Airborne Fungal Spore Review, New Advances and Automatisation

Optimizing an integrated biovigilance toolbox to study the spatial distribution and dynamic changes of airborne mycobiota, with a focus on cereal rust fungi in western Canada

In the face of evolving agricultural practices and climate change, tools towards an integrated biovigilance platform to combat crop diseases, spore sampling, DNA diagnostics and predictive trajectory modelling were optimized. These tools revealed microbial dynamics and were validated by monitoring cereal rust fungal pathogens affecting wheat, oats, barley and rye across four growing seasons (2015-2018) in British Columbia and during the 2018 season in southern Alberta. ITS2 metabarcoding revealed disparity in aeromycobiota diversity and compositional structure across the Canadian Rocky Mountains, suggesting a barrier effect on air flow and pathogen dispersal. A novel bioinformatics classifier and curated cereal rust fungal ITS2 database, corroborated by real-time PCR, enhanced the precision of cereal rust fungal species identification. Random Forest modelling identified crop and land-use diversification as well as atmospheric pressure and moisture as key factors in rust distribution. As a valuable addition to explain observed differences and patterns in rust fungus distribution, trajectory HYSPLIT modelling tracked rust fungal urediniospores' northeastward dispersal from the Pacific Northwest towards southern British Columbia and Alberta, indicating multiple potential origins. Our Canadian case study exemplifies the power of an advanced biovigilance toolbox towards developing an early-warning system for farmers to detect and mitigate impending disease outbreaks.

Mycological Methods for Routine Air Sampling and Interpretation of Results in Operating Theaters

Many infectious diseases are transmitted via the air and are, therefore, particularly difficult to combat. These infections include various invasive mycoses caused by molds. The usual route of infection is the inhalation of conidia. In hospitals, infection can also occur through the deposition of conidia in otherwise sterile anatomical sites during surgical and other invasive procedures. Therefore, knowledge of airborne mold concentrations can lead to measures to protect patients from fungal infections. The literature on this topic contains insufficient and sometimes ambiguous information. This is evidenced by the fact that there are no international recommendations or guidelines defining the methodology of air sampling and the interpretation of the results obtained. Surgical departments, intensive care units and medical mycology laboratories are, therefore, left to their own devices, leading to significant differences in the implementation of mycological surveillance in hospitals. The aim of this mini-review is to provide an overview of the current methods of air sampling and interpretation of results used in medical mycology laboratories.

Using qPCR and microscopy to assess the impact of harvesting and weather conditions on the relationship between Alternaria alternata and Alternaria spp. spores in rural and urban atmospheres

Alternaria is a plant pathogen and human allergen. Alternaria alternata is one of the most abundant fungal spores in the air. The purpose of this study was to examine whether Alternaria spp. spore concentrations can be used to predict the abundance and spatio-temporal pattern of A. alternata spores in the air. This was investigated by testing the hypothesis that A. alternata dominates airborne Alternaria spp. spores and varies spatio-temporally. Secondarily, we aimed at investigating the relationship between airborne Alternaria spp. spores and the DNA profile of A. alternata spores between two proximate (~ 7 km apart) sites. These were examined by sampling Alternaria spp. spores using Burkard 7-day and cyclone samplers for the period 2016-2018 at Worcester and Lakeside campuses of the University of Worcester, UK. Daily Alternaria spp. spores from the Burkard traps were identified using optical microscopy whilst A. alternata from the cyclone samples was detected and quantified using quantitative polymerase chain reaction (qPCR). The results showed that either A. alternata or other Alternaria species spores dominate the airborne Alternaria spore concentrations, generally depending on weather conditions. Furthermore, although Alternaria spp. spore concentrations were similar for the two proximate sites, A. alternata spore concentrations significantly varied for those sites and it is highly likely that the airborne samples contained large amounts of small fragments of A. alternata. Overall, the study shows that there is a higher abundance of airborne Alternaria allergen than reported by aerobiological networks and the majority is likely to be from spore and hyphal fragments.

Differences in microbial community composition and factors affecting different particulate matter during autumn in three cities of Xinjiang, China

Environmental pollution has become an issue of increasing concern in China, owing to the country's rapid economic development. Atmospheric particulate matter (PM) is known to be an important parameter in air quality monitoring; further, bioaerosol forms a crucial component of PM. As the climatic environments in the north and south of Xinjiang, China, are significantly different, here, atmospheric PM samples collected from three cities, Shihezi, Yining, and Tumushuk, located in different directions, were analysed for a better understanding of the spatial distribution patterns of microbial community composition of Xinjiang. The16s rDNA and 18 s rDNA were used to locate bacteria and fungi in PM_2.5, PM₁₀, and total suspended particulate matter (TSP) at the species level and genus level, and the microbial communities with the top 15 abundances were selected for analysis. The reports indicate that the most abundant group in Shihezi and Yining was Cenchrus_americanus, which belongs to Proteobacteria. The remaining 14 dominant species had their own distribution pattern in each city. The most dominant strain in Tumushuk was Bacillus_taeanensis, but this strain was not detected in Yining and Shihezi. Similarly, the most predominant fungus in Tumushuk (Microdorylaimus_miser under Myriophyllum) was not detected in the other two cities. The analysis of the effect of environmental impact factors on bacteria and fungi revealed that the impact factors such as temperature, humidity, and wind speed had a greater effect on microorganisms, while O₃ had a negative correlation with most microorganisms, owing to its toxicity. Overall, the results of this study show that short-range transported air masses have a greater impact on local pollutants and microorganisms.

What's New in Prevention of Invasive Fungal Diseases during Hospital Construction and Renovation Work: An Overview

The goal of the overview was to give insight into the recent data of invasive fungal diseases (IFDs) associated with construction and renovation in healthcare settings as well as the recent evidence about available prevention and infection control measures. The number of studies describing IFD outbreaks associated with construction or renovation is on the rise again. Applying adequate prevention measures is still a challenge not just for healthcare workers but also for architects and construction workers as well. The role of multidisciplinary teams in the planning and monitoring of prevention measures cannot be overemphasized. Dust control is an inevitable part of every prevention plan. HEPA filters are helpful in the prevention of fungal outbreaks in hematologic patients, but further studies are needed to clarify the extent in which they contribute as specific control measures. The cut-off value for a "threating" level of fungal spore contamination still remains to be defined. The value of antifungal prophylaxis is difficult to assess because other preventive measures are simultaneously applied. Recommendations are still based on few meta-analyses, a large number of descriptive reports, and the opinion of respective authorities. Outbreak reports in the literature are a valuable resource and should be used for education as well as for preparing outbreak investigations.

Seasonal variation of airborne fungal diversity and community structure in urban outdoor environments in Tianjin, China

Airborne fungi are ubiquitous in human living environments and may be a source of respiratory problems, allergies, and other health issues. A 12 months study was performed to investigate the diversity, concentration and community structure of culturable airborne fungi in different outdoor environments of Tianjin City, using an HAS-100B air sampler. A total of 1,015 fungal strains belonging to 175 species and 82 genera of Ascomycota 92.5%, Basidiomycota 7%, and Mucoromycota 0.3% were isolated and identified using morphological and molecular analysis. The most abundant fungal genera were Alternaria 35%, Cladosporium 18%, Penicillium 5.6%, Talaromyces 3.9%, Didymella 3%, and Aspergillus 2.8%, while the most frequently occurring species were A. alternata (24.7%), C. cladosporioides (11%), A. tenuissima (5.3%), P. oxalicum (4.53%), and T. funiculosus (2.66%). The fungal concentration ranged from 0 to 340 CFU/m³ during the whole study. Environmental factors, including temperature, relative humidity, wind speed, and air pressure exerted a varying effect on the presence and concentration of different fungal taxa. The four analyzed seasons showed significantly different airborne fungal communities, which were more strongly influenced by air temperature and relative humidity in spring and summer, whereas wind speed and air pressure had a stronger effect in autumn and winter. Fungal communities from green and busy sites did not show significant differences over the four analyzed seasons, which may be due to the effect of the surrounding environments characterized by high human activities on the air of the relatively small parks present in Tianjin. The present study provided valuable information on the seasonal dynamics and the environmental factors shaping the diversity and concentration of the analyzed outdoor airborne fungal communities, which can be of help for air quality monitoring, microbial contamination control, and health risk assessment in urban environments.

Recovery of the soil fungal microbiome after steam disinfection to manage the plant pathogen Fusarium solani

Soil disinfection using high temperatures via steam is a promising approach to manage plant pathogens, pests, and weeds. Soil steaming is a viable option for growers who are moving away from dependence on chemical soil fumigants, especially in plant nursery or high tunnel environments. However, there are few studies that investigate how soil steaming causes substantial disturbance to the soil by killing both target pathogens and other soil biota. Steaming treatments also change the trajectory of the soil microbiome as it reassembles over time. Growers are interested in the health of soils after using steam-disinfection, especially if a virulent pathogen colonizes the soil and then flourishes in a situation where there are very few microbes to suppress its growth. Should recruitment of a virulent pathogen occur in the soil, this could have devasting effects on seed germination, seedling establishment and survival. Beneficial microbes are often used to prevent the colonization of plant pathogens, especially after a soil-steaming event. Here, we experimentally test how soil fungal communities assemble after steaming disinfection. We introduce to steam-treated soil Fusarium solani, an important fungal pathogen of soybean and Trichoderma harzianum, a known beneficial fungus used for soilborne pathogen suppression. Results show that F. solani significantly affects the relative abundance and diversity of the soil fungal microbiome, however, T. harzianum does not mitigate the amount of F. solani in the steam treated soil. Within the T. harzianum microbial addition, the soil fungal communities were similar to the control (steaming only). This result suggests inoculating the soil with T. harzianum does not drastically alter the assembly trajectory of the soil fungal microbiome. Other soil amendments such as a combination of Trichoderma spp. or other genera could suppress F. solani growth and shift soil microbiome composition and function post-steaming, however, more experimental research is needed.

A Modified Spectroscopic Approach for the Real-Time Detection of Pollen and Fungal Spores at a Semi-Urban Site Using the WIBS-4+, Part I

The real-time monitoring of primary biological aerosol particles (PBAP) such as pollen and fungal spores has received much attention in recent years as a result of their health and climatic effects. In this study, the Wideband Integrated Bioaerosol Sensor (WIBS) 4+ model was evaluated for its ability to sample and detect ambient fungal spore and pollen concentrations, compared to the traditional Hirst volumetric method. Although the determination of total pollen and fungal spore ambient concentrations are of interest, the selective detection of individual pollen/fungal spore types are often of greater allergenic/agricultural concern. To aid in this endeavour, modifications were made to the WIBS-4 instrument to target chlorophyll fluorescence. Two additional fluorescence channels (FL4 and FL5 channels) were combined with the standard WIBS channels (FL1, FL2, FL3). The purpose of this modification is to help discriminate between grass and herb pollen from other pollen. The WIBS-4+ was able to successfully detect and differentiate between different bioaerosol classes. The addition of the FL4 and FL5 channels also allowed for the improved differentiation between tree (R² = 0.8), herbaceous (R² = 0.6) and grass (R² = 0.4) pollen and fungal spores (R² = 0.8). Both grass and herbaceous pollen types showed a high correlation with D type particles, showing strong fluorescence in the FL4 channel. The additional fluorescent data that were introduced also improved clustering attempts, making k-means clustering a comparable solution for this high-resolution data.

Aerobiological modelling II: A review of long-range transport models

The long-range atmospheric transport models of pollen and fungal spores require four modules for their development: (i) Meteorological module: which contain the meteorological model, and it can be coupled to transport model with the same output configuration (spatio-temporal resolution), or uncoupled does not necessarily have the same output parameters. (ii) Emission module: settles the mass fluxes of bioaerosol, it can be done with a complex parameterization integrating phenological models and meteorological factors or by a simple emission factor. (iii) Sources of emission module, specifically refers to forestry/agronomy maps or, in the case of herbs and fungi, to potential geographical areas of emission. Obtaining the highest possible resolution in these maps allows establishing greater reliability in the modelling. (iv) Atmospheric transport module, with its respective established output parameters. The review and subsequent analysis presented in this article, were performed on published electronic scientific articles from 1998 to 2016. Of a total of 101 models applied found in 64 articles, 33 % performed forward modelling (using 15 different models) and 67 % made backward modelling (with three different models). The 88 % of the cases were applied to pollen (13 taxa) and 12 % to fungal spores (3 taxa). Regarding the emission module, 22 % used parametrization (four different parameters) and 10 % emission factors. The most used transport model was HYSPLIT (59 %: 56 % backward and 3 % forward) following by SILAM 10 % (all forward). Main conclusions were that the models of long-range transport of pollen and fungal spores had high technical-scientific requirements to development and that the major limitations were the establishment of the flow and the source of the emission.

Numerical Simulation of Aspergillus Niger Spore Deposition in Nasal Cavities of a Population in Northwest China

Background: As common pathogens in the human respiratory tract, fungal-spore-related health risks have been challenging to evaluate properly. This paper presents numerical simulations of particle deposition of Aspergillus niger spores in human nasal cavities. Methods: 30 healthy adults (including 60 nasal chambers) who lived in northwest China were recruited to conduct a nasal cavity numerical simulation using computational fluid dynamics–discrete phase model (CFD-DPM). The deposition rate in each anatomic area and its influencing variables, such as body position and respiratory flow rate, were analyzed. Results: (1) Under a resting condition, only about 5.57% ± 1.51% Aspergillus niger spores were deposited in the nasal cavity, while most of them escaped from the nasopharynx, and 0.31% ± 0.20% spores entered the maxillary sinus; (2) under an exercising condition, spores deposited in the nasal cavity were about 2.09 times as many as that in the resting state; (3) in a lying position, the A. niger spores deposited evenly on the lateral wall of the nasal cavity and the sinus when compared with a standing position. However, the deposition rate in each anatomic area did not change significantly.