Browsing by Subject "fungi"

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  • de Vries, Ronald; Mäkelä, Miia Riitta; Hilden, Sari Kristiina; Kämper, Jörg (2018)
  • Vitkainen, Orvo; Ahti, Teuvo; Kuusinen, Mikko; Lommi, Sampsa; Ulvinen, Tauno (Helsingin yliopiston luonnontieeteellisen keskusmuseon kasvimuseo, 1997)
    Norrlinia; 6
  • Tanskanen, Ville (Helsingin yliopisto, 2020)
    Microbial volatile organic compounds are emitted by diverse set of microbial organisms and they are known to cause health hazards when present in indoor air. Early detection of fungal contaminated buildings and species present is crucial to prevent health problems caused by fungal secondary metabolites. This thesis focuses on analysing emission profiles of different insulation materials and fungal cultures, which allows, in further studies, to develop efficient new ways to detect fungi from contaminated buildings. Studied insulation materials consisted of cellulose and glass wool, which were analysed in multiple different conditions. Humidity of atmosphere was varied between 0-10 microliters and temperature was varied between 30°C and 40°C. In fungal emission profile study 24 different cultures were analysed in two different atmospheres, ambient and micro- aerophilic, and in multiple different inoculums. Analysis for both insulation materials and fungal cultures was done using headspace solid phase microextraction Arrow -tool and headspace in tube extraction –tool together with gas chromatography – mass spectrometry. One goal for this thesis was also test suitability of these methods for detection of fungal secondary metabolites. Comprehensive fungal emission profiles were successfully formed and new information from behaviour of insulation materials in different settings was found. In addition, new information about analysis methods and fungal behaviour in different atmospheres was found. Headspace solid phase microextraction Arrow with gas chromatography – mass spectrometry was found to be efficient, sensitive and timesaving method for indoor air study purposes. There were also many potential fungal culture specific biomarker compounds found for further study purposes.
  • Korpelainen, Helena; Pietiläinen, Maria (2017)
    In the present study, we conducted DNA metabarcoding (the nuclear ITS2 region) for indoor fungal samples originating from two nursery schools with a suspected mould problem (sampling before and after renovation), from two university buildings, and from an old farmhouse. Good-quality sequences were obtained, and the results showed that DNA metabarcoding provides high resolution in fungal identification. The pooled proportions of sequences representing filamentous ascomycetes, filamentous basidiomycetes, yeasts, and other fungi equalled 62.3%, 8.0%, 28.3%, and 1.4%, respectively, and the total number of fungal genera found during the study was 585. When comparing fungal diversities and taxonomic composition between different types of buildings, no obvious pattern was detected. The average pairwise values of Sorensen(Chao) indices that were used to compare similarities for taxon composition between samples among the samples from the two university buildings, two nurseries, and farmhouse equaled 0.693, 0.736, 0.852, 0.928, and 0.981, respectively, while the mean similarity index for all samples was 0.864. We discovered that making explicit conclusions on the relationship between the indoor air quality and mycoflora is complicated by the lack of appropriate indicators for air quality and by the occurrence of wide spatial and temporal changes in diversity and compositions among samples.
  • Koskinen, Janne; Roslin, Tomas; Nyman, Tommi; Abrego, Nerea; Michell, Craig; Vesterinen, Eero J. (2019)
    Fruiting bodies of fungi constitute an important resource for thousands of other taxa. The structure of these diverse assemblages has traditionally been studied with labour-intensive methods involving cultivation and morphology-based species identification, to which molecular information might offer convenient complements. To overcome challenges in DNA extraction and PCR associated with the complex chemical properties of fruiting bodies, we developed a pipeline applicable for extracting amplifiable total DNA from soft fungal samples of any size. Our protocol purifies DNA in two sequential steps: (a) initial salt-isopropanol extraction of all nucleic acids in the sample is followed by (b) an extra clean-up step using solid-phase reversible immobilization (SPRI) magnetic beads. The protocol proved highly efficient, with practically all of our samples-regardless of biomass or other properties-being successfully PCR-amplified using metabarcoding primers and subsequently sequenced. As a proof of concept, we apply our methods to address a topical ecological question: is host specificity a major characteristic of fungus-associated communities, that is, do different fungus species harbour different communities of associated organisms? Based on an analysis of 312 fungal fruiting bodies representing 10 species in five genera from three orders, we show that molecular methods are suitable for studying this rich natural microcosm. Comparing to previous knowledge based on rearing and morphology-based identifications, we find a species-rich assemblage characterized by a low degree of host specialization. Our method opens up new horizons for molecular analyses of fungus-associated interaction webs and communities.
  • Väre, Henry Uolevi (2017)
    Finnish botanists and mycologists have studied Arctic areas and timberline regions since the beginning of the 18th century. Most expeditions to the Kola Peninsula were made between 1800 and 1917 and until 1945 to Lapponia petsamoensis on the western rim of the Kola Peninsula. Since those years, these areas have been part of the Soviet Union or Russia. Svalbard and Newfoundland and Labrador have been studied repeatedly as well, Svalbard since the 1860s and Newfoundland and Labrador since the 1930s. This article focuses on Finnish collections. These are deposited in the herbaria of Helsinki, Turku, and Oulu universities, except materials from the Nordenskiold expeditions, which were mainly deposited in Stockholm. Concerning the Kola Peninsula, collections at Helsinki are the most extensive. The exact number of specimens is not known, but by rough estimation, the number is about 60 000, with an additional 110 000 observations included in the database. These expeditions have provided material to describe 305 new taxa to science, viz. 47 algae, 78 bryophytes, 25 fungi, 136 lichens, and 19 vascular plants. This number is an underestimate, as many new species have been described in several separate taxonomic articles. At least 63 persons have contributed to making these collections to Finnish herbaria. Of those, 52 are of Finnish nationality.
  • Terhonen, Eeva; Blumenstein, Kathrin; Kovalchuk, Andriy; Asiegbu, Fred O. (2019)
    Terrestrial plants including forest trees are generally known to live in close association with microbial organisms. The inherent features of this close association can be commensalism, parasitism or mutualism. The term microbiota has been used to describe this ecological community of plant-associated pathogenic, mutualistic, endophytic and commensal microorganisms. Many of these microbiota inhabiting forest trees could have a potential impact on the health of, and disease progression in, forest biomes. Comparatively, studies on forest tree microbiomes and their roles in mutualism and disease lag far behind parallel work on crop and human microbiome projects. Very recently, our understanding of plant and tree microbiomes has been enriched due to novel technological advances using metabarcoding, metagenomics, metatranscriptomics and metaproteomics approaches. In addition, the availability of massive DNA databases (e.g., NCBI (USA), EMBL (Europe), DDBJ (Japan), UNITE (Estonia)) as well as powerful computational and bioinformatics tools has helped to facilitate data mining by researchers across diverse disciplines. Available data demonstrate that plant phyllosphere bacterial communities are dominated by members of only a few phyla (Proteobacteria, Actinobacteria, Bacteroidetes). In bulk forest soil, the dominant fungal group is Basidiomycota, whereas Ascomycota is the most prevalent group within plant tissues. The current challenge, however, is how to harness and link the acquired knowledge on microbiomes for translational forest management. Among tree-associated microorganisms, endophytic fungal biota are attracting a lot of attention for their beneficial health- and growth-promoting effects, and were preferentially discussed in this review.
  • Truchy, Amélie; Sarremejane, Romain; Muotka, Timo; Mykrä, Heikki; Angeler, David G.; Lehosmaa, Kaisa; Huusko, Ari; Johnson, Richard K.; Sponseller, Ryan A.; McKie, Brendan G. (Wiley Online Library, 2020)
    Global Change Biology 26 6 (2020)
    Ongoing climate change is increasing the occurrence and intensity of drought episodes worldwide, including in boreal regions not previously regarded as drought prone, and where the impacts of drought remain poorly understood. Ecological connectivity is one factor that might influence community structure and ecosystem functioning post-drought, by facilitating the recovery of sensitive species via dispersal at both local (e.g. a nearby habitat patch) and regional (from other systems within the same region) scales. In an outdoor mesocosm experiment, we investigated how impacts of drought on boreal stream ecosystems are altered by the spatial arrangement of local habitat patches within stream channels, and variation in ecological connectivity with a regional species pool. We measured basal ecosystem processes underlying carbon and nutrient cycling: (a) algal biomass accrual; (b) microbial respiration; and (c) decomposition of organic matter, and sampled communities of aquatic fungi and benthic invertebrates. An 8-day drought event had strong impacts on both community structure and ecosystem functioning, including algal accrual, leaf decomposition and microbial respiration, with many of these impacts persisting even after water levels had been restored for 3.5 weeks. Enhanced connectivity with the regional species pool and increased aggregation of habitat patches also affected multiple response variables, especially those associated with microbes, and in some cases reduced the effects of drought to a small extent. This indicates that spatial processes might play a role in the resilience of communities and ecosystem functioning, given enough time. These effects were however insufficient to facilitate significant recovery in algal growth before seasonal dieback began in autumn. The limited resilience of ecosystem functioning in our experiment suggests that even short-term droughts can have extended consequences for stream ecosystems in the world's vast boreal region, and especially on the ecosystem processes and services mediated by algal biofilms.
  • Liu, Xinxin; Hui, Nan; Kontro, Merja H. (2020)
    The triazine herbicide atrazine easily leaches with water through soil layers into groundwater, where it is persistent. Its behavior during short-term transport is poorly understood, and there is no in situ remediation method for it. The aim of this study was to investigate whether water circulation, or circulation combined with bioaugmentation (Pseudomonassp. ADP, or four isolates from atrazine-contaminated sediments) alone or with biostimulation (Na-citrate), could enhance atrazine dissipation in subsurface sediment-water systems. Atrazine concentrations (100 mg L-1) in the liquid phase of sediment slurries and in the circulating water of sediment columns were followed for 10 days. Atrazine was rapidly degraded to 53-64 mg L(-1)in the slurries, and further to 10-18 mg L(-1)in the circulating water, by the inherent microbes of sediments collected from 13.6 m in an atrazine-contaminated aquifer. Bioaugmentation without or with biostimulation had minor effects on atrazine degradation. The microbial number simultaneously increased in the slurries from 1.0 x 10(3)to 0.8-1.0 x 10(8)cfu mL(-1), and in the circulating water from 0.1-1.0 x 10(2)to 0.24-8.8 x 10(4)cfu mL(-1). In sediments without added atrazine, the cultivable microbial numbers remained low at 0.82-8.0 x 10(4)cfu mL(-1)in the slurries, and at 0.1-2.8 x 10(3)cfu mL(-1)in the circulating water. The cultivated microorganisms belonged to the nine generaAcinetobacter,Burkholderia,Methylobacterium,Pseudomonas,Rhodococcus,Sphingomonas,Streptomyces,VariovoraxandWilliamsia; i.e., biodiversity was low. Water flow through the sediments released adsorbed and complex-bound atrazine for microbial degradation, though the residual concentration of 10-64 mg L(-1)was high and could contaminate large groundwater volumes from a point source, e.g., during heavy rain or flooding.
  • Peng, Mao; Aguilar-Pontes, Maria V.; de Vries, Ronald P.; Mäkelä, Miia R. (2018)
    Aspergillus niger is one of the most widely used fungi to study the conversion of the lignocellulosic feedstocks into fermentable sugars. Understanding the sugar uptake system of A. niger is essential to improve the efficiency of the process of fungal plant biomass degradation. In this study, we report a comprehensive characterization of the sugar transportome of A. niger by combining phylogenetic and comparative transcriptomic analyses. We identified 86 putative sugar transporter (ST) genes based on a conserved protein domain search. All these candidates were then classified into nine subfamilies and their functional motifs and possible sugar-specificity were annotated according to phylogenetic analysis and literature mining. Furthermore, we comparatively analyzed the ST gene expression on a large set of fungal growth conditions including mono-, di- and polysaccharides, and mutants of transcriptional regulators. This revealed that transporter genes from the same phylogenetic clade displayed very diverse expression patterns and were regulated by different transcriptional factors. The genome-wide study of STs of A. niger provides new insights into the mechanisms underlying an extremely flexible metabolism and high nutritional versatility of A. niger and will facilitate further biochemical characterization and industrial applications of these candidate STs.
  • Valkonen, M.; Täubel, M.; Pekkanen, J.; Tischer, C.; Rintala, H.; Zock, J. -P.; Casas, L.; Probst-Hensch, N.; Forsberg, B.; Holm, M.; Janson, C.; Pin, I.; Gislason, T.; Jarvis, D.; Heinrich, J.; Hyvärinen, A. (2018)
    Microbial exposures in homes of asthmatic adults have been rarely investigated; specificities and implications for respiratory health are not well understood. The objectives of this study were to investigate associations of microbial levels with asthma status, asthma symptoms, bronchial hyperresponsiveness (BHR), and atopy. Mattress dust samples of 199 asthmatics and 198 control subjects from 7 European countries participating in the European Community Respiratory Health Survey II study were analyzed for fungal and bacterial cell wall components and individual taxa. We observed trends for protective associations of higher levels of mostly bacterial markers. Increased levels of muramic acid, a cell wall component predominant in Gram-positive bacteria, tended to be inversely associated with asthma (OR's for different quartiles: II 0.71 [0.39-1.30], III 0.44 [0.23-0.82], and IV 0.60 [0.31-1.18] P for trend .07) and with asthma score (P for trend .06) and with atopy (P for trend .02). These associations were more pronounced in northern Europe. This study among adults across Europe supports a potential protective effect of Gram-positive bacteria in mattress dust and points out that this may be more pronounced in areas where microbial exposure levels are generally lower.
  • Borovichev, Evgeny; Kozhin, Mikhail; Ignashov, Pavel A.; Kirillova, Natalya R.; Kopeina, Ekaterina; Kravchenko, Alexei; Kuznetsov, Oleg; Kutenkov, Stanislav; Melekhin, Aleksey V.; Popova, Ksenia B.; Razumovskaya, Anna V.; Sennikov, Alexander; Fadeeva, Margarita; Khimich, Yulia (2020)
  • Linnakoski, Riikka; Forbes, Kristian M. (2019)
  • Lindstrom, Stafva; Timonen, Sari; Sundstrom, Liselotte (2021)
    In a subarctic climate, the seasonal shifts in temperature, precipitation, and plant cover drive the temporal changes in the microbial communities in the topsoil, forcing soil microbes to adapt or decline. Many organisms, such as mound-building ants, survive the cold winter owing to the favorable microclimate in their nest mounds. We have previously shown that the microbial communities in the nest of the ant Formica exsecta are significantly different from those in the surrounding bulk soil. In the current study, we identified taxa, which were consistently present in the nests over a study period of three years. Some taxa were also significantly enriched in the nest samples compared with spatially corresponding reference soils. We show that the bacterial communities in ant nests are temporally stable across years, whereas the fungal communities show greater variation. It seems that the activities of the ants contribute to unique biochemical processes in the secluded nest environment, and create opportunities for symbiotic interactions between the ants and the microbes. Over time, the microbial communities may come to diverge, due to drift and selection, especially given the long lifespan (up to 30 years) of the ant colonies.
  • Palomäki, Anne (Helsingin yliopisto, 2019)
    In nutrient poor boreal peatlands, a significant proportion of photosynthesis-derived carbon of mycorrhizal plants is allocated to their fungal symbionts in exchange for nutrients. The soil carbon cycle is intertwined and affected by inputs of e.g. nitrogen and sulfur, whose amounts both in the soil and atmosphere have increased since the Industrial Revolution. In addition, as stated in the recent Global Warming of 1.5 °C -report (IPCC 2018) global warming is likely to reach 1.5 °C above pre-industrial levels before 2052. In this study, data from ericoid mycorrhizal fungi (ErMF) abundance, enzyme activities and the fungal taxa associated with them under increased warming and nutrient depositions were connected. This thesis is part of the Nitro-Erica -project of Natural Resources Institute Finland (LUKE) and it has been funded by the Academy of Finland (SA286731). Root fragments of Vaccinium oxycoccos L. and Andromeda polifolia L. were observed under a light microscope to determine the abundance of all root associated fungi, ErMF and dark septate endophytes (DSE). Fluorometric and photometric assays were used to study the ability of the fungi to degrade organic material and scavenge nutrients. Finally, direct PCR and Sanger sequencing were used to learn the dominant fungal taxa in the roots. A decrease in the abundance of ErMF and DSE was observed, indicating the possibility of a reduction in the carbon sink potential of peatlands through a decrease in the number of fungi. An increase in acid phosphatase activity under nitrogen deposition was observed in the two plants, which was expected as boreal peatlands are often nitrogen limited. In contrast, sulfur deposition suppressed the activity of all carbon acquiring enzymes which we concluded was likely to be the result of the sulfur inhibiting the growth of two parasitic fungi that greatly contributed to the overall high activity of carbon acquiring enzymes. More research is needed to gain a comprehensive understanding of the fungal abundance, communities and their functioning in peatlands under the changing environmental conditions.
  • Purhonen, Jenna; Nerea, Abrego; Komonen, Atte; Huhtinen, Seppo; Kotiranta, Heikki; Læssøe, Thomas; Halme, Panu (Nature Publishing Group, 2021)
    Scientific Reports 11: 1
    The general negative impact of forestry on wood-inhabiting fungal diversity is well recognized, yet the effect of forest naturalness is poorly disentangled among different fungal groups inhabiting dead wood of different tree species. We studied the relationship between forest naturalness, log characteristics and diversity of different fungal morpho-groups inhabiting large decaying logs of similar quality in spruce dominated boreal forests. We sampled all non-lichenized fruitbodies from birch, spruce, pine and aspen in 12 semi-natural forest sites of varying level of naturalness. The overall fungal community composition was mostly determined by host tree species. However, when assessing the relevance of the environmental variables separately for each tree species, the most important variable varied, naturalness being the most important explanatory variable for fungi inhabiting pine and aspen. More strikingly, the overall species richness increased as the forest naturalness increased, both at the site and log levels. At the site scale, the pattern was mostly driven by the discoid and pyrenoid morpho-groups inhabiting pine, whereas at the log scale, it was driven by pileate and resupinate morpho-groups inhabiting spruce. Although our study demonstrates that formerly managed protected forests serve as effective conservation areas for most wood-inhabiting fungal groups, it also shows that conservation planning and management should account for group- or host tree -specific responses.