration of PepBiotics required to interfere with growth or metabolic activity varied between different fungal species or even between isolates of the same fungal species. This study shows that PepBiotics display strong potential for use as novel antifungal compounds to fight a large variety of clinically relevant fungal species.

From colony to rodlet: "A six meter long portrait of the xerophilic fungus Aspergillus restrictus decorates the hall of the Westerdijk institute."

The extreme xerophilic fungus Aspergillus restrictus is used as a model for a large artwork created out of five microscopic pictures in total measuring 80 cm by 624 cm. The artwork is printed on aluminium and located at the entrance of the Westerdijk Institute, Utrecht, The Netherlands. The first picture is made from a colony of the fungus, which has a dimension of 1 cm and the last picture shows details of ornamentation on conidia and phialides of the fungus. The first two pictures of the artwork are made using a unique method of light microscopy in which many hundreds of pictures are made at different focal depths resulting in high detail and resolution of the pictures. For three other pictures, cryo-electron scanning microscopy was used including both a conventional system for lower magnification and a field emission scanning electron microscope for high resolution micrographs. The range of magnification is, at real size, between 78 and 63,000 times. When the observer passes the artwork it acts like a virtual microscope, just by walking past it you zoom-in to the smallest possible details. This coherent increase of magnification of one fungus, with very high quality light- and electron microscopy micrographs, shows different layers of fungal organization and emergent properties. These include the occurrence of secondary outcrops of hyphae and conidiophores in a colony; the formation of a stipe on a thin aerial hyphae; the presence and formation of characteristic structures on stipes, vesicles and phialides and a continuous zone between the forming conidia and phialides.

Comparing thermal inactivation to a combined process of moderate heat and high pressure: Effect on ascospores in strawberry puree

High pressure processing is a mild preservation process that inactivates pathogenic and spoilage micro-organisms in food products, but preserves the fresh characteristics of a product. Compared to untreated product, an enhanced shelf life is obtained during refrigerated storage. Knowledge on the use of high pressure pasteurisation aimed for ambient storage is limited. The aim of this research was to investigate if a combination of high pressure and moderate heat could be used to produce a shelf-stable high-acid fruit product. Ascospores of the heat resistant fungi Talaromyces macrosporus and Aspergillus fischeri were added to fresh strawberry puree that served as a model system. The effect of the processing steps and storage at ambient temperature for 2 weeks was studied on viability of the ascospores. A preheating step at 69 °C/2 min resulted in full or partial activation of A. fischeri and T. macrosporus spores, respectively. The pressure build-up by the process without any holding time resulted in additional activation of spores. A combination of moderate heat (maximum 85-90 °C) and high pressure (500-700 MPa) for holding times up to 13 min inactivated these highly resistant spores much faster than a heat treatment alone. At T_max = 85 °C and 600 MPa the spores of T. macrosporus and A. fischeri were inactivated by 5.0 and 5.5 log₁₀ after 13 and 7 min, respectively. At T_max = 85 °C the heat treatment alone did not reduce the viability of these spores up to 60 min of treatment. At T_max = 90 °C the holding time of the combined pressure-heat treatment could be reduced to obtain the same degree of inactivation of the heat resistant fungi. In addition, treated and untreated ascospores in strawberry puree were stored for 14 days at room temperature to evaluate delayed outgrowth of spores. Untreated ascospores of A. fischeri were activated by storage in the puree. However, at conditions combining high pressure ≥ 600 MPa with T_max ≥ 85 °C for 13 min, heat resistant fungi were successfully inactivated. This research showed that a combination of moderate heat and pressure can drastically improve the effectiveness to inactivate heat-resistant ascospores in a high-acid fruit product compared to a heat treatment, potentially resulting in a better product quality.

The Third International Symposium on Fungal Stress - ISFUS

Stress is a normal part of life for fungi, which can survive in environments considered inhospitable or hostile for other organisms. Due to the ability of fungi to respond to, survive in, and transform the environment, even under severe stresses, many researchers are exploring the mechanisms that enable fungi to adapt to stress. The International Symposium on Fungal Stress (ISFUS) brings together leading scientists from around the world who research fungal stress. This article discusses presentations given at the third ISFUS, held in São José dos Campos, São Paulo, Brazil in 2019, thereby summarizing the state-of-the-art knowledge on fungal stress, a field that includes microbiology, agriculture, ecology, biotechnology, medicine, and astrobiology.

The most heat-resistant conidia observed to date are formed by distinct strains of Paecilomyces variotii

Fungi colonize habitats by means of spores. These cells are stress‐resistant compared with growing fungal cells. Fungal conidia, asexual spores, formed by cosmopolitan fungal genera like Penicillium, Aspergillus and Peacilomyces are dispersed by air. They are present in places where food products are stored and as a result, they cause food spoilage. Here, we determined the heterogeneity of heat resistance of conidia between and within strains of Paecilomyces variotii, a spoiler of foods such as margarine, fruit juices, canned fruits and non‐carbonized sodas. Out of 108 strains, 31 isolates showed a conidial survival >10% after a 10‐min‐heat treatment at 59°C. Three strains with different conidial heat resistance were selected for further phenotyping. Conidia of DTO 212‐C5 and DTO 032‐I3 showed 0.3% and 2.6% survival in the screening respectively, while survival of DTO 217‐A2 conidia was >10%. The decimal reduction times of these strains at 60°C (D₆₀ value) were 3.7 ± 0.08, 5.5 ± 0.35 and 22.9 ± 2.00 min respectively. Further in‐depth analysis revealed that the three strains showed differences in morphology, spore size distributions, compatible solute compositions and growth under salt stress. Conidia of DTO 217‐A2 are the most heat‐resistant reported so far. The ecological consequences of this heterogeneity of resistance, including food spoilage, are discussed.

Hydrophobin gene deletion and environmental growth conditions impact mechanical properties of mycelium by affecting the density of the material

Filamentous fungi colonize substrates by forming a mycelium. This network of hyphae can be used as a bio-based material. Here, we assessed the impact of environmental growth conditions and deletion of the hydrophobin gene sc3 on material properties of the mycelium of the mushroom forming fungus Schizophyllum commune. Thermogravimetric analysis showed that Δsc3 mycelium retained more water with increasing temperature when compared to the wild type. The Young's modulus (E) of the mycelium ranged between 438 and 913 MPa when the wild type strain was grown in the dark or in the light at low or high CO₂ levels. This was accompanied by a maximum tensile strength (σ) of 5.1-9.6 MPa. In contrast, E and σ of the Δsc3 strain were 3-4- fold higher with values of 1237-2727 MPa and 15.6-40.4 MPa, respectively. These values correlated with mycelium density, while no differences in chemical composition of the mycelia were observed as shown by ATR-FTIR. Together, genetic modification and environmental growth conditions impact mechanical properties of the mycelium by affecting the density of the mycelium. As a result, mechanical properties of wild type mycelium were similar to those of natural materials, while those of Δsc3 were more similar to thermoplastics.

Functional optics of glossy buttercup flowers

Buttercup (Ranunculus spp.) flowers are exceptional because they feature a distinct gloss (mirror-like reflection) in addition to their matte-yellow coloration. We investigated the optical properties of yellow petals of several Ranunculus and related species using (micro)spectrophotometry and anatomical methods. The contribution of different petal structures to the overall visual signal was quantified using a recently developed optical model. We show that the coloration of glossy buttercup flowers is due to a rare combination of structural and pigmentary coloration. A very flat, pigment-filled upper epidermis acts as a thin-film reflector yielding the gloss, and additionally serves as a filter for light backscattered by the strongly scattering starch and mesophyll layers, which yields the matte-yellow colour. We discuss the evolution of the gloss and its two likely functions: it provides a strong visual signal to insect pollinators and increases the reflection of sunlight to the centre of the flower in order to heat the reproductive organs.

Physically Triggered Morphology Changes in a Novel Acremonium Isolate Cultivated in Precisely Engineered Microfabricated Environments

Fungi are strongly affected by their physical environment. Microfabrication offers the possibility of creating new culture environments and ecosystems with defined characteristics. Here, we report the isolation of a novel member of the fungal genus Acremonium using a microengineered cultivation chip. This isolate was unusual in that it organizes into macroscopic structures when initially cultivated within microwells with a porous aluminum oxide (PAO) base. These “templated mycelial bundles” (TMB) were formed from masses of parallel hyphae with side branching suppressed. TMB were highly hydrated, facilitating the passive movement of solutes along the bundle. By using a range of culture chips, it was deduced that the critical factors in triggering the TMB were growth in microwells from 50 to 300 μm in diameter with a PAO base. Cultivation experiments, using spores and pigments as tracking agents, indicate that bulk growth of the TMB occurs at the base. TMB morphology is highly coherent and is maintained after growing out of the microwells. TMB can explore their environment by developing unbundled lateral hyphae; TMB only followed if nutrients were available. Because of the ease of fabricating numerous microstructures, we suggest this is a productive approach for exploring morphology and growth in multicellular microorganisms and microbial communities.

Putting the waste out: a proposed mechanism for transmission of the mycoparasite Escovopsis between leafcutter ant colonies

The attine ant system is a remarkable example of symbiosis. An antagonistic partner within this system is the fungal parasite Escovopsis, a genus specific to the fungal gardens of the Attini. Escovopsis parasitizes the Leucoagaricus symbiont that leaf-cutting ants (Acromyrmex, Atta) have been farming over the past 8-12 Myr. However, it has been a puzzle how Escovopsis reaches its host. During a seasonal survey of nests of Acromyrmex subterraneus subterraneus in Atlantic rainforest in Brazil, Escovopsis was detected in all the sampled fungal garden waste tips or middens (n = 111). Middens were built strategically; always below the nest entrances. Here, we report the first evidence of a putative mechanism for horizontal transmission of Escovopsis between attine colonies. It is posited that leaf-cutting ants pick up the spores from soil and litter during foraging and vector the mycoparasite between attine colonies. Field and laboratory experiments, using At. laevigata and Ac. subterraneus subterraneus, confirm that Escovopsis spores are phoretic, and have an inbuilt dormancy, broken by the presence of their Leucoagaricus host. However, in the coevolutionary arms race, Atta ants may lose out-despite most species in the genus investing in a more advanced waste disposal system-due to the insanitary habits of their Acromyrmex neighbours.

Glycerol enhances fungal germination at the water-activity limit for life

For the most-extreme fungal xerophiles, metabolic activity and cell division typically halts between 0.700 and 0.640 water activity (approximately 70.0-64.0% relative humidity). Here, we investigate whether glycerol can enhance xerophile germination under acute water-activity regimes, using an experimental system which represents the biophysical limit of Earth's biosphere. Spores from a variety of species, including Aspergillus penicillioides, Eurotium halophilicum, Xerochrysium xerophilum (formerly Chrysosporium xerophilum) and Xeromyces bisporus, were produced by cultures growing on media supplemented with glycerol (and contained up to 189 mg glycerol g dry spores-1 ). The ability of these spores to germinate, and the kinetics of germination, were then determined on a range of media designed to recreate stresses experienced in microbial habitats or anthropogenic systems (with water-activities from 0.765 to 0.575). For A. penicillioides, Eurotium amstelodami, E. halophilicum, X. xerophilum and X. bisporus, germination occurred at lower water-activities than previously recorded (0.640, 0.685, 0.651, 0.664 and 0.637 respectively). In addition, the kinetics of germination at low water-activities were substantially faster than those reported previously. Extrapolations indicated theoretical water-activity minima below these values; as low as 0.570 for A. penicillioides and X. bisporus. Glycerol is present at high concentrations (up to molar levels) in many types of microbial habitat. We discuss the likely role of glycerol in expanding the water-activity limit for microbial cell function in relation to temporal constraints and location of the microbial cell or habitat. The findings reported here have also critical implications for understanding the extremes of Earth's biosphere; for understanding the potency of disease-causing microorganisms; and in biotechnologies that operate at the limits of microbial function.

Aspergillus section Nidulantes (formerly Emericella): Polyphasic taxonomy, chemistry and biology

Aspergillus section Nidulantes includes species with striking morphological characters, such as biseriate conidiophores with brown-pigmented stipes, and if present, the production of ascomata embedded in masses of Hülle cells with often reddish brown ascospores. The majority of species in this section have a sexual state, which were named Emericella in the dual name nomenclature system. In the present study, strains belonging to subgenus Nidulantes were subjected to multilocus molecular phylogenetic analyses using internal transcribed spacer region (ITS), partial β-tubulin (BenA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) sequences. Nine sections are accepted in subgenus Nidulantes including the new section Cavernicolus. A polyphasic approach using morphological characters, extrolites, physiological characters and phylogeny was applied to investigate the taxonomy of section Nidulantes. Based on this approach, section Nidulantes is subdivided in seven clades and 65 species, and 10 species are described here as new. Morphological characters including colour, shape, size, and ornamentation of ascospores, shape and size of conidia and vesicles, growth temperatures are important for identifying species. Many species of section Nidulantes produce the carcinogenic mycotoxin sterigmatocystin. The most important mycotoxins in Aspergillus section Nidulantes are aflatoxins, sterigmatocystin, emestrin, fumitremorgins, asteltoxins, and paxillin while other extrolites are useful drugs or drug lead candidates such as echinocandins, mulundocandins, calbistrins, varitriols, variecolins and terrain. Aflatoxin B₁ is produced by four species: A. astellatus, A. miraensis, A. olivicola, and A. venezuelensis.

The Indoor Fungus Cladosporium halotolerans Survives Humidity Dynamics Markedly Better than Aspergillus niger and Penicillium rubens despite Less Growth at Lowered Steady-State Water Activity

Indoor fungi cause damage in houses and are a potential threat to human health. Indoor fungal growth requires water, for which the terms water activity (aw) and relative humidity (RH) are used. The ability of the fungi Aspergillus niger, Cladosporium halotolerans, and Penicillium rubens at different developmental stages to survive changes in aw dynamics was studied. Fungi grown on media with high aw were transferred to a controlled environment with low RH and incubated for 1 week. Growth of all developmental stages was halted during incubation at RHs below 75%, while growth continued at 84% RH. Swollen conidia, germlings, and microcolonies of A. niger and P. rubens could not reinitiate growth when retransferred from an RH below 75% to a medium with high aw All developmental stages of C. halotolerans showed growth after retransfer from 75% RH. Dormant conidia survived retransfer to medium with high aw in all cases. In addition, retransfer from 84% RH to medium with high aw resulted in burst hyphal tips for Aspergillus and Penicillium Cell damage of hyphae of these fungi after incubation at 75% RH was already visible after 2 h, as observed by staining with the fluorescent dye TOTO-1. Thus, C. halotolerans is more resistant to aw dynamics than A. niger and P. rubens, despite its limited growth compared to that of these fungi at a lowered steady-state aw The survival strategy of this phylloplane fungus in response to the dynamics of aw is discussed in relation to its morphology as studied by cryo-scanning electron microscopy (cryo-SEM).

IMPORTANCE

Indoor fungi cause structural and cosmetic damage in houses and are a potential threat to human health. Growth depends on water, which is available only at certain periods of the day (e.g., during cooking or showering). Knowing why fungi can or cannot survive indoors is important for finding novel ways of prevention. Until now, the ability of fungi to grow on media with little available water at steady state (unchanging conditions) has been important for evaluating whether a fungus can grow indoors. In the present study, we found that the fungus Cladosporium halotolerans, a common indoor fungus, is more resistant to changes in available water than the fungi Aspergillus niger and Penicillium rubens, despite the fact that the latter fungi can grow on media with low water availability. We concluded that the ability of fungi to deal with changes in humidity is at least as important as the ability to grow on low-water media.

Water-, pH- and temperature relations of germination for the extreme xerophiles Xeromyces bisporus (FRR 0025), Aspergillus penicillioides (JH06THJ) and Eurotium halophilicum (FRR 2471)

Water activity, temperature and pH are determinants for biotic activity of cellular systems, biosphere function and, indeed, for all life processes. This study was carried out at high concentrations of glycerol, which concurrently reduces water activity and acts as a stress protectant, to characterize the biophysical capabilities of the most extremely xerophilic organisms known. These were the fungal xerophiles: Xeromyces bisporus (FRR 0025), Aspergillus penicillioides (JH06THJ) and Eurotium halophilicum (FRR 2471). High‐glycerol spores were produced and germination was determined using 38 media in the 0.995–0.637 water activity range, 33 media in the 2.80–9.80 pH range and 10 incubation temperatures, from 2 to 50°C. Water activity was modified by supplementing media with glycerol+sucrose, glycerol+NaCl and glycerol+NaCl+sucrose which are known to be biologically permissive for X. bisporus, A. penicillioides and E. halophilicum respectively. The windows and rates for spore germination were quantified for water activity, pH and temperature; symmetry/asymmetry of the germination profiles were then determined in relation to supra‐ and sub‐optimal conditions; and pH‐ and temperature optima for extreme xerophilicity were quantified. The windows for spore germination were ~1 to 0.637 water activity, pH 2.80–9.80 and > 10 and < 44°C, depending on strain. Germination profiles in relation to water activity and temperature were asymmetrical because conditions known to entropically disorder cellular macromolecules, i.e. supra‐optimal water activity and high temperatures, were severely inhibitory. Implications of these processes were considered in relation to the in‐situ ecology of extreme conditions and environments; the study also raises a number of unanswered questions which suggest the need for new lines of experimentation.

Fungal spores for dispersion in space and time

Spores are an integral part of the life cycle of the gross majority of fungi. Their morphology and the mode of formation are both highly variable among the fungi, as is their resistance to stressors. The main aim for spores is to be dispersed, both in space, by various mechanisms or in time, by an extended period of dormancy. Some fungal ascospores belong to the most stress-resistant eukaryotic cells described to date. Stabilization is a process in which biomolecules and complexes thereof are protected by different types of molecules against heat, drought, or other molecules. This review discusses the most important compounds that are known to protect fungal spores and also addresses the biophysics of cell protection. It further covers the phenomena of dormancy, breaking of dormancy, and early germination. Germination is the transition from a dormant cell toward a vegetative cell and includes a number of specific changes. Finally, the applied aspects of spore biology are discussed.

Hydrophilins in the filamentous fungus Neosartorya fischeri (Aspergillus fischeri) have protective activity against several types of microbial water stress

Hydrophilins are proteins that occur in all domains of life and protect cells and organisms against drought and other stresses. They include most of the late embryogenesis abundant (LEA) proteins and the heat shock protein (HSP) Hsp12. Here, the role of a predicted LEA-like protein (LeamA) and two Hsp12 proteins (Hsp12A and Hsp12B) of Neosartorya fischeri was studied. This filamentous fungus forms ascospores that belong to the most stress-resistant eukaryotic cells described to date. Heterologous expression of LeamA, Hsp12A and Hsp12B resulted in increased tolerance against salt and osmotic stress in Escherichia coli. These proteins were also shown to protect lactate dehydrogenase against dry heat and freeze-thaw cycles in vitro. Deletion of leamA caused diminished viability of sexual ascospores after drought and heat. This is the first report on functionality of Hsp12 and putative LeamA proteins derived from filamentous fungi, and their possible role in N. fischeri ascospore resistance against desiccation, high temperature and osmotic stress is discussed.

Xerotolerant Cladosporium sphaerospermum Are Predominant on Indoor Surfaces Compared to Other Cladosporium Species

Indoor fungi are a major cause of cosmetic and structural damage of buildings worldwide and prolonged exposure of these fungi poses a health risk. Aspergillus, Penicillium and Cladosporium species are the most predominant fungi in indoor environments. Cladosporium species predominate under ambient conditions. A total of 123 Cladosporium isolates originating from indoor air and indoor surfaces of archives, industrial factories, laboratories, and other buildings from four continents were identified by sequencing the internal transcribed spacer (ITS), and a part of the translation elongation factor 1α gene (TEF) and actin gene (ACT). Species from the Cladosporium sphaerospermum species complex were most predominant representing 44.7% of all isolates, while the Cladosporium cladosporioides and Cladosporium herbarum species complexes represented 33.3% and 22.0%, respectively. The contribution of the C. sphaerospermum species complex was 23.1% and 58.2% in the indoor air and isolates from indoor surfaces, respectively. Isolates from this species complex showed growth at lower water activity (≥ 0.82) when compared to species from the C. cladosporioides and C. herbarum species complexes (≥ 0.85). Together, these data indicate that xerotolerance provide the C. sphaerospermum species complex advantage in colonizing indoor surfaces. As a consequence, C. sphaerospermum are proposed to be the most predominant fungus at these locations under ambient conditions. Findings are discussed in relation to the specificity of allergy test, as the current species of Cladosporium used to develop these tests are not the predominant indoor species.

Food preparation with mucoralean fungi: A potential biosafety issue?

Mucorales have been used for production of fermented food in Asia and Africa since time immemorial. Particularly Rhizopus species are rapidly growing, active producers of lipases and proteases and occur naturally during the first stages of soybean fermentation. Two biosafety issues have been raised in recent literature: (1) pathogenicity, Rhizopus species being prevalent opportunists causing erosive infections in severely compromised patients, and (2) toxicity, strains harbouring endosymbiotic Burkholderia producing toxic secondary metabolites. At the molecular level, based on different gene markers, species identity was found between strains used for food processing and clinical strains. In this study, we screened for bacterial symbionts in 64 Rhizopus strains by light microscopy, 16S rRNA sequencing, and HPLC. Seven strains (11 %) carried bacteria identified as Burkholderia rhizoxinica and Burkholderia endofungorum, and an unknown Burkholderia species. The Burkholderia isolates proved to be able to produce toxic rhizoxins. Strains with endosymbionts originated from food, soil, and a clinical source, and thus their presence could not be linked to particular habitats. The presence of Burkholderia in Rhizopus producing toxins could not be excluded as a potential risk for human health. In contrast, given the type of diseases caused by Rhizopus species, we regard the practical risk of infection via the food industry as negligible.

Common but different: The expanding realm of Cladosporium

The genus Cladosporium (Cladosporiaceae, Dothideomycetes), which represents one of the largest genera of dematiaceous hyphomycetes, has been intensively investigated during the past decade. In the process, three major species complexes (C. cladosporioides, C. herbarum and C. sphaerospermum) were resolved based on morphology and DNA phylogeny, and a monographic revision of the genus (s. lat.) published reflecting the current taxonomic status quo. In the present study a further 19 new species are described based on phylogenetic characters (nuclear ribosomal RNA gene operon, including the internal transcribed spacer regions ITS1 and ITS2, as well as partial actin and translation elongation factor 1-α gene sequences) and morphological differences. For a selection of the species with ornamented conidia, scanning electron microscopic photos were prepared to illustrate the different types of surface ornamentation. Surprisingly, during this study Cladosporium ramotenellum was found to be a quite common saprobic species, being widely distributed and occurring on various substrates. Therefore, an emended species description is provided. Furthermore, the host range and distribution data for several previously described species are also expanded.

Fungal stress biology: a preface to the Fungal Stress Responses special edition

There is currently an urgent need to increase global food security, reverse the trends of increasing cancer rates, protect environmental health, and mitigate climate change. Toward these ends, it is imperative to improve soil health and crop productivity, reduce food spoilage, reduce pesticide usage by increasing the use of biological control, optimize bioremediation of polluted sites, and generate energy from sustainable sources such as biofuels. This review focuses on fungi that can help provide solutions to such problems. We discuss key aspects of fungal stress biology in the context of the papers published in this Special Issue of Current Genetics. This area of biology has relevance to pure and applied research on fungal (and indeed other) systems, including biological control of insect pests, roles of saprotrophic fungi in agriculture and forestry, mycotoxin contamination of the food-supply chain, optimization of microbial fermentations including those used for bioethanol production, plant pathology, the limits of life on Earth, and astrobiology.

Is there a common water-activity limit for the three domains of life?

Archaea and Bacteria constitute a majority of life systems on Earth but have long been considered inferior to Eukarya in terms of solute tolerance. Whereas the most halophilic prokaryotes are known for an ability to multiply at saturated NaCl (water activity (a(w)) 0.755) some xerophilic fungi can germinate, usually at high-sugar concentrations, at values as low as 0.650-0.605 a(w). Here, we present evidence that halophilic prokayotes can grow down to water activities of <0.755 for Halanaerobium lacusrosei (0.748), Halobacterium strain 004.1 (0.728), Halobacterium sp. NRC-1 and Halococcus morrhuae (0.717), Haloquadratum walsbyi (0.709), Halococcus salifodinae (0.693), Halobacterium noricense (0.687), Natrinema pallidum (0.681) and haloarchaeal strains GN-2 and GN-5 (0.635 a(w)). Furthermore, extrapolation of growth curves (prone to giving conservative estimates) indicated theoretical minima down to 0.611 aw for extreme, obligately halophilic Archaea and Bacteria. These were compared with minima for the most solute-tolerant Bacteria in high-sugar (or other non-saline) media (Mycobacterium spp., Tetragenococcus halophilus, Saccharibacter floricola, Staphylococcus aureus and so on) and eukaryotic microbes in saline (Wallemia spp., Basipetospora halophila, Dunaliella spp. and so on) and high-sugar substrates (for example, Xeromyces bisporus, Zygosaccharomyces rouxii, Aspergillus and Eurotium spp.). We also manipulated the balance of chaotropic and kosmotropic stressors for the extreme, xerophilic fungi Aspergillus penicilloides and X. bisporus and, via this approach, their established water-activity limits for mycelial growth (∼0.65) were reduced to 0.640. Furthermore, extrapolations indicated theoretical limits of 0.632 and 0.636 a(w) for A. penicilloides and X. bisporus, respectively. Collectively, these findings suggest that there is a common water-activity limit that is determined by physicochemical constraints for the three domains of life.

Functionality and prevalence of trehalose-based oligosaccharides as novel compatible solutes in ascospores of Neosartorya fischeri (Aspergillus fischeri) and other fungi

Ascospores of Neosartorya, Byssochlamys and Talaromyces can be regarded as the most stress-resistant eukaryotic cells. They can survive exposure at temperatures as high as 85°C for 100 min or more. Neosartorya fischeri ascospores are more viscous and more resistant to the combined stress of heat and desiccation than the ascospores of Talaromyces macrosporus which contain predominantly trehalose. These ascospores contain trehalose-based oligosaccharides (TOS) that are novel compatible solutes, which are accumulated to high levels. These compounds are also found in other members of the genus Neosartorya and in some other genera within the order Eurotiales that also include Byssochlamys and Talaromyces. The presence of oligosaccharides was observed in species that had a relatively high growth temperature. TOS glasses have a higher glass transition temperature (Tg ) than trehalose, and they form a stable glass with crystallizing molecules, such as mannitol. Our data indicate that TOS are important for prolonged stabilization of cells against stress. The possible unique role of these solutes in protection against dry heat conditions is discussed.

Nutrient limitation leads to penetrative growth into agar and affects aroma formation in Pichia fabianii, P. kudriavzevii and Saccharomyces cerevisiae

Among fermentative yeast species, Saccharomyces cerevisiae is most frequently used as a model organism, although other yeast species may have special features that make them interesting candidates to apply in food-fermentation processes. In this study, we used three yeast species isolated from fermented masau (Ziziphus mauritiana) fruit, S. cerevisiae 131, Pichia fabianii 65 and Pichia kudriavzevii 129, and determined the impact of nitrogen and/or glucose limitation on surface growth mode and the production of volatile organic compounds (VOCs). All three species displayed significant changes in growth mode in all nutrient-limited conditions, signified by the formation of metafilaments or pseudohyphae. The timing of the transition was found to be species-specific. Transition in growth mode is suggested to be linked to the production of certain fusel alcohols, such as phenylethyl alcohol, which serve as quorum-sensing molecules. Interestingly, we did not observe concomitant increased production of phenylethyl alcohol and filamentous growth. Notably, a broader range of esters was found only for the Pichia spp. grown on nitrogen-limited agar for 21 days compared to nutrient-rich agar, and when grown on glucose- and glucose- plus nitrogen-limited agar. Our data suggest that for the Pichia spp., the formation of esters may play an important role in the switch in growth mode upon nitrogen limitation. Further biological or ecological implications of ester formation are discussed.

Genome and physiology of the ascomycete filamentous fungus Xeromyces bisporus, the most xerophilic organism isolated to date

Xeromyces bisporus can grow on sugary substrates down to 0.61, an extremely low water activity. Its genome size is approximately 22 Mb. Gene clusters encoding for secondary metabolites were conspicuously absent; secondary metabolites were not detected experimentally. Thus, in its 'dry' but nutrient-rich environment, X. bisporus appears to have relinquished abilities for combative interactions. Elements to sense/signal osmotic stress, e.g. HogA pathway, were present in X. bisporus. However, transcriptomes at optimal (∼ 0.89) versus low aw (0.68) revealed differential expression of only a few stress-related genes; among these, certain (not all) steps for glycerol synthesis were upregulated. Xeromyces bisporus increased glycerol production during hypo- and hyper-osmotic stress, and much of its wet weight comprised water and rinsable solutes; leaked solutes may form a protective slime. Xeromyces bisporus and other food-borne moulds increased membrane fatty acid saturation as water activity decreased. Such modifications did not appear to be transcriptionally regulated in X. bisporus; however, genes modulating sterols, phospholipids and the cell wall were differentially expressed. Xeromyces bisporus was previously proposed to be a 'chaophile', preferring solutes that disorder biomolecular structures. Both X. bisporus and the closely related xerophile, Xerochrysium xerophilum, with low membrane unsaturation indices, could represent a phylogenetic cluster of 'chaophiles'.

A decrease in bulk water and mannitol and accumulation of trehalose and trehalose-based oligosaccharides define a two-stage maturation process towards extreme stress resistance in ascospores of Neosartorya fischeri (Aspergillus fischeri)

Fungal propagules survive stresses better than vegetative cells. Neosartorya fischeri, an Aspergillus teleomorph, forms ascospores that survive high temperatures or drying followed by heat. Not much is known about maturation and development of extreme stress resistance in fungal cells. This study provides a novel two-step model for the acquisition of extreme stress resistance and entry into dormancy. Ascospores of 11- and 15-day-old cultures exhibited heat resistance, physiological activity, accumulation of compatible solutes and a steep increase in cytoplasmic viscosity. Electron spin resonance spectroscopy indicated that this stage is associated with the removal of bulk water and an increase of chemical stability. Older ascospores from 15- to 50-day-old cultures showed no changes in compatible solute content and cytoplasmic viscosity, but did exhibit a further increase of heat resistance and redox stability with age. This stage was also characterized by changes in the composition of the mixture of compatible solutes. Mannitol levels decreased and the relative quantities of trehalose and trehalose-based oligosaccharides increased. Dormant ascospores of N. fischeri survive in low-water habitats. After activation of the germination process, the stress resistance decreases, compatible solutes are degraded and the cellular viscosity drops. After 5 h, the hydrated cells enter the vegetative stage and redox stability has decreased notably.