Cohort Study of Airway Mycobiome in Adult Cystic Fibrosis Patients: Differences in Community Structure between Fungi and Bacteria Reveal Predominance of Transient Fungal Elements

The respiratory mycobiome is an important but understudied component of the human microbiota. Like bacteria, fungi can cause severe lung diseases, but their infection rates are much lower. This study compared the bacterial and fungal communities of sputum samples from a large cohort of 56 adult patients with cystic fibrosis (CF) during nonexacerbation periods and under continuous antibiotic treatment. Molecular fingerprinting based on single-strand conformation polymorphism (SSCP) analysis revealed fundamental differences between bacterial and fungal communities. Both groups of microorganisms were taxonomically classified by identification of gene sequences (16S rRNA and internal transcript spacer), and prevalences of single taxa were determined for the entire cohort. Major bacterial pathogens were frequently observed, whereas fungi of known pathogenicity in CF were detected only in low numbers. Fungal species richness increased without reaching a constant level (saturation), whereas bacterial richness showed saturation after 50 patients were analyzed. In contrast to bacteria, a large number of fungal species were observed together with high fluctuations over time and among patients. These findings demonstrated that the mycobiome was dominated by transient species, which strongly suggested that the main driving force was their presence in inhaled air rather than colonization. Considering the high exposure of human airways to fungal spores, we concluded that fungi have low colonization abilities in CF, and colonization by pathogenic fungal species may be considered a rare event. A comprehensive understanding of the conditions promoting fungal colonization may offer the opportunity to prevent colonization and substantially reduce or even eliminate fungus-related disease progression in CF.

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Hypothesis and Theory: Fungal Spores in Stemflow and Potential Bark Sources

Frontiers in Forests and Global Change ◽

10.3389/ffgc.2021.623758 ◽

2021 ◽

Vol 4 ◽

Author(s):

Donát Magyar ◽

John T. Van Stan ◽

Kandikere R. Sridhar

Keyword(s):

Species Composition ◽

Fungal Spores ◽

Complex Function ◽

Chemical Properties ◽

Fungal Species ◽

Tree Canopy ◽

Fungal Colonization ◽

Palm Species ◽

Conidial Concentration ◽

Bark Structure

The study of stemflow fungi began over 50 years ago. Past work has been performed in different climatic regions of the world, with different sampling methods, by mycologists focusing on different taxonomical groups. Therefore, we aim to synthesize this work to delineate major conclusions and emerging hypothesis. Here, we present: (1) a systematic compilation of observations on stemflow conidial concentration, flux, and species composition; (2) an evaluation of the methods underlying these observations; (3) a testable theory to understand spatiotemporal dynamics in stemflow (including honeydews) conidial assemblages, with a focus on their relationship to bark structure and microhabitats; and (4) a discussion of major hypotheses based on past observations and new data. This represents a knowledge gap in our understanding of fungal dispersal mechanisms in forests, in a spatially-concentrated hydrologic flux that interacts with habitats throughout the forest microbiome. The literature synthesis and new data represent observations for 228 fungal species’ conidia in stemflow collected from 58 tree species, 6 palm species, and 1 bamboo species. Hypothetical relationships were identified regarding stemflow production and conidial concentration, flux, and species composition. These relationships appear to be driven by bark physico-chemical properties, tree canopy setting, the diversity of in-canopy microenvironments (e.g., tree holes, bark fissures, and epiphytes), and several possible conidia exchange processes (teleomorph aerosols, epi-faunal exchanges, fungal colonization of canopy microhabitats, and droplet impacts, etc.). The review reveals a more complex function of stemflow fungi, having a role in self-cleaning tree surfaces (which play air quality-related ecoservices themselves), and, on the other hand, these fungi may have a role in the protection of the host plant.

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Rock Surface Fungi in Deep Continental Biosphere—Exploration of Microbial Community Formation with Subsurface In Situ Biofilm Trap

Microorganisms ◽

10.3390/microorganisms9010064 ◽

2020 ◽

Vol 9 (1) ◽

pp. 64

Author(s):

Maija Nuppunen-Puputti ◽

Riikka Kietäväinen ◽

Lotta Purkamo ◽

Pauliina Rajala ◽

Merja Itävaara ◽

...

Keyword(s):

Significant Proportion ◽

Debaryomyces Hansenii ◽

Fungal Communities ◽

Fungal Colonization ◽

Rock Surface ◽

Mica Schist ◽

Deep Subsurface ◽

Bacterial Phyla ◽

In Situ Conditions

Fungi have an important role in nutrient cycling in most ecosystems on Earth, yet their ecology and functionality in deep continental subsurface remain unknown. Here, we report the first observations of active fungal colonization of mica schist in the deep continental biosphere and the ability of deep subsurface fungi to attach to rock surfaces under in situ conditions in groundwater at 500 and 967 m depth in Precambrian bedrock. We present an in situ subsurface biofilm trap, designed to reveal sessile microbial communities on rock surface in deep continental groundwater, using Outokumpu Deep Drill Hole, in eastern Finland, as a test site. The observed fungal phyla in Outokumpu subsurface were Basidiomycota, Ascomycota, and Mortierellomycota. In addition, significant proportion of the community represented unclassified Fungi. Sessile fungal communities on mica schist surfaces differed from the planktic fungal communities. The main bacterial phyla were Firmicutes, Proteobacteria, and Actinobacteriota. Biofilm formation on rock surfaces is a slow process and our results indicate that fungal and bacterial communities dominate the early surface attachment process, when pristine mineral surfaces are exposed to deep subsurface ecosystems. Various fungi showed statistically significant cross-kingdom correlation with both thiosulfate and sulfate reducing bacteria, e.g., SRB2 with fungi Debaryomyces hansenii.

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First Speleomycological Study on the Occurrence of Psychrophilic and Psychrotolerant Aeromycota in the Brestovská Cave (Western Tatras Mts., Slovakia) and First Reports for Some Species at Underground Sites

Biology ◽

10.3390/biology10060497 ◽

2021 ◽

Vol 10 (6) ◽

pp. 497

Author(s):

Rafał Ogórek ◽

Mateusz Speruda ◽

Justyna Borzęcka ◽

Agata Piecuch ◽

Magdalena Cal

Keyword(s):

Global Warming ◽

Immune System ◽

Biological Material ◽

Fungal Spores ◽

Airborne Fungi ◽

Fungal Species ◽

Air Samples ◽

Cold Adapted ◽

First Report

Most underground ecosystems are heterotrophic, fungi in these objects are dispersed in the air in the form of spores, and they may be potentially hazardous to mammals. Research in underground sites has focused on mesophilic airborne fungi and only a few concerned cold-adapted species. Therefore, the goal of our research was the first report of psychrophilic and psychrotolerant aeromycota in the Brestovská Cave using culture-based techniques with genetic and phenotypic identification. Plates with PDA medium containing sampled biological material were incubated at 8 ± 0.5 °C. The density of mycobiota inside the cave ranged from 37.4 to 71 CFU 1 m−3 of air and 63.3 CFU 1 m−3 of air outside the cave. Thus, the level of fungal spores did not exceed the standards for the mycological quality of the air. A total of 18 species were isolated during the study, and some species may be potentially dangerous to people with weakened immune system. All fungal species were present inside the cave and only seven of them were outside. Cladosporium cladosporioides dominated in the external air samples and Mortierella parvispora was cultured most frequently from internal air samples. To our knowledge, this is the first discovery of the fungal species such as Coniothyrium pyrinum, Cystobasidium laryngis, Filobasidium wieringae, Leucosporidium drummii, M. parvispora, Mrakia blollopis, Nakazawaea holstii, and Vishniacozyma victoriae in the air inside the underground sites. Moreover, C. pyrinum, C. laryngis, L. drummii, M. blollopis, and N. holstii have never been detected in any component of the underground ecosystems. There are possible reasons explaining the detection of those species, but global warming is the most likely.

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Prevalence of Aspergillus fumigatus and other fungal species in the sputum of adult patients with cystic fibrosis

Mycoses ◽

10.1046/j.1439-0507.2003.00830.x ◽

2003 ◽

Vol 46 (1-2) ◽

pp. 19-23 ◽

Cited By ~ 134

Author(s):

N. Bakare ◽

V. Rickerts ◽

J. Bargon ◽

G. Just-Nübling

Keyword(s):

Cystic Fibrosis ◽

Aspergillus Fumigatus ◽

Fungal Species ◽

Adult Patients

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ePS02.2 Fungal colonization in a cystic fibrosis adult population

Journal of Cystic Fibrosis ◽

10.1016/s1569-1993(15)30139-9 ◽

2015 ◽

Vol 14 ◽

pp. S44

Author(s):

G. Freire ◽

C. Lopes ◽

F. Freitas ◽

P. Azevedo

Keyword(s):

Cystic Fibrosis ◽

Adult Population ◽

Fungal Colonization

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Different Amplicon Targets for Sequencing-Based Studies of Fungal Diversity

Applied and Environmental Microbiology ◽

10.1128/aem.00905-17 ◽

2017 ◽

Vol 83 (17) ◽

Cited By ~ 40

Author(s):

Francesca De Filippis ◽

Manolo Laiola ◽

Giuseppe Blaiotta ◽

Danilo Ercolini

Keyword(s):

Microbial Ecology ◽

High Throughput ◽

Biological Samples ◽

Fungal Diversity ◽

High Throughput Sequencing ◽

Amplicon Sequencing ◽

Fungal Species ◽

Fungal Communities ◽

Its2 Region ◽

Mock Community

ABSTRACT Target-gene amplicon sequencing is the most exploited high-throughput sequencing application in microbial ecology. The targets are taxonomically relevant genes, with 16S rRNA being the gold standard for bacteria. As for fungi, the most commonly used target is the internal transcribed spacer (ITS). However, the uneven ITS length among species may promote preferential amplification and sequencing and incorrect estimation of their abundance. Therefore, the use of different targets is desirable. We evaluated the use of three different target amplicons for the characterization of fungal diversity. After an in silico primer evaluation, we compared three amplicons (the ITS1-ITS2 region [ITS1-2], 18S ribosomal small subunit RNA, and the D1/D2 domain of the 26S ribosomal large subunit RNA), using biological samples and a mock community of common fungal species. All three targets allowed for accurate identification of the species present. Nevertheless, high heterogeneity in ITS1-2 length was found, and this caused an overestimation of the abundance of species with a shorter ITS, while both 18S and 26S amplicons allowed for more reliable quantification. We demonstrated that ITS1-2 amplicon sequencing, although widely used, may lead to an incorrect evaluation of fungal communities, and efforts should be made to promote the use of different targets in sequencing-based microbial ecology studies. IMPORTANCE Amplicon-sequencing approaches for fungi may rely on different targets affecting the diversity and abundance of the fungal species. An increasing number of studies will address fungal diversity by high-throughput amplicon sequencing. The description of the communities must be accurate and reliable in order to draw useful insights and to address both ecological and biological questions. By analyzing a mock community and several biological samples, we demonstrate that using different amplicon targets may change the results of fungal microbiota analysis, and we highlight how a careful choice of the target is fundamental for a thorough description of the fungal communities.

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Studies on the arbuscular mycorrhizal fungal association in some medicinal plant species of paithal hills, western ghats kannur district, kerala

Kongunadu Research Journal ◽

10.26524/krj.2020.19 ◽

2020 ◽

Vol 7 (2) ◽

pp. 30-38

Author(s):

Santhoshkumar S ◽

Nagarajan N ◽

Sree Priya S

Keyword(s):

Plant Species ◽

Root Colonization ◽

Rhizosphere Soil ◽

Fungal Spores ◽

Arbuscular Mycorrhizal ◽

Soil Samples ◽

Fungal Colonization ◽

The Family ◽

Spore Population ◽

Arbuscular Mycorrhizal Fungal

In the present study to analyzed that the arbuscular mycorrhizal fungal spores in root colonization and spore population in rhizosphere soils samples in various medicinal at Paithal hills,Western Ghats of Kannur district, Kerala, India. Root and rhizosphere soil samples were collected during the month of August, 2018-March, 2019 from the surface to 30 cm depth as well as pH were also recorded. Totally 30 plant species belonging to 19 families were collected and identified. The present result showed arbuscular mycorrhizal spore population in the rhizosphere soil and root colonization of all the plant species. A total of 19 AM fungal spores were recovered from the rhizosphere soil samples in this study region. The Glomus was dominant had seen in rhizosphere soil samples in all the medicinal plant species. The maximum spore population was found in the rhizosphere soil samples of Mimosa pudica (590/100g of soil) which belongs to the family Mimosaceae and the lowest spore population was observed in the Terminalia bellirica 135/100g of soil) belongs to Combretaceae family. The highest 78 % AM fungal colonization was found in roots of Euphorbia hirta belongs to the family Euphorbiaceae. While the lowest 11 % AM fungal colonization was found in the root of Sida acuta belongs to the family Malvaceae.

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Molds in museum environments: Biodeterioration of art photographs and wooden sculptures

Archives of Biological Sciences ◽

10.2298/abs1303955g ◽

2013 ◽

Vol 65 (3) ◽

pp. 955-962 ◽

Cited By ~ 19

Author(s):

Milica Ljaljevic-Grbic ◽

M. Stupar ◽

Jelena Vukojevic ◽

Ivana Maricic ◽

Natasa Bungur

Keyword(s):

Aspergillus Niger ◽

Indoor Air ◽

Trichoderma Viride ◽

Fungal Species ◽

Chaetomium Globosum ◽

Fungal Colonization ◽

Cellulolytic Activity ◽

Cultural Center ◽

Fungal Propagules ◽

Alternaria Sp

Pieces of art stored in museum depots and display rooms are subject to fungal colonization that leads to bio-deterioration processes. Deteriorated wooden sculptures and art photographs temporarily stored in the quarantine room of the Cultural Center of Belgrade were subject to mycological analyses. Twelve fungal species were identified on the wooden substratum and five species were detected on photograph surfaces. Trichoderma viride, Chaetomium globosum and Alternaria sp. were the fungi with proven cellulolytic activity detected on the examined cellulose substrata. Indoor air mycobiota were estimated to 210.09 ? 8.06 CFU m-3, and the conidia of fungus Aspergillus niger were the dominant fungal propagules in the air of the examined room.

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Diversity, host-specificity and stability of sponge-associated fungal communities of co-occurring sponges

PeerJ ◽

10.7717/peerj.4965 ◽

2018 ◽

Vol 6 ◽

pp. e4965 ◽

Cited By ~ 7

Author(s):

Mary T.H.D. Nguyen ◽

Torsten Thomas

Keyword(s):

Host Specificity ◽

Horizontal Transmission ◽

Critical Role ◽

Fungal Species ◽

Fungal Communities ◽

Sponge Species ◽

Fungal Community Composition ◽

Potential Core ◽

Community Profiling ◽

Surrounding Seawater

Fungi play a critical role in a range of ecosystems; however, their interactions and functions in marine hosts, and particular sponges, is poorly understood. Here we assess the fungal community composition of three co-occurring sponges (Cymbastela concentrica, Scopalina sp., Tedania anhelans) and the surrounding seawater over two time points to help elucidate host-specificity, stability and potential core members, which may shed light into the ecological function of fungi in sponges. The results showed that ITS-amplicon-based community profiling likely provides a more realistic assessment of fungal diversity in sponges than cultivation-dependent approaches. The sponges studied here were found to contain phylogenetically diverse fungi (eight fungal classes were observed), including members of the family Togniniaceae and the genus Acrostalagmus, that have so far not been reported to be cultured from sponges. Fungal communities within any given sponge species were found to be highly variable compared to bacterial communities, and influenced in structure by the community of the surrounding seawater, especially considering temporal variation. Nevertheless, the sponge species studied here contained a few “variable/core” fungi that appeared in multiple biological replicates and were enriched in their relative abundance compared to seawater communities. These fungi were the same or highly similar to fungal species detected in sponges around the world, which suggests a prevalence of horizontal transmission where selectivity and enrichment of some fungi occur for those that can survive and/or exploit the sponge environment. Our current sparse knowledge about sponge-associated fungi thus indicate that fungal communities may perhaps not play as an important ecological role in the sponge holobiont compared to bacterial or archaeal symbionts.

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Wild Apple-Associated Fungi and Bacteria Compete to Colonize the Larval Gut of an Invasive Wood-Borer Agrilus mali in Tianshan Forests

Frontiers in Microbiology ◽

10.3389/fmicb.2021.743831 ◽

2021 ◽

Vol 12 ◽

Author(s):

Tohir A. Bozorov ◽

Zokir O. Toshmatov ◽

Gulnaz Kahar ◽

Daoyuan Zhang ◽

Hua Shao ◽

...

Keyword(s):

Gut Microbiota ◽

Inhibitory Concentration ◽

Fungal Species ◽

Gut Bacteria ◽

Recent Analysis ◽

Fungal Colonization ◽

Antifungal Compound ◽

Concentration Method ◽

Malus Sieversii ◽

Wood Borer

The gut microflora of insects plays important roles throughout their lives. Different foods and geographic locations change gut bacterial communities. The invasive wood-borer Agrilus mali causes extensive mortality of wild apple, Malus sieversii, which is considered a progenitor of all cultivated apples, in Tianshan forests. Recent analysis showed that the gut microbiota of larvae collected from Tianshan forests showed rich bacterial diversity but the absence of fungal species. In this study, we explored the antagonistic ability of the gut bacteria to address this absence of fungi in the larval gut. The results demonstrated that the gut bacteria were able to selectively inhibit wild apple tree-associated fungi. Among them, Pseudomonas synxantha showed strong antagonistic ability, producing antifungal compounds. Using different analytical methods, such as column chromatography, mass spectrometry, HPLC, and NMR, an antifungal compound, phenazine-1-carboxylic acid (PCA), was identified. Activity of the compound was determined by the minimum inhibitory concentration method and electron microscopy. Moreover, our study showed that the gut bacteria could originate from noninfested apple microflora during infestation. Overall, the results showed that in newly invaded locations, A. mali larvae changed their gut microbiota and adopted new gut bacteria that prevented fungal colonization in the gut.

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