Contributions of the peroxisome and β-oxidation cycle to biotin synthesis in fungi

The first step in the synthesis of the bicyclic rings of D-biotin is mediated by 8-amino-7-oxononanoate (AON) synthase, which catalyzes the decarboxylative condensation of l-alanine and pimelate thioester. We found that the Aspergillus nidulans AON synthase, encoded by the bioF gene, is a peroxisomal enzyme with a type 1 peroxisomal targeting sequence (PTS1). Localization of AON to the peroxisome was essential for biotin synthesis because expression of a cytosolic AON variant or deletion of pexE, encoding the PTS1 receptor, rendered A. nidulans a biotin auxotroph. AON synthases with PTS1 are found throughout the fungal kingdom, in ascomycetes, basidiomycetes, and members of basal fungal lineages but not in representatives of the Saccharomyces species complex, including Saccharomyces cerevisiae. A. nidulans mutants defective in the peroxisomal acyl-CoA oxidase AoxA or the multifunctional protein FoxA showed a strong decrease in colonial growth rate in biotin-deficient medium, whereas partial growth recovery occurred with pimelic acid supplementation. These results indicate that pimeloyl-CoA is the in vivo substrate of AON synthase and that it is generated in the peroxisome via the β-oxidation cycle in A. nidulans and probably in a broad range of fungi. However, the β-oxidation cycle is not essential for biotin synthesis in S. cerevisiae or Escherichia coli. These results suggest that alternative pathways for synthesis of the pimelate intermediate exist in bacteria and eukaryotes and that Saccharomyces species use a pathway different from that used by the majority of fungi.     

From A to Z and back? Multicompartment proteins in the sarcomere

Sarcomeres, the smallest contractile units of striated muscle, are conventionally perceived as the most regular macromolecular assemblies in biology, with precisely assigned localizations for their constituent proteins. However, recent studies have revealed complex multiple locations for several sarcomere proteins within the sarcomere and other cellular compartments such as the nucleus. Several of these proteins appear to relocalize in response to mechanical stimuli. Here, we review the emerging role of these protein networks as dynamic information switchboards that communicate between the contractile machinery and the nucleus to central pathways controlling cell survival, protein breakdown, gene expression and extracellular signaling.     

Using fossils to determine an amber source: aphids and crane flies in Chinese or Baltic amber?

Aphids and crane flies in amber purported to have originated in China were examined. Six aphid specimens were characterised and determined to be conspecific with Germaraphis defuncta Heie, originally described from Baltic amber. Two crane flies from the same collection were identified as Cheilotrichia minuta and Rhabdomastix brevis, species also previously described from Baltic amber. This study shows that when the locality of an amber source is ambiguous, fossils can be used to determine the true province.     

Aquatic fungi in relation to the physical and chemical parameters of water quality in the Augustów Canal

The objective of this study was to determine the effects of physical and chemical water quality parameters in the Augustów Canal on the abundance and taxonomic diversity of aquatic fungi. The studies were conducted in the hydrological year 2012 along the environmentally valuable area of the Augustów Canal. The mean abundance of fungi was 2 160 ± 1840 CFU ml⁻¹. The lowest abundances were observed in the uppermost part of the canal, and the highest abundances in the southern part. A total of 38 species were identified, including 13 potentially pathogenic fungi, which predominated in the central region of the canal, called the natural lake part. Redundancy analysis (RDA) indicated that variation in water chemistry caused significant changes to fungal species diversity. The results showed that fungal species diversity and abundance in the canal were particularly dependent on the extent of water pollution, as indicated by chloride and sulphate(VI) ions and electrolytic conductivity. Other water quality parameters that influenced the development of aquatic fungi were organic matter and algal biomass, responsible for water eutrophication. We propose that mycoplankton be considered a sensitive biological indicator of water quality.     

Mycoremediation (bioremediation with fungi) – growing mushrooms to clean the earth

Abstract

Some of the prospects of using fungi, principally white-rot fungi, for cleaning contaminated land are surveyed. That white-rot fungi are so effective in degrading a wide range of organic molecules is due to their release of extra-cellular lignin-modifying enzymes, with a low substrate-specificity, so they can act upon various molecules that are broadly similar to lignin. The enzymes present in the system employed for degrading lignin include lignin-peroxidase (LiP), manganese peroxidase (MnP), various H₂O₂ producing enzymes and laccase. The degradation can be augmented by adding carbon sources such as sawdust, straw and corn cob at polluted sites.     

Can Antarctic lichens acclimatize to changes in temperature?

The Antarctic Peninsula, a tundra biome dominated by lichens and bryophytes, is an ecozone undergoing rapid temperature shifts. Such changes may demand a high physiological plasticity of the local lichen species to maintain their role as key drivers in this pristine habitat. This study examines the response of net photosynthesis and respiration to increasing temperatures for three Antarctic lichen species with different ecological response amplitudes. We hypothesize that negative effects caused by increased temperatures can be mitigated by thermal acclimation of respiration and/or photosynthesis. The fully controlled growth chamber experiment simulated intermediate and extreme temperature increases over the time course of 6 weeks. Results showed that, in contrast to our hypothesis, none of the species was able to down‐regulate temperature‐driven respiratory losses through thermal acclimation of respiration. Instead, severe effects on photobiont vitality demonstrated that temperatures around 15°C mark the upper limit for the two species restricted to the Antarctic, and when mycobiont demands exceeded the photobiont capacity they could not survive within the lichen thallus. In contrast, the widespread lichen species was able to recover its homoeostasis by rapidly increasing net photosynthesis. We conclude that to understand the complete lichen response, acclimation processes of both symbionts, the photo‐ and the mycobiont, have to be evaluated separately. As a result, we postulate that any acclimation processes in lichen are species‐specific. This, together with the high degree of response variability and sensitivity to temperature in different species that co‐occur spatially close, complicates any predictions regarding future community composition in the Antarctic. Nevertheless, our results suggest that species with a broad ecological amplitude may be favoured with on‐going changes in temperature.     

Influenza Seasonality in the Tropics and Subtropics – When to Vaccinate?

BackgroundThe timing of the biannual WHO influenza vaccine composition selection and production cycle has been historically directed to the influenza seasonality patterns in the temperate regions of the northern and southern hemispheres. Influenza activity, however, is poorly understood in the tropics with multiple peaks and identifiable year-round activity. The evidence-base needed to take informed decisions on vaccination timing and vaccine formulation is often lacking for the tropics and subtropics. This paper aims to assess influenza seasonality in the tropics and subtropics. It explores geographical grouping of countries into vaccination zones based on optimal timing of influenza vaccination.MethodsInfluenza seasonality was assessed by different analytic approaches (weekly proportion of positive cases, time series analysis, etc.) using FluNet and national surveillance data. In case of discordance in the seasonality assessment, consensus was built through discussions with in-country experts. Countries with similar onset periods of their primary influenza season were grouped into geographical zones.ResultsThe number and period of peak activity was ascertained for 70 of the 138 countries in the tropics and subtropics. Thirty-seven countries had one and seventeen countries had two distinct peaks. Countries near the equator had secondary peaks or even identifiable year-round activity. The main influenza season in most of South America and Asia started between April and June. The start of the main season varied widely in Africa (October and December in northern Africa, April and June in Southern Africa and a mixed pattern in tropical Africa). Eight “influenza vaccination zones” (two each in America and Asia, and four in Africa and Middle East) were defined with recommendations for vaccination timing and vaccine formulation. The main limitation of our study is that FluNet and national surveillance data may lack the granularity to detect sub-national variability in seasonality patterns.ConclusionDistinct influenza seasonality patterns, though complex, could be ascertained for most countries in the tropics and subtropics using national surveillance data. It may be possible to group countries into zones based on similar recommendations for vaccine timing and formulation.     

Phylogeny and taxonomy of the ‘manna lichens’

We present ataxonomic revision of the ‘manna lichens’ based on morphological, chemical, ecological and molecular data. A large number of herbarium specimens and fresh collections were examined. Phylogenetic analyses were performed using nuclear ribosomal (nrITS, nrLSU) and mitochondrial small subunit (mtSSU) sequences. Some notable phenotypic characters were plotted on the phylogenetic tree, and the analysis reveals that some of these characters are useful for genus and species level distinction of certain ‘manna lichens.’ Phylogeny of the Megasporaceae was revised using a combined data set of nrLSU and mtSSU and performing parsimony and Bayesian analyses. Five genera (Aspicilia, Circinaria, Lobothallia, Megaspora and Sagedia) are recognized. Further, the relationships of five presumably closely related genera of ‘manna lichens’, namely Agrestia (vagrant), Aspicilia (crustose) Circinaria (crustose), Chlorangium (vagrant) and Sphaerothallia (vagrant) with different growth forms were analysed. The analyses revealed that ‘manna lichens’ do not form a monophyletic group but occur in different clades within the genus Circinaria. The genera Agrestia, Chlorangium and Sphaerothallia are assigned as new synonyms under the genus Circinaria and no vagrant or erratic species remain in the genus Aspicilia. The analyses also show that five new erratic, vagrant and crustose species can be recognized. In this study two ‘manna lichens’, viz. Circinaria rostamii sp. nov. (Azerbaijan, Iran and Turkey), and Circinaria gyrosa sp. nov. (Armenia, Azerbaijan, Iran, Turkey, Turkmenistan and Spain) are described as new to science. Three potentially new species with crustose and erratic forms need additional study. Aspicilia fruticolosofoliacea is reduced to synonymy under C. alpicola, and a lectotype is designated for C. aspera. Thirteen new combinations in Circinaria are presented. The phenomenon of vagrancy is briefly discussed, and the biogeography of the ‘manna lichens’ is outlined. Illustrations, distribution maps, and an identification key to the species are provided.     

Approaching the taxonomic affiliation of unidentified sequences in public databases – an example from the mycorrhizal fungi

Background  

During the last few years, DNA sequence analysis has become one of the primary means of taxonomic identification of species, particularly so for species that are minute or otherwise lack distinct, readily obtainable morphological characters. Although the number of sequences available for comparison in public databases such as GenBank increases exponentially, only a minuscule fraction of all organisms have been sequenced, leaving taxon sampling a momentous problem for sequence-based taxonomic identification. When querying GenBank with a set of unidentified sequences, a considerable proportion typically lack fully identified matches, forming an ever-mounting pile of sequences that the researcher will have to monitor manually in the hope that new, clarifying sequences have been submitted by other researchers. To alleviate these concerns, a project to automatically monitor select unidentified sequences in GenBank for taxonomic progress through repeated local BLAST searches was initiated. Mycorrhizal fungi – a field where species identification often is prohibitively complex – and the much usedITSlocus were chosen as test bed.     

Occurrence of endophyte fungi on grasses in Poland – Review

The first reports from Pfannmöller et al. (1994) and Lewis (2000) regarding the level of Neotyphodium colonization of grasses in Poland identified ratios ranging from 20 % to 60 %. To date, the studies of endophytes in Poland have focused mainly on the rate of endophyte infection in subsequent years of plantation use, the effect of endophytes on turf performance and the occurrence of endophytes in cultivars of meadow fescue, tall fescue and perennial ryegrass. The aforementioned studies were mainly conducted on breeding varieties of grasses. From 2007 to 2009, intensive studies on Neotyphodium occurrence in ecotypes of wild grasses in Poland were conducted. The results suggest that Neotyphodium species are quite common in Poland and colonize roughly 70 % of semi-natural, used or abandoned grasslands. In this paper we review studies that have been conducted thus far in Poland regarding the occurrence of Neotyphodium spp. in grasses.     

Wood decay fungi and their bacterial interaction partners in the built environment – A systematic review on fungal bacteria interactions in dead wood and timber

Microbial biodeterioration of timber and woody material in buildings can cause costly restoration procedures. Here, we focus on Serpula lacrymans (commonly known as dry-rot) the fungus causing the most severe damages to buildings in Europe. Although its morphology, lifestyle, and dispersal have been intensively studied, research on microorganisms sharing the same habitat and interacting with the dry-rot fungus is not as comprehensive. Bacteria have long been known to inhabit dead wood, and several studies have shown their association to fungi. However, their identity, ecology, and putative interactions with co-existing fungi in dead wood remains largely underexplored. The interactions of bacterial and fungi have considerable impact on all partners involved covering the full spectrum between antagonistic and beneficial. Fungi are highly capable of manipulating the microbial community in their surroundings (e.g. via pH manipulation) and bacteria, in turn, can influence fungi by affecting the outcomes of (antagonistic) interactions or preventing fungal feedback inhibition via consumption of breakdown products. Associated bacteria on the other side could play an essential role for the fungus as bacteria can exert significant influence on fungal physiology and behaviour. This minireview summarizes the current knowledge on bacterial-fungal interactions in dead wood with a special focus on dry-rot and proposes possible bacterial-fungal interaction (BFI) mechanisms based on examples from soil or decomposing wood from forests.     

Problems in application of the terms ‘blastic’ and ‘thallic’ to modes of conidiogenesis in some onygenalean fungi

A woman suffering from acute tubulo-interstitial nephritis was admitted to the hospital ten days after deliberate intoxication by ingestion of Cortinarius orellanus. Orellanine, the main toxin responsible for orellanine poisoning, was detected in biological fluids and renal biopsies. It was assayed by direct spectrofluorimetry on two-dimensional thin-layer chromatograms after specific photodecomposition into orelline. The orellanine concentration was 6.12 mg/l in the plasma (10 days after ingestion). Orellanine levels in renal biopsies were 7 g per 25 mm³ of the first biopsy (13 days after ingestion) and 24 g per 8 mm³ of the second biopsy (6 months later).Taken in part from the doctorate thesis of S. Rapior.     

How diverse were ferns in the Baltic amber forest?

Diverse temperate forest types and a high atmospheric humidity have recently been suggested for the Eocene source area of Baltic amber. However, ferns are astonishingly rare as inclusions in this amber, which is in contrast to other seed‐free land plants, fungi, and lichens. Moreover, the identities of some of the few described putative fern taxa are dubious, and some fossils were even assigned to the Paleozoic seed fern genera Alethopteris, Pecopteris and to the form genus Sphenopteris containing Paleozoic and Mesozoic fern‐like leaf fossils. Here, we review previously described fern inclusions from Baltic amber and identify further fern‐like leaf inclusions as belonging to the extant angiosperm genus Comptonia (sweet ferns, Myricaceae). We conclude that only one taxon, Matonia striata (Matoniaceae), can with confidence be identified as a Polypodiopsida representative. Although “Pecopteris” humboldtiana is so far only known as sterile foliage, its leaf morphology strongly suggests that also this taxon belongs to the Polypodiopsida rather than to any other tracheophyte lineage. We propose accommodating “Pecopteris” humboldtiana in the new genus Berendtiopteris. “Alethopteris” serrata and “Sphenopteris” phyllocladoides are not to be regarded as evidence of ferns from Baltic amber. Reinvestigation of the holotypes of these two taxa did not reveal to which tracheophyte lineages these fossils belong. We suggest that the scarcity of fern remains from Baltic amber may reflect both a relatively low fern diversity in the source area of the fossil resin, and an absence or rarity of epiphytic and climbing ferns as observed in modern temperate forest ecosystems.     

Do ectomycorrhizal fungi exhibit adaptive tolerance to potentially toxic metals in the environment ?

The effects of potentially toxic metals on ectomycorrhizal (ECM) fungi and their higher plant hosts are examined in this review. Investigations at a species and community level have revealed wide inter- and intraspecific variation in sensitivity to metals. Adaptive and constitutive mechanisms of ECM tolerance are proposed and discussed in relation to proven tolerance mechanisms in bacteria, yeasts and plants. Problems with methodology and research priorities are highlighted. These include the need for a detailed understanding of the genetic basis of tolerance in the ECM symbiosis, and for studies of ECM community dynamics in polluted sites.