Robert A. Samson

Fleming’s penicillin producing strain is not Penicillium chrysogenum but P. rubens

Penicillium chrysogenum is a commonly occurring mould in indoor environments and foods, and has gained much attention for its use in the production of the antibiotic penicillin. Phylogenetic analysis of the most important penicillin producing P. chrysogenum isolates revealed the presence of two highly supported clades, and we show here that these two clades represent two species, P. chrysogenum and P. rubens. These species are phenotypically similar, but extrolite analysis shows that P. chrysogenum produces secalonic acid D and F and/or a metabolite related to lumpidin, while P. rubens does not produce these metabolites. Fleming’s original penicillin producing strain and the full genome sequenced strain of P. chrysogenum are re-identified as P. rubens. Furthermore, the well-known claim that Alexander Fleming misidentified the original penicillin producing strain as P. rubrum is discussed.

Impact of ionic liquids on extreme microbial biotypes from soil

This work aims at identifying, amongst extreme soil biotypes at locations of high salinity and high hydrocarbon load, microbial strains able to survive short or long-term exposure to the presence of selected ionic liquids. We have evaluated the impact of ionic liquids on the diversity of the soil microbiota to identify which microbial strains have higher survival rates towards ionic liquids, and consequently those which might possibly play a major role in their biotic fate. To the best of our knowledge, this is the first study of this kind. Soils, from a region in Portugal (Aveiro) were sampled and the bacterial and fungal strains able to survive after exposure to high concentrations of selected ionic liquids were isolated and further characterised. We have mainly focused on two types of cations: imidazolium – the most commonly used; and cholinium – generally perceived as benign. The surviving microbial strains were isolated and taxonomically identified, and the ionic liquid degradation was analysed during their cultivation. The continuing exposure of the microbial strains to petroleum hydrocarbons is likely to be the basis for their acquired resistance to some imidazolium salts; also, the higher capacity of fungi – compared to bacteria – to grow, even during their exposure to these liquid salts, became evident in this study.

Five new Penicillium species in section Sclerotiora: a tribute to the Dutch Royal family

Current literature accepts 17 species in Penicillium section Sclerotiora. Several produce colonies in bright yellow to orange colours and have monoverticillate conidiophores, apart from P. herquei, P. malachiteum and P. nodositatum, which are biverticillate. The focus of this paper is to refine the concepts of the species currently accepted in the section and introduce five new species, named after the Dutch Royal family as P. vanoranjei, P. maximae, P. amaliae, P. alexiae and P. arianeae. Penicillium vanoranjei produces orange (Dutch = oranje) colonies in culture, and is named after Willem-Alexander Claus George Ferdinand, ‘Zijne Koninklijke Hoogheid de Prins van Oranje’ (translated from Dutch as: ‘His Royal Highness the Prince of Orange’) and his family, to coincide with his coronation. We review the current taxonomic positions of P. lilacinoechinulatum and P. nodositatum, both currently considered to be synonyms of P. bilaiae. Sequence data generated in this study show that both species are phylogenetically distinct. Penicillium lilacinoechinulatum is closely related to P. amaliae sp. nov., whereas P. nodositatum does not belong to Penicillium sensu stricto. All species were compared morphologically and phylogenetically, based on β-tubulin and calmodulin DNA data. A table summarising the morphological characters of all species is included, together with photomicrographs and recommended DNA markers for identification.

Molecular Diversity of Aspergillus and Penicillium Species on Fruits and Vegetables

Publisher Summary This chapter provides an overview on the genetic diversity and mycotoxin production abilities of Penicillium and Aspergillus species on fruits and vegetables. Species of Aspergillus and Penicillium are generally not known as plant pathogens causing field diseases because of the production of numerous conidia, they easily infect fruits and vegetables and develop as post-harvest contaminants. Each species in Aspergillus and Penicillium genera has its specific habitat and many data on their association with fruits and vegetables are available. Aspergilli and penicillia are frequently encountered on fruits and vegetables. The most notorious plant pathogens are Penicillium expansum, Aspergillus niger and A. flavus that cause various plant diseases. Aspergilli and penicillia can also contaminate fruits and vegetables at different stages including harvest, processing and handling. Post-harvest contamination can lead to changes in the quality and nutritional value of fruits and vegetables. The most important aspect of food spoilage caused by these organisms is the formation of mycotoxins, which have harmful effects on human and animal health. Mycotoxin contamination of fruits including grapes, figs, treenuts, and peanuts is the economically most important.

2 Fungal Spoilage of Crops and Food

Food products are a rich nutrient source that will attract both bacterial and fungal colonizers. Food spoilage is a major threat for our food stock and is responsible for enormous losses worldwide, which makes it a research area that is very relevant with respect to the increasing demand on food during the next decennia.

A phylogenetic revision of Penicillium sect. Exilicaulis, including nine new species from fynbos in South Africa.

A survey of the fynbos biome in South Africa resulted in the isolation of 61 Penicillium species from Protea repens infructescences, air, and soil samples. Fourteen of these belong to Penicillium sect. Exilicaulis and therefore we considered it an opportunity to re-evaluate the taxonomy of the section. Phylogenetic comparisons of the ITS, β-tubulin, calmodulin and RPB2 gene regions of the 76 section Exilicaulis species, revealed 52 distinct species, including nine new species from fynbos. Morphological comparisons confirmed the novelty for most of these, however, new species closely related to P. rubefaciens did not show significant or consistent morphological differences and we thus placed a bias on phylogenetic data applying the Genealogical Concordance Phylogenetic Species Recognition (GCPSR) concept. In this paper we describe the nine new species and update the accepted species list and resolve synonyms in the section. Importantly, we reveal that P. citreosulfuratum is the correct name for the clade previously considered to represent P. toxicarium fide Serra et al. (2008). The nine new species are: Penicillium atrolazulinum, P. consobrinum, P. cravenianum, P. hemitrachum, P. pagulum, P. repensicola, P. momoii, P. subturcoseum, and P. xanthomelinii spp. nov.

Understanding fungal functional biodiversity during the mitigation of environmentally dispersed pentachlorophenol in cork oak forest soils

Pentachlorophenol (PCP) is globally dispersed and contamination of soil with this biocide adversely affects its functional biodiversity, particularly of fungi - key colonizers. Their functional role as a community is poorly understood, although a few pathways have been already elucidated in pure cultures. This constitutes here our main challenge - elucidate how fungi influence the pollutant mitigation processes in forest soils. Circumstantial evidence exists that cork oak forests in N. W. Tunisia - economically critical managed forests are likely to be contaminated with PCP, but the scientific evidence has previously been lacking. Our data illustrate significant forest contamination through the detection of undefined active sources of PCP. By solving the taxonomic diversity and the PCP-derived metabolomes of both the cultivable fungi and the fungal community, we demonstrate here that most strains (predominantly penicillia) participate in the pollutant biotic degradation. They form an array of degradation intermediates and by-products, including several hydroquinone, resorcinol and catechol derivatives, either chlorinated or not. The degradation pathway of the fungal community includes uncharacterized derivatives, e.g. tetrachloroguaiacol isomers. Our study highlights fungi key role in the mineralization and short lifetime of PCP in forest soils and provide novel tools to monitor its degradation in other fungi dominated food webs.

The fungal composition of natural biofinishes on oil-treated wood

BackgroundBiofinished wood is considered to be a decorative and protective material for outdoor constructions, showing advantages compared to traditional treated wood in terms of sustainability and self-repair. Natural dark wood staining fungi are essential to biofinish formation on wood. Although all sorts of outdoor situated timber are subjected to fungal staining, the homogenous dark staining called biofinish has only been detected on specific vegetable oil-treated substrates. Revealing the fungal composition of various natural biofinishes on wood is a first step to understand and control biofinish formation for industrial application.ResultsA culture-based survey of fungi in natural biofinishes on oil-treated wood samples showed the common wood stain fungus Aureobasidium and the recently described genus Superstratomyces to be predominant constituents. A culture-independent approach, based on amplification of the internal transcribed spacer regions, cloning and Sanger sequencing, resulted in clone libraries of two types of biofinishes. Aureobasidium was present in both biofinish types, but was only predominant in biofinishes on pine sapwood treated with raw linseed oil. Most cloned sequences of the other biofinish type (pine sapwood treated with olive oil) could not be identified. In addition, a more in-depth overview of the fungal composition of biofinishes was obtained with Illumina amplicon sequencing that targeted the internal transcribed spacer region 1. All investigated samples, that varied in wood species, (oil) treatments and exposure times, contained Aureobasidium and this genus was predominant in the biofinishes on pine sapwood treated with raw linseed oil. Lapidomyces was the predominant genus in most of the other biofinishes and present in all other samples. Surprisingly, Superstratomyces, which was predominantly detected by the cultivation-based approach, could not be found with the Illumina sequencing approach, while Lapidomyces was not detected in the culture-based approach.ConclusionsOverall, the culture-based approach and two culture-independent methods that were used in this study revealed that natural biofinishes were composed of multiple fungal genera always containing the common wood staining mould Aureobasidium. Besides Aureobasidium, the use of other fungal genera for the production of biofinished wood has to be considered.