Yeasts of the soil - obscure but precious

Benefits of fungal-to-bacterial quorum quenching as anti-biofouling strategy in membrane bioreactors for wastewater treatment and water reuse

This study addresses membrane biofouling in membrane bioreactors (MBRs) by exploring fungal-to-bacterial quorum quenching (QQ) strategies. While most research has been focused on bacterial-to-bacterial QQ tactics, this study identified fungal strain Vanrija sp. MS1, which is capable of degrading N-acyl-homoserine lactones (signaling molecules of Gram-negative bacteria). To determine the benefits of fungal over bacterial strains, after immobilization on fluidizing spherical beads in an MBR, MS1 significantly reduced the fouling rate by 1.8-fold compared to control MBR, decreased extracellular polymeric substance levels in the biofilm during MBR operation, and favorably changed microbial community and bacterial network, resulting in biofouling mitigation. It is noteworthy that, unlike Rhodococcus sp. BH4, MS1 enhanced QQ activity when switching from neutral to acidic conditions. These results suggest that MS1 has the potential for the effective treatment of acidic industrial wastewater sources such as semiconductor and secondary battery wastewater using MBRs.

Gypsum Cave Biofilm Communities are Strongly Influenced by Bat- And Arthropod-Related Fungi

The Gypsum Karst of Sorbas, Almeria, southeast Spain, includes a few caves whose entrances are open and allow the entry and roosting of numerous bats. Caves are characterized by their diversity of gypsum speleothems, such as stalactites, coralloids, gypsum crusts, etc. Colored biofilms can be observed on the walls of most caves, among which the Covadura and C3 caves were studied. The objective was to determine the influence that bat mycobiomes may have on the fungal communities of biofilms. The results indicate that the fungi retrieved from white and yellow biofilms in Covadura Cave (Ascomycota, Mortierellomycota, Basidiomycota) showed a wide diversity, depending on their location, and were highly influenced by the bat population, the guano and the arthropods that thrive in the guano, while C3 Cave was more strongly influenced by soil- and arthropod-related fungi (Ascomycota, Mortierellomycota), due to the absence of roosting bats.

Wild and partially synanthropic bird yeast diversity, in vitro virulence, and antifungal susceptibility of Candida parapsilosis and Candida tropicalis strains isolated from feces

Yeast complexes in the fecal samples of wild (Dendrocopos major, Picus viridis) and partially synanthropic (Bombycilla garrulus, Garrulus glandarius, Pica pica, and Pyrrhula pyrrhula) birds were studied in a forest ecosystem during winter. A total of 18 yeast species were identified: 16 ascomycetes and two basidiomycetes belonging to five subphyla of fungi: Saccharomycotina (15), Pezizomycotina (1), Agaricomycotina (1), and Pucciniomycotina (1). Most yeast species were found in the fecal samples of P. pyrrhula (Candida parapsilosis, C. zeylanoides, Debaryomyces hansenii, Hanseniaspora uvarum, Metschnikowia pulcherrima, Meyerozyma carpophila, M. guilliermondii, Rhodotorula mucilaginosa); the lowest number of yeast species was observed in the feces of B. garrulus (C. parapsilosis, C. zeylanoides, Met. pulcherrima, and Rh. mucilaginosa). The opportunistic species of the genus Candida were found only in feces of partially synanthropic birds: C. parapsilosis was observed in the feces of B. garrulus, G. glandarius, P. pica, and P. pyrrhula; its relative abundance was 69.3%, 49.1%, 10.5%, and 1.1%, respectively; C. tropicalis was observed in the feces of P. pica and G. glandarius; its relative abundance was 54.6% and 7.1%, respectively. Strains of C. parapsilosis and C. tropicalis isolated from the feces of partially synanthropic birds were evaluated for their susceptibility to conventional antifungal agents (fluconazole, voriconazole, amphotericin B) and hydrolytic activity. A total of 160 strains were studied. Resistance to fluconazole was detected in 86.8% of C. parapsilosis strains and in 87% of C. tropicalis strains; resistance to voriconazole was detected in 71.7% of C. parapsilosis and in 66.7% of C. tropicalis strains, and the lowest percentage of resistant strains was detected to amphotericin B, 2.8% and 3.7% in C. parapsilosis and C. tropicalis strains, respectively. Multiresistance was detected in one strain of C. parapsilosis isolated from P. pica feces and in one strain of C. tropicalis isolated from G. glandarius feces. Phospholipase and hemolysin activities in the strains of C. parapsilosis were low (mean Pz values of 0.93 and 0.91, respectively); protease activity was moderate (mean Pz value of 0.53). The ability to produce hydrolytic enzymes was higher in the isolated strains of C. tropicalis. The mean Pz values of phospholipase and hemolysin activities were moderate (mean Pz values of 0.63 and 0.60, respectively), whereas protease activity was high (mean Pz value of 0.32). Thus, wild and partially synanthropic birds play an important role in disseminating of various yeast species. These yeasts can enter the topsoil via feces and contribute to the formation of allochthonous and uneven soil yeast diversity in natural ecosystems. In addition, partially synanthropic birds can be vectors of virulent strains of opportunistic Candida species from urban environments to natural biotopes.

Yeast-insect interactions in southern Africa: Tapping the diversity of yeasts for modern bioprocessing

Yeast-insect interactions are one of the most interesting long-standing relationships whose research has contributed to our understanding of yeast biodiversity and their industrial applications. Although insect-derived yeast strains are exploited for industrial fermentations, only a limited number of such applications has been documented. The search for novel yeasts from insects is attractive to augment the currently domesticated and commercialized production strains. More specifically, there is potential in tapping the insects native to southern Africa. Southern Africa is home to a disproportionately high fraction of global biodiversity with a cluster of biomes and a broad climate range. This review presents arguments on the roles of the mutualistic relationship between yeasts and insects, the presence of diverse pristine environments and a long history of spontaneous food and beverage fermentations as the potential source of novelty. The review further discusses the recent advances in novelty of industrial strains of insect origin, as well as various ancient and modern-day industries that could be improved by use yeasts from insect origin. The major focus of the review is on the relationship between insects and yeasts in southern African ecosystems as a potential source of novel industrial yeast strains for modern bioprocesses.

A Second Fungal Outbreak in Castañar Cave, Spain, Discloses the Fragility of Subsurface Ecosystems

Castañar is a cave with strict visitor control measures since it was open to public visits in 2003. However, in recent years, the cave suffered two fungal outbreaks, the first in 2008 and controlled by cleaning the contaminated sediments and subsequent closure of the cave until 2014. The cave was reopened but limited to a maximum of 450 visitors/year. Despite these restrictions on visit, the cave experienced a second outbreak in 2021, originating from the installation of a steel grating walkway, aiming at protecting the ground sediments from the visitors' footsteps. Here, we conducted an analysis using Next-Generation Sequencing and culture-dependent techniques to investigate the fungal communities related to the second outbreak and compare with those present before the cave suffered the outbreak. The results show that the most abundant fungi involved in the 2021 outbreak were already detected in 2020, and even in 2008 and 2009, although the main species that originating both outbreaks were different, likely due to the different carbon sources introduced into the cave.

Culturable yeast diversity in urban topsoil influenced by various anthropogenic impacts

In urban ecosystems, processes associated with anthropogenic influences almost always lead to changes in soil micromycete complexes. The taxonomic structure of soil micromycete complexes is an important informative parameter of soil bioindication in the ecological control of urban environments. Unicellular fungi, such as culturable yeasts, are a very suitable and promising object of microbiological research for monitoring urban topsoil. This review aims to give an overview of the yeast communities in urban topsoil in different areas of Moscow (heating main area, household waste storage and disposal area, highway area) and to discuss the changes in the taxonomic structure of culturable yeast complexes depending on the type and intensity of anthropogenic impact.

Analysis of rhizosphere fungal community of agricultural crops cultivated in laboratory experiments on Chernevaya taiga soil

Chernevaya taiga of Western Siberia, Russia, is a unique ecosystem characterized by fertile soil, exceptionally large herbaceous plant sizes, and extraordinarily rapid rates of plant residue degradation. We expected that growing crops on soil collected from Chernevaya taiga, which has never been used for agricultural purposes before, would result in a distinct rhizospheric fungal community. This community could potentially yield novel, potent biostimulators and biocontrol fungi for modern agriculture. To check this idea, we used high-throughput ITS sequencing to examine the microbial communities in the rhizosphere of spring wheat and radish grown in greenhouse experiments on Chernevaya and control soils. Additionally, representative fungal strains were isolated and assessed for their ability to promote growth in wheat seedlings. The study revealed that the most abundant phyla in the rhizospheric fungal community were Mortierellomycota, primarily consisting of Mortierella species, and Ascomycota. Mucor and Umbelopsis comprised the majority of Mucoromycota in the control soils. Fusarium and Oidiodendron, two potentially plant-pathogenic fungi, were only found in the rhizosphere of crops grown in the control soil. Conversely, Chernevaya soil contained a diverse range of potential biocontrol fungi for plants. Tested novel fungal isolates showed a stimulating effect on the development of wheat seedlings and positively affected their rate of biomass accumulation. The results of the study demonstrate that the soil of Chernevaya taiga do indeed contain fungi with prominent potential to stimulate agricultural plants growth.

Assessment of soil yeasts Papiliotrema laurentii S-08 and Saitozyma podzolica S-77 for plant growth promotion and biocontrol of Fusarium wilt of brinjal

AIM

This study aimed to determine the efficacy of the soil yeasts Papiliotrema laurentii S-08 and Saitozyma podzolica S-77 for plant growth promotion (PGP) and biocontrol of wilt disease in brinjal plants while applying yeasts individually or as a consortium in pot experiments.

METHODS AND RESULTS

The yeasts were tested for various PGP characteristics and antagonistic activity against the phytopathogen Fusarium oxysporum f. sp. melongenae. Both the yeast isolates demonstrated some PGP attributes as well as inhibited the growth of the phytopathogen. A gas chromatography-mass spectrometry analysis of the yeast metabolites revealed the presence of several antifungal compounds. The pot experiment performed under nursery conditions showed that applying these yeasts, individually or in consortium, decreased the percent disease incidence in brinjal seedlings while significantly enhancing their growth parameters.

CONCLUSION

Papiliotrema laurentii S-08 and S. podzolica S-77 can be used in brinjal plants as plant growth promoters and also as biocontrol agents against the brinjal wilt disease.

Effects of temporal and spatial scales on soil yeast communities in the peach orchard

Shihezi Reclamation Area is located at the southern edge of the Junggar Basin, with natural, soil, and climatic conditions unique to the production of peaches. In turn, peach orchards have accumulated rich microbial resources. As an important taxon of soil fungi, the diversity and community structure changes of yeast in the soil of peach orchards on spatial and temporal scales are still unknown. Here, we aimed to investigate the changes in yeast diversity and community structure in non-rhizosphere and rhizosphere soils of peach trees of different ages in the peach orchard and the factors affecting them, as well as the changes in the yeast co-occurrence network in the peach orchard at spatial and temporal scales. High-through put sequencing results showed that a total of 114 yeast genera were detected in all soil samples, belonging to Ascomycota (60 genera) and Basidiomycota (54 genera). The most dominant genus, Cryptococcus, was present in greater than 10% abundance in each sample. Overall, the differences in yeast diversity between non-rhizosphere and rhizosphere soil of peach trees at 3, 8 and 15 years were not significant. Principal coordinate analysis (PCoA) showed that differences in yeast community structure were more pronounced at the temporal scale compared to the spatial scale. The results of soil physical and chemical analysis showed that the 15-year-old peach rhizosphere soil had the lowest pH, while the OM, TN, and TP contents increased significantly. Redundancy analysis showed that soil pH and CO were key factors contributing to changes in soil yeast community structure in the peach orchard at both spatial and temporal scales. The results of co-occurrence network analysis showed that the peach orchard soil yeast network showed synergistic effects as a whole, and the degree of interactions and connection tightness of the 15-year-old peach orchard soil yeast network were significantly higher than the 3- and 8-year-old ones on the time scale. The results reveal the distribution pattern and mechanism of action of yeast communities in peach orchard soils, which can help to develop effective soil management strategies and improve the stability of soil microecology, thus promoting crop growth.

Soybean and Cotton Spermosphere Soil Microbiome Shows Dominance of Soilborne Copiotrophs

The spermosphere is the transient, immediate zone of soil around imbibing and germinating seeds. It represents a habitat where there is contact between seed-associated microbes and soil microbes, but it is studied less than other plant habitats. Previous studies on spermosphere microbiology were primarily culture based or did not sample the spermosphere soil as initially defined in space and time. Thus, the objectives of this study were to develop an efficient strategy to collect spermosphere soils around imbibing soybean and cotton in nonsterile soil and investigate changes in microbial communities. The method employed sufficiently collected spermosphere soil as initially defined in space by constraining the soil sampled with a cork borer and confining the soil to a 12-well microtiter plate. Spermosphere prokaryote composition changed over time and depended on the crop within 6 h after seeds were sown. By 12 to 18 h, crops had unique microbial communities in spermosphere soils. Prokaryote evenness dropped following seed imbibition, with the proliferation of copiotrophic soil bacteria. Due to their long history of plant growth promotion, prokaryote operational taxonomic units (OTUs) in Bacillus, Paenibacillus, Burkholderia, Massilia, Azospirillum, and Pseudomonas were notable organisms enriched. Fungi and prokaryotes were hub taxa in cotton and soybean spermosphere networks. Additionally, the enriched taxa were not hubs in networks, suggesting that other taxa besides those enriched may be important for spermosphere communities. Overall, this study advances knowledge in the assembly of the plant microbiome early in a plant's life, which may have plant health implications in more mature plant growth stages. IMPORTANCE The central hypothesis of this research was that plant species and seed exudate release would alter the assembly of microbes in the spermosphere soil. Our research investigated the response of microbes to the initial burst of nutrients into the spermosphere soil, filling knowledge gaps from previous studies that pregerminated seeds under sterile conditions. We identified several copiotrophic bacterial lineages with a long history of plant growth promotion proliferating in response to the initial exudate release. With a comparative network approach, we show that these copiotrophic bacteria are not central to networks, demonstrating that other microbes (including fungi) may be important for community structure. This study improves knowledge on microbial dynamics in the understudied spermosphere and helps inform solutions for biologically or ecologically motivated solutions to spermosphere pathogens.

Nonbacterial Microflora in Wastewater Treatment Plants: an Underappreciated Potential Source of Pathogens

Wastewater treatment plants (WWTPs) receive and treat large volumes of domestic, industrial, and urban wastewater containing pathogenic and nonpathogenic microorganisms, chemical compounds, heavy metals, and other potentially hazardous substances. WWTPs play an essential role in preserving human, animal, and environmental health by removing many of these toxic and infectious agents, particularly biological hazards. Wastewater contains complex consortiums of bacterial, viral, archaeal, and eukaryotic species, and while bacteria in WWTP have been extensively studied, the temporal and spatial distribution of nonbacterial microflora (viruses, archaea, and eukaryotes) is less understood. In this study, we analyzed the viral, archaeal, and eukaryotic microflora in wastewater throughout a treatment plant (raw influent, effluent, oxidation pond water, and oxidation pond sediment) in Aotearoa (New Zealand) using Illumina shotgun metagenomic sequencing. Our results suggest a similar trend across many taxa, with an increase in relative abundance in oxidation pond samples compared to influent and effluent samples, except for archaea, which had the opposite trend. Additionally, some microbial families, such as Podoviridae bacteriophages and Apicomplexa alveolates, appeared largely unaffected by the treatment process, with their relative abundance remaining stable throughout. Several groups encompassing pathogenic species, such as Leishmania, Plasmodium, Toxoplasma, Apicomplexa, Cryptococcus, Botrytis, and Ustilago, were identified. If present, these potentially pathogenic species could be a threat to human and animal health and agricultural productivity; therefore, further investigation is warranted. These nonbacterial pathogens should be considered when assessing the potential for vector transmission, distribution of biosolids to land, and discharge of treated wastewater to waterways or land. IMPORTANCE Nonbacterial microflora in wastewater remain understudied compared to their bacterial counterparts despite their importance in the wastewater treatment process. In this study, we report the temporal and spatial distributions of DNA viruses, archaea, protozoa, and fungi in raw wastewater influent, effluent, oxidation pond water, and oxidation pond sediments by using shotgun metagenomic sequencing. Our study indicated the presence of groups of nonbacterial taxa which encompass pathogenic species that may have potential to cause disease in humans, animals, and agricultural crops. We also observed higher alpha diversity in viruses, archaea, and fungi in effluent samples than in influent samples. This suggests that the resident microflora in the wastewater treatment plant may be making a greater contribution to the diversity of taxa observed in wastewater effluent than previously thought. This study provides important insights to better understand the potential human, animal, and environmental health impacts of discharged treated wastewater.

The composition of environmental microbiota in three tree fruit packing facilities changed over seasons and contained taxa indicative of L. monocytogenes contamination

BACKGROUND

Listeria monocytogenes can survive in cold and wet environments, such as tree fruit packing facilities and it has been implicated in outbreaks and recalls of tree fruit products. However, little is known about microbiota that co-occurs with L. monocytogenes and its stability over seasons in tree fruit packing environments. In this 2-year longitudinal study, we aimed to characterize spatial and seasonal changes in microbiota composition and identify taxa indicative of L. monocytogenes contamination in wet processing areas of three tree fruit packing facilities (F1, F2, F3).

METHODS

A total of 189 samples were collected during two apple packing seasons from floors under the washing, drying, and waxing areas. The presence of L. monocytogenes was determined using a standard culturing method, and environmental microbiota was characterized using amplicon sequencing. PERMANOVA was used to compare microbiota composition among facilities over two seasons, and abundance-occupancy analysis was used to identify shared and temporal core microbiota. Differential abundance analysis and random forest were applied to detect taxa indicative of L. monocytogenes contamination. Lastly, three L. monocytogenes-positive samples were sequenced using shotgun metagenomics with Nanopore MinION, as a proof-of-concept for direct detection of L. monocytogenes' DNA in environmental samples.

RESULTS

The occurrence of L. monocytogenes significantly increased from 28% in year 1 to 46% in year 2 in F1, and from 41% in year 1 to 92% in year 2 in F3, while all samples collected from F2 were L. monocytogenes-positive in both years. Samples collected from three facilities had a significantly different microbiota composition in both years, but the composition of each facility changed over years. A subset of bacterial taxa including Pseudomonas, Stenotrophomonas, and Microbacterium, and fungal taxa, including Yarrowia, Kurtzmaniella, Cystobasidium, Paraphoma, and Cutaneotrichosporon, were identified as potential indicators of L. monocytogenes within the monitored environments. Lastly, the DNA of L. monocytogenes was detected through direct Nanopore sequencing of metagenomic DNA extracted from environmental samples.

CONCLUSIONS

This study demonstrated that a cross-sectional sampling strategy may not accurately reflect the representative microbiota of food processing facilities. Our findings also suggest that specific microorganisms are indicative of L. monocytogenes, warranting further investigation of their role in the survival and persistence of L. monocytogenes. Video Abstract.

Mycobiota of Mexican Maize Landraces with Auxin-Producing Yeasts That Improve Plant Growth and Root Development

Compared to agrochemicals, bioinoculants based on plant microbiomes are a sustainable option for increasing crop yields and soil fertility. From the Mexican maize landrace "Raza cónico" (red and blue varieties), we identified yeasts and evaluated in vitro their ability to promote plant growth. Auxin production was detected from yeast isolates and confirmed using Arabidopsis thaliana plants. Inoculation tests were performed on maize, and morphological parameters were measured. Eighty-seven yeast strains were obtained (50 from blue corn and 37 from red corn). These were associated with three families of Ascomycota (Dothideaceae, Debaryomycetaceae, and Metschnikowiaceae) and five families of Basidiomycota (Sporidiobolaceae, Filobasidiaceae, Piskurozymaceae, Tremellaceae, and Rhynchogastremataceae), and, in turn, distributed in 10 genera (Clavispora, Rhodotorula, Papiliotrema, Candida, Suhomyces, Soliccocozyma, Saitozyma Holtermaniella, Naganishia, and Aeurobasidium). We identified strains that solubilized phosphate and produced siderophores, proteases, pectinases, and cellulases but did not produce amylases. Solicoccozyma sp. RY31, C. lusitaniae Y11, R. glutinis Y23, and Naganishia sp. Y52 produced auxins from L-Trp (11.9-52 µg/mL) and root exudates (1.3-22.5 µg/mL). Furthermore, they stimulated the root development of A. thaliana. Inoculation of auxin-producing yeasts caused a 1.5-fold increase in maize plant height, fresh weight, and root length compared to uninoculated controls. Overall, maize landraces harbor plant growth-promoting yeasts and have the potential for use as agricultural biofertilizers.

Micro-fractionation shows microbial community changes in soil particles below 20 μm

Introduction

Micro-scale analysis of microbes in soil is essential to the overall understanding of microbial organization, interactions, and ecosystem functioning. Soil fractionation according to its aggregated structure has been used to access microbial habitats. While bacterial communities have been extensively described, little is known about the fungal communities at scales relevant to microbial interactions.

Methods

We applied a gentle soil fractionation method to preserve stable aggregated structures within the range of micro-aggregates and studied fungal and bacterial communities as well as nitrogen cycling potentials in the pristine Rothamsted Park Grass soil (bulk soil) as well as in its particle size fractions (PSFs; >250 μm, 250–63 μm, 63–20 μm, 20–2 μm, <2 μm, and supernatant).

Results

Overall bacterial and fungal community structures changed in PSFs below 20 μm. The relative abundance of Basidiomycota decreased with decreasing particle size over the entire measure range, while Ascomycota showed an increase and Mucoromycota became more prominent in particles below 20 μm. Bacterial diversity was found highest in the < 2 μm fraction, but only a few taxa were washed-off during the procedure and found in supernatant samples. These taxa have been associated with exopolysaccharide production and biofilm formation (e.g., Pseudomonas, Massilia, Mucilaginibacter, Edaphobaculum, Duganella, Janthinobacterium, and Variovorax). The potential for nitrogen reduction was found elevated in bigger aggregates.

Discussion

The observed changes below 20 μm particle are in line with scales where microbes operate and interact, highlighting the potential to focus on little researched sub-fractions of micro-aggregates. The applied method shows potential for use in studies focusing on the role of microbial biofilms in soil and might also be adapted to research various other soil microbial functions. Technical advances in combination with micro-sampling methods in soil promise valuable output in soil studies when particles below 20 μm are included.

Comparative toxicological assessment of three soils polluted with different levels of hydrocarbons and heavy metals using in vitro and in vivo approaches

The biological effects induced by the pollutants present in soils, together with the chemical and physical characterizations, are good indicators to provide a general overview of their quality. However, the existence of studies where the toxicity associated to soils contaminated with mixtures of pollutants applying both in vitro and in vivo models are scarce. In this work, three soils (namely, Soil 001, Soil 002 and Soil 013) polluted with different concentrations of hydrocarbons and heavy metals were evaluated using different organisms representative of human (HepG2 human cell line) and environmental exposure (the yeast Saccharomyces cerevisiae, the Gram-negative bacterium Pseudomonas putida and, for the in vivo evaluation, the annelid Enchytraeus crypticus). In vitro assays showed that the soluble fraction of the Soil 001, which presented the highest levels of heavy metals, represented a great impact in the viability of the HepG2 cells and S. cerevisiae, while organic extracts from Soils 002 and 013 caused a slight decrease in the viability of HepG2 cells. In addition, in vivo experiments showed that Soils 001 and 013 affected the survival and the reproduction of E. crypticus. Altogether, these results provide a general overview of the potential hazards associated to three specific contaminated sites in a variety of organisms, showing how different concentrations of similar pollutants affect them, and highlights the relevance of testing both organic and soluble extracts when in vitro safety assays of soils are performed.

Legacy effects of fumigation on soil bacterial and fungal communities and their response to metam sodium application

BACKGROUND

Soil microorganisms are integral to maintaining soil health and crop productivity, but fumigation used to suppress soilborne diseases may affect soil microbiota. Currently, little is known about the legacy effects of soil fumigation on soil microbial communities and their response to fumigation at the production scale. Here, 16S rRNA gene and internal transcribed spacer amplicon sequencing was used to characterize the bacterial and fungal communities in soils from intensively managed crop fields with and without previous exposure to metam sodium (MS) fumigation. The effect of fumigation history, soil series, and rotation crop diversity on microbial community variation was estimated and the response of the soil microbiome to MS application in an open microcosm system was documented.

RESULTS

We found that previous MS fumigation reduced soil bacterial diversity but did not affect microbial richness and fungal diversity. Fumigation history, soil series, and rotation crop diversity were the main contributors to the variation in microbial β-diversity. Between fumigated and non-fumigated soils, predominant bacterial and fungal taxa were similar; however, their relative abundance varied with fumigation history. In particular, the abundance of Basidiomycete yeasts was decreased in fumigated soils. MS fumigation also altered soil bacterial and fungal co-occurrence network structure and associations. In microcosms, application of MS reduced soil microbial richness and bacterial diversity. Soil microbial β-diversity was also affected but microbial communities of the microcosm soils were always similar to that of the field soils used to establish the microcosms. MS application also induced changes in relative abundance of several predominant bacterial and fungal genera based on a soil's previous fumigation exposure.

CONCLUSIONS

The legacy effects of MS fumigation are more pronounced on soil bacterial diversity, β-diversity and networks. Repeated fumigant applications shift soil microbial compositions and may contribute to differential MS sensitivity among soil microorganisms. Following MS application, microbial richness and bacterial diversity decreases, but microbial β-diversity was similar to that of the field soils used to establish the microcosms in the short-term (< 6 weeks). The responses of soil microbiome to MS fumigation are context dependent and rely on abiotic, biotic, and agricultural management practices.

Discovery of Oleaginous Yeast from Mountain Forest Soil in Thailand

As an interesting alternative microbial platform for the sustainable synthesis of oleochemical building blocks and biofuels, oleaginous yeasts are increasing in both quantity and diversity. In this study, oleaginous yeast species from northern Thailand were discovered to add to the topology. A total of 127 yeast strains were isolated from 22 forest soil samples collected from mountainous areas. They were identified by an analysis of the D1/D2 domain of the large subunit rRNA (LSU rRNA) gene sequences to be 13 species. The most frequently isolated species were Lipomyces tetrasporus and Lipomyces starkeyi. Based on the cellular lipid content determination, 78 strains of ten yeast species, and two potential new yeast that which accumulated over 20% of dry biomass, were found to be oleaginous yeast strains. Among the oleaginous species detected, Papiliotrema terrestris and Papiliotrema flavescens have never been reported as oleaginous yeast before. In addition, none of the species in the genera Piskurozyma and Hannaella were found to be oleaginous yeast. L. tetrasporus SWU-NGP 2-5 accumulated the highest lipid content of 74.26% dry biomass, whereas Lipomyces mesembrius SWU-NGP 14-6 revealed the highest lipid quantity at 5.20 ± 0.03 g L-1. The fatty acid profiles of the selected oleaginous yeasts varied depending on the strain and suitability for biodiesel production.

Soil Microbiome Influences on Seedling Establishment and Growth of Prosopis chilensis and Prosopis tamarugo from Northern Chile

Prosopis chilensis and Prosopis tamarugo, two woody legumes adapted to the arid regions of Chile, have a declining distribution due to the lack of new seedling establishment. This study investigated the potential of both species to establish in soil collected from four locations in Chile, within and outside the species distribution, and to assess the role of the root-colonizing microbiome in seedling establishment and growth. Seedling survival, height, and water potential were measured to assess establishment success and growth. 16S and ITS2 amplicon sequencing was used to characterize the composition of microbial communities from the different soils and to assess the ability of both Prosopis species to recruit bacteria and fungi from the different soils. Both species were established on three of the four soils. P. tamarugo seedlings showed significantly higher survival in foreign soils and maintained significantly higher water potential in Mediterranean soils. Amplicon sequencing showed that the four soils harbored distinct microbial communities. Root-associated microbial composition indicated that P. chilensis preferentially recruited mycorrhizal fungal partners while P. tamarugo recruited abundant bacteria with known salt-protective functions. Our results suggest that a combination of edaphic properties and microbial soil legacy are potential factors mediating the Prosopis establishment success in different soils.

Homogeneous selection is stronger for fungi in deeper peat than in shallow peat in the low-temperature fens of China

Peatlands have accumulated enormous amounts of carbon over millennia, and climate changes threatens the release of this carbon into the atmosphere. Fungi are crucial drivers of global carbon cycling because they are the principal decomposer of organic matter in peatlands. However, the fungal community composition and ecological preferences in peat remain unclear, which restricts our ability to evaluate the role of the fungal community in peat biogeochemical functions. We investigated 54 soils from 6 low-temperature peatlands across China to fill this knowledge gap. The peat was divided into above-water table (AWT) and below-water table (BWT) layers based on the water table fluctuation. We investigated fungal community assembly processes and drivers for each peat layer. The results showed that fungal communities differed significantly among peat layers. The relative abundance of symbiotrophs was significantly higher in the AWT (17.4%) than in the BWT (9.0%), while the abundances of yeast and litter saprotrophs were obviously lower in the AWT than in the BWT. Our results revealed that the assemblage of both fungal taxonomic and phylogenetic communities was mainly governed by stochastic processes in both AWT (87.8%) and BWT (58.6%) layers. However, in the BWT, the relative importance of deterministic processes (28.4%) significantly increased, indicating a potential deterministic environmental selection induced by permanently anaerobic condition. Mean annual precipitation and mean annual temperature were the most critical drives for the assemblage of the fungal community in the BWT. These observations collectively indicate that fungal community assembly is depth-dependent, implying different community assembly mechanisms and ecological functions along the peat profile. These findings highlight the importance of climate driven deep peat fungal community composition assemblages and suggest the potential to project the changes in fungal diversity with ongoing climate change.

Changes in urban soil yeast communities after a reduction in household waste during the COVID-19 pandemic

The soils of streets, urban parks and suburban areas were examined for yeasts in the summer of 2020 on the territory of the southern cities of Russia and the Republic of Crimea: Krasnodar, Maykop, Sochi and Simferopol. The results of this study are compared with the results of a previous study carried out in these cities in 2019. This study was conducted three months after the lockdown due to the COVID-19 pandemic, which led to a sustained decline in household waste deposition in these areas. The number of tourists visiting these southern cities decreased significantly, and the number of walkers and visitors to urban parks fell sharply. In 2020, after the decline of household waste loads, the yeast abundance was slightly but reliably higher than in 2019. A total of 30 yeast species were observed - 11 ascomycetes and 19 basidiomycetes. This was more than in 2019 and was caused by twice as many autochthonous basidiomycetous yeast species (natural core community), which were found in urban soils only after the reduction in household waste in the environment - Apiotrichum dulcitum, A. laibachii, Saitozyma podzolica Solicoccozyma terricola. And at the same time, the proportion of clinically significant (opportunistic) yeasts, Candida sake and Meyerozyma guilliermondii, was much lower in 2020 than in 2019. Thus, the observed changes in yeast communities in urban soils could be a short-time response of the microbial community to a reduction in household waste.

Uncovering the Yeast Communities in Fungus-Growing Ant Colonies

Yeast-insect interactions are compelling models to study the evolution, ecology, and diversification of yeasts. Fungus-growing (attine) ants are prominent insects in the Neotropics that evolved an ancient fungiculture of basidiomycete fungi over 55-65 million years, supplying an environment for a hidden yeast diversity. Here we assessed the yeast diversity in the attine ant environment by thoroughly sampling fungus gardens across four out of five ant fungiculture systems: Acromyrmex coronatus and Mycetomoellerius tucumanus standing for leaf-cutting and higher-attine fungicultures, respectively; Apterostigma sp., Mycetophylax sp., and Mycocepurus goeldii as ants from the lower-attine fungiculture. Among the fungus gardens of all fungus-growing ants examined, we found taxonomically unique and diverse microbial yeast communities across the different fungicultures. Ascomycete yeasts were the core taxa in fungus garden samples, with Saccharomycetales as the most frequent order. The genera Aureobasidium, Candida, Papiliotrema, Starmerella, and Sugiyamaella had the highest incidence in fungus gardens. Despite the expected similarity within the same fungiculture system, colonies of the same ant species differed in community structure. Among Saccharomycotina yeasts, few were distinguishable as killer yeasts, with a classical inhibition pattern for the killer phenotype, differing from earlier observations in this environment, which should be further investigated. Yeast mycobiome in fungus gardens is distinct between colonies of the same fungiculture and each ant colony harbors a distinguished and unique yeast community. Fungus gardens of attine ants are emergent environments to study the diversity and ecology of yeasts associated with insects.

Does Organomineral Fertilizer Combined with Phosphate-Solubilizing Bacteria in Sugarcane Modulate Soil Microbial Community and Functions?

Soil bacterial and fungal communities are suitable soil ecosystem health indicators due to their sensitivity to management practices and their role in soil ecosystem processes. Here, information on composition and functions of bacterial and fungal communities were evaluated at two phenological stages of sugarcane (six and twelve months, equivalent to the most intensive vegetative stage and to final maturation, respectively) when organomineral fertilizer, combined with phosphate-solubilizing bacteria (PSB), was added into the soil. Organic compost enriched with apatite (C + A) or phosphorite (C + P) and compost without phosphate enrichment (C) were used in the presence or absence of PSB. In addition, we used a control fertilized with soluble triple superphosphate. The differences were more related to the sampling period than to the type of organomineral fertilizer, being observed higher available phosphorus at six months than at twelve months. Only in the C treatment we observed the presence of Bacillaceae and Planococcaceae, while Pseudomonadaceae were only prevalent in inoculated C + A. As for fungi, the genera Chaetomium and Achroiostachys were only present in inoculated C + P, while the genus Naganishia was most evident in inoculated C + A and in uninoculated C + P. Soliccocozyma represented 75% of the total fungal abundance in uninoculated C while in inoculated C, it represented 45%. The bacterial community was more related to the degradation of easily decomposable organic compounds, while the fungal community was more related to degradation of complex organic compounds. Although the microbial community showed a resilient trait, subtle changes were detected in microbial community composition and function, and this may be related to the increase in yield observed.

Native Non-Saccharomyces Yeasts as a Tool to Produce Distinctive and Diverse Tamjanika Grape Wines

The enological potential of two previously characterized indigenous yeast isolates, Hanseniaspora uvarum S-2 and Candida famata WB-1, in pure and sequential inoculation with commercial yeast Saccharomyces cerevisiae QA23 were analyzed in industrial-scale vinification of the grape variety Tamjanika. Their contribution to the quality and aroma profile was investigated by quantifying volatile compounds and wine sensory evaluation. Both yeast isolates were able to complete alcoholic fermentation, to reduce ethanol concentration up to 1.06% v/v (in monoculture) in comparation to S. cerevisiae QA23, and to enhance aroma and sensory profile. Based on calculated odor activity values (OAV), p-cymene, ethyl hexanoate, ethyl octanoate, and ethyl decanoate were the major aroma volatile compounds in all Tamjanika wine samples. Analyzed yeast strains significantly affected relative contribution of volatile compounds and can be considered responsible for the differences and uniqueness of the obtained wine samples. Besides confirmation of good enological and fermentative characteristics, selected isolates can be characterized as high ester-producing strains with potential to enhance the floral and fruity aromas of wine. The present study represents a further step toward the use of indigenous yeast isolates at industrial-scale fermentation in order to ensure the regional signature of Tamjanika wine.

Exploring Yeast Diversity to Produce Lipid-Based Biofuels from Agro-Forestry and Industrial Organic Residues

Exploration of yeast diversity for the sustainable production of biofuels, in particular biodiesel, is gaining momentum in recent years. However, sustainable, and economically viable bioprocesses require yeast strains exhibiting: (i) high tolerance to multiple bioprocess-related stresses, including the various chemical inhibitors present in hydrolysates from lignocellulosic biomass and residues; (ii) the ability to efficiently consume all the major carbon sources present; (iii) the capacity to produce lipids with adequate composition in high yields. More than 160 non-conventional (non-Saccharomyces) yeast species are described as oleaginous, but only a smaller group are relatively well characterised, including Lipomyces starkeyi, Yarrowia lipolytica, Rhodotorula toruloides, Rhodotorula glutinis, Cutaneotrichosporonoleaginosus and Cutaneotrichosporon cutaneum. This article provides an overview of lipid production by oleaginous yeasts focusing on yeast diversity, metabolism, and other microbiological issues related to the toxicity and tolerance to multiple challenging stresses limiting bioprocess performance. This is essential knowledge to better understand and guide the rational improvement of yeast performance either by genetic manipulation or by exploring yeast physiology and optimal process conditions. Examples gathered from the literature showing the potential of different oleaginous yeasts/process conditions to produce oils for biodiesel from agro-forestry and industrial organic residues are provided.

The crude oil biodegradation activity of Candida strains isolated from oil-reservoirs soils in Saudi Arabia

Crude oil (petroleum) is a naturally occurring complex composed of hydrocarbon deposits and other organic materials. Bioremediation of crude oil-polluted sites is restricted by the biodiversity of indigenous microflora. They possess complementary substrates required for degrading the different hydrocarbons. In the current study, four yeast strains were isolated from different oil reservoirs in Riyadh, Saudi Arabia. The oil-biodegradation ability of these isolates showed variable oxidation effects on multiple hydrocarbons. The scanning electron microscopy (SEM) images showed morphological changes in Candida isolates compared to the original structures. The drop-collapse and oil emulsification assays showed that yeast strains affected the physical properties of tested hydrocarbons. The content of biosurfactants produced by isolated strains was quantified in the presence of different hydrocarbons to confirm the oil displacement activity. The recovery assays included acid precipitation, solvent extraction, ammonium sulfate, and zinc sulfate precipitation methods. All these methods revealed that the amount of biosurfactants correlates to the type of tested hydrocarbons, where the highest amount was produced in crude oil contaminated samples. In conclusion, the study highlights the importance of Candida isolated from contaminated soils for bioremediation of petroleum oil pollution. That raises the need for further analyses on the microbes/hydrocarbon degradation dynamics.

A global microbiome survey of vineyard soils highlights the microbial dimension of viticultural terroirs

The microbial biodiversity found in different vitivinicultural regions is an important determinant of wine terroir. It should be studied and preserved, although it may, in the future, be subjected to manipulation by precision agriculture and oenology. Here, we conducted a global survey of vineyards' soil microbial communities. We analysed soil samples from 200 vineyards on four continents to establish the basis for the development of a vineyard soil microbiome's map, representing microbial biogeographical patterns on a global scale. This study describes vineyard microbial communities worldwide and establishes links between vineyard locations and microbial biodiversity on different scales: between continents, countries, and between different regions within the same country. Climate data correlates with fungal alpha diversity but not with prokaryotes alpha diversity, while spatial distance, on a global and national scale, is the main variable explaining beta-diversity in fungal and prokaryotes communities. Proteobacteria, Actinobacteria and Acidobacteria phyla, and Archaea genus Nitrososphaera dominate prokaryotic communities in soil samples while the overall fungal community is dominated by the genera Solicoccozyma, Mortierella and Alternaria. Finally, we used microbiome data to develop a predictive model based on random forest analyses to discriminate between microbial patterns and to predict the geographical source of the samples with reasonable precision.

Search for Cryptococcus neoformans/gattii Complexes and Related Genera (Filobasidium, Holtermanniella, Naganishia, Papiliotrema, Solicoccozyma, Vishniacozyma) spp. Biotope: Two Years Surveillance of Wild Avian Fauna in Southern France

Fungi belonging to the Cryptococcus genus and related genera (Filobasidium, Holtermanniella, Naganishia, Papiliotrema, Solicoccozyma, Vishniacozyma) are encapsulated yeasts found in either the environment or animal sources. However, the precise biotopes of most species remain poorly defined. To assess whether wild birds from southern France can carry or spread the most pathogenic species (i.e., species belonging to the C. neoformans and C. gattii complexes), as well as lesser-studied species (non-neoformans/gattii Cryptococcus and former Cryptococcus spp.), 669 birds belonging to 89 species received for care over a two-year period at the Centre de Protection de la Faune Sauvage of Villeveyrac (Bird Protection League nongovernmental organization (NGO) care center) were sampled. Samples were cultured, and Cryptococcus and former Cryptococcus yeasts were identified by PCR sequencing. The purpose was to evaluate whether there was any health risk to local populations or care personnel in aviaries and gather new data on the ecological niches of lesser-known species. One hundred and seven birds (16%) were found to be positive for at least one Cryptococcus or former Cryptococcus species. No yeasts belonging to the highly pathogenic C. neoformans or C. gattii complexes were isolated. However, diversity was notable, with 20 different Cryptococcus or former Cryptococcus species identified. Furthermore, most bird–yeast species associations found in this study have never been described before.

Yeasts from temperate forests

Yeasts are ubiquitous in temperate forests. While this broad habitat is well-defined, the yeasts inhabiting it and their life cycles, niches, and contributions to ecosystem functioning are less understood. Yeasts are present on nearly all sampled substrates in temperate forests worldwide. They associate with soils, macroorganisms, and other habitats, and no doubt contribute to broader ecosystem-wide processes. Researchers have gathered information leading to hypotheses about yeasts' niches and their life cycles based on physiological observations in the laboratory as well as genomic analyses, but the challenge remains to test these hypotheses in the forests themselves. Here we summarize the habitat and global patterns of yeast diversity, give some information on a handful of well-studied temperate forest yeast genera, discuss the various strategies to isolate forest yeasts, and explain temperate forest yeasts' contributions to biotechnology. We close with a summary of the many future directions and outstanding questions facing researchers in temperate forest yeast ecology. Yeasts present an exciting opportunity to better understand the hidden world of microbial ecology in this threatened and global habitat.

Degradation activity of fungal communities on avocado peel (Persea americana Mill.) in a solid-state process: mycobiota successions and trophic guild shifts

To explore the capability of soil mycobiota to degrade avocado peel waste and identify relevant successions and trophic guild shifts, fungal communities from three environments with different land uses were evaluated in a solid-state process. Soil samples used as inoculum were collected from a pristine mature tropical forest, a traditionally managed Mayan land, and an intensively managed monospecific avocado plantation. Soil-substrate mixes were evaluated for 52 weeks to evaluate organic matter decay and the carbon-to-nitrogen ratio. Amplicon-based high-throughput sequencing from internally transcribed spacer (ITS) analysis revealed significant differences in fungal communities widely dominated by Fusarium sp. and Clonostachys sp.; however, less represented taxa showed relevant shifts concomitantly with organic matter content drops. Trophic guild assignment revealed different behaviors in fungal communities between treatments over the 52 weeks, suggesting distinct preconditioning of fungal communities in these environments. Overall, the results lead to the identification of promising degradation moments and inoculum sources for further consortia enrichment or bioprospecting efforts.

Trends in yeast diversity discovery

Yeasts, usually defined as unicellular fungi, occur in various fungal lineages. Hence, they are not a taxonomic unit, but rather represent a fungal lifestyle shared by several unrelated lineages. Although the discovery of new yeast species occurs at an increasing speed, at the current rate it will likely take hundreds of years, if ever, before they will all be documented. Many parts of the earth, including many threatened habitats, remain unsampled for yeasts and many others are only superficially studied. Cold habitats, such as glaciers, are home to a specific community of cold-adapted yeasts, and, hence, there is some urgency to study such environments at locations where they might disappear soon due to anthropogenic climate change. The same is true for yeast communities in various natural forests that are impacted by deforestation and forest conversion. Many countries of the so-called Global South have not been sampled for yeasts, despite their economic promise. However, extensive research activity in Asia, especially China, has yielded many taxonomic novelties. Comparative genomics studies have demonstrated the presence of yeast species with a hybrid origin, many of them isolated from clinical or industrial environments. DNA-metabarcoding studies have demonstrated the prevalence, and in some cases dominance, of yeast species in soils and marine waters worldwide, including some surprising distributions, such as the unexpected and likely common presence of Malassezia yeasts in marine habitats.

Baseline Data of the Fungal Phytobiome of Three Sorghum (Sorghum bicolor) Cultivars in South Africa using Targeted Environmental Sequencing

Plant-associated fungi, or the mycobiome, inhabit plant surfaces above ground, reside in plant tissues as endophytes, or are rhizosphere in the narrow zone of soil surrounding plant roots. Studies have characterized mycobiomes of various plant species, but little is known about the sorghum mycobiome, especially in Africa, despite sorghum being one of the most important indigenous and commercial cereals in Africa. In this study, the mycobiome associated with above- and below-ground tissues of three commercial sorghum cultivars, as well as from rhizosphere and surrounding bulk soil samples, were sequenced using targeted sequencing with the Illumina MiSeq platform. Relative abundance differences between fungal communities were found between above-ground and below-ground niches, with most differences mostly in the dominant MOTUs, such as Davidiellaceae sp. (Cladosporium), Didymellaceae sp. 1 (Phoma), Fusarium, Cryptococcus and Mucor. Above-ground communities also appeared to be more diverse than below-ground communities, and plants harboured the most diversity. A considerable number of MOTUs were shared between the cultivars although, especially for NS5511, their abundances often differed. Several of the detected fungal groups include species that are plant pathogens of sorghum, such as Fusarium, and, at low levels, Alternaria and the Ustilaginomycetes. Findings from this study illustrate the usefulness of targeted sequencing of the ITS rDNA gene region (ITS2) to survey and monitor sorghum fungal communities and those from associated soils. This knowledge may provide tools for disease management and crop production and improvement.

Azole-Resilient Biofilms and Non-wild Type C. albicans Among Candida Species Isolated from Agricultural Soils Cultivated with Azole Fungicides: an Environmental Issue?

This study aimed to identify Candida spp. from agricultural soils cultivated with azole fungicides and investigate their susceptibility to clinical (fluconazole, itraconazole, voriconazole, and amphotericin B) and agricultural (tetraconazole and tebuconazole) antifungals in planktonic form. Additionally, Candida biofilm-forming ability and biofilm susceptibility to agricultural antifungals and voriconazole were analyzed. Species identification was performed by phenotypic and molecular assays. The susceptibility of planktonic cells was evaluated by the broth microdilution method. The biofilm metabolic activity was evaluated by the XTT reduction assay. The recovered Candida spp. were identified as C. parapsilosis sensu stricto (n = 14), C. albicans (n = 5), C. tropicalis (n = 2), C. fermentati (n = 1), and C. metapsilosis (n = 2). Minimum inhibitory concentration ranges for clinical and agricultural antifungals were ≤ 0.03-4 μg/mL and 1-128 μg/mL, respectively. Two and one C. albicans strains were considered non-wild type for voriconazole and fluconazole, respectively. All strains were biofilm producers. The minimum biofilm inhibitory concentration ranges for tetraconazole and tebuconazole were 128-> 1024 μg/mL, while for voriconazole was 512-> 1024 μg/mL. In summary, this study shows that non-wild type and azole-resilient biofilm-producing Candida species colonize agricultural soils cultivated with azole fungicides.

Global patterns in culturable soil yeast diversity

Yeasts, broadly defined as unicellular fungi, fulfill essential roles in soil ecosystems as decomposers and nutrition sources for fellow soil-dwellers. Broad-scale investigations of soil yeasts pose a methodological challenge as metagenomics are of limited use for identifying this group of fungi. Here we characterize global soil yeast diversity using fungal DNA barcoding on 1473 yeasts cultured from 3826 soil samples obtained from nine countries in six continents. We identify mean annual precipitation and international air travel as two significant correlates with soil yeast community structure and composition worldwide. Evidence for anthropogenic influences on soil yeast communities, directly via travel and indirectly via altered rainfall patterns resulting from climate change, is concerning as we found common infectious yeasts frequently distributed in soil in several countries. Our discovery of 41 putative novel species highlights the continued need for culture-based studies to advance our knowledge of environmental yeast diversity.

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Mean annual rainfall is a positive predictor of global soil yeast diversity

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International travel predicts number of shared yeast species between countries

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41 novel yeast species were discovered from soils in eight countries

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Continued culture-based studies are needed to investigate soil yeast populations

Equine grass sickness (a multiple systems neuropathy) is associated with alterations in the gastrointestinal mycobiome

BACKGROUND

Equine grass sickness (EGS) is a multiple systems neuropathy of grazing horses of unknown aetiology. An apparently identical disease occurs in cats, dogs, rabbits, hares, sheep, alpacas and llamas. Many of the risk factors for EGS are consistent with it being a pasture mycotoxicosis. To identify potential causal fungi, the gastrointestinal mycobiota of EGS horses were evaluated using targeted amplicon sequencing, and compared with those of two control groups. Samples were collected post mortem from up to 5 sites in the gastrointestinal tracts of EGS horses (EGS group; 150 samples from 54 horses) and from control horses that were not grazing EGS pastures and that had been euthanased for reasons other than neurologic and gastrointestinal diseases (CTRL group; 67 samples from 31 horses). Faecal samples were also collected from healthy control horses that were co-grazing pastures with EGS horses at disease onset (CoG group; 48 samples from 48 horses).

RESULTS

Mycobiota at all 5 gastrointestinal sites comprised large numbers of fungi exhibiting diverse taxonomy, growth morphology, trophic mode and ecological guild. FUNGuild analysis parsed most phylotypes as ingested environmental microfungi, agaricoids and yeasts, with only 1% as gastrointestinal adapted animal endosymbionts. Mycobiota richness varied throughout the gastrointestinal tract and was greater in EGS horses. There were significant inter-group and inter-site differences in mycobiota structure. A large number of phylotypes were differentially abundant among groups. Key phylotypes (n = 56) associated with EGS were identified that had high abundance and high prevalence in EGS samples, significantly increased abundance in EGS samples, and were important determinants of the inter-group differences in mycobiota structure. Many key phylotypes were extremophiles and/or were predicted to produce cytotoxic and/or neurotoxic extrolites.

CONCLUSIONS

This is the first reported molecular characterisation of the gastrointestinal mycobiota of grazing horses. Key phylotypes associated with EGS were identified. Further work is required to determine whether neurotoxic extrolites from key phylotypes contribute to EGS aetiology or whether the association of key phylotypes and EGS is a consequence of disease or is non-causal.

The Mycobiota of High Altitude Pear Orchards Soil in Colombia

Simple Summary

Soil fungi are extremely important in the agro-environment. They are among the main decomposers of organic matter, contributing to carbon, nitrogen, and phosphorous cycles. They often establish positive relationships with plants, protecting them from pathogens and abiotic stresses. This study aimed to uncover the soil fungal communities of two high altitude pear orchards with biomolecular techniques. We found a rich and diverse assemblage, dominated by fungi belonging to Ascomycota and Mortierellomycota. Most of the found species were novel records for soil fungi in Colombia. The most common fungal genera were Mortierella, Fusarium, Pseudaleria and Cylindrocarpon. Among the identified fungi, some species are known to be bioactive, with promising activities as biocontrol agents, plant-growth promoters, and producers of valuable substances. These results could contribute for a more attentive management of Colombian pear orchards in future and an enrichment of knowledge on Colombian biodiversity.

Abstract

In Colombia, the cultivation of deciduous fruit trees such as pear is expanding for socio-economic reasons and is becoming more and more important for the local population. Since organized cultivation is slowly replacing sustenance cultivation, scientific information on the present agro-environment is needed to proceed in this change in an organic and environmentally friendly way. In particular, this study is an accurate description of the mycobiota present in the bulk soil of two different high altitude pear orchards in the Colombian Andes. The metabarcoding of soil samples allowed an in-depth analysis of the whole fungal community. The fungal assemblage was generally dominated by Ascomycota and secondly by Mortierellomycota. As observed in other studies in Colombia, the genus Mortierella was found to be especially abundant. The soil of the different pear orchards appeared to host quite different fungal communities according to the soil physico-chemical properties. The common mycobiota contained 35 fungal species, including several species of Mortierella, Humicola, Solicoccozyma and Exophiala. Moreover, most of the identified fungal species (79%) were recorded for the first time in Colombian soils, thus adding important information on soil biodiversity regarding both Colombia and pear orchards.

Soil yeast abundance and diversity assessment in a hot climatic region, semi-arid ecosystem

Background and Objectives

Yeasts are an important portion of microbial communities of soil due to their bioactivity for ecosystem safety. Soil yeast abundance and diversity are likely to be affected under harsh environmental and climatic conditions. In Iraq, human activity and climatic changes especially high temperature which may alter microbial communities in soil. Very little is known about yeast abundance and diversity in a hot climatic region.

Materials and Methods

By PCR technique, soil yeast abundance and diversity were investigated under extreme environmental and climatic conditions, as well as the effects of soil properties and vegetation cover in semi-arid lands.

Results

In all, 126 yeast strains were isolated and identified as belonging to 13 genera and 26 known species. The maximum quantity of yeast was 0.8 × 10² CFU g^-1 of soil, with significantly varied in abundance and diversity depending on soil properties and presence of vegetation.

Conclusion

The results show that soil yeast abundance in these regions was significantly decreased. However, semi-arid lands are still rich in yeast diversity, and many species have adapted to survive in such conditions.

How Tillage and Crop Rotation Change the Distribution Pattern of Fungi

Massive sequencing of fungal communities showed that climatic factors, followed by edaphic and spatial variables, are feasible predictors of fungal richness and community composition. This study, based on a long-term field experiment with tillage and no-tillage management since 1995 and with a crop rotation introduced in 2009, confirmed that tillage practices shape soil properties and impact soil fungal communities. Results highlighted higher biodiversity of saprotrophic fungi in soil sites with low disturbance and an inverse correlation between the biodiversity of ectomycorrhizal and saprotrophic fungi. We speculated how their mutual exclusion could be due to a substrate-mediated niche partitioning or by space segregation. Moreover, where the soil was ploughed, the species were evenly distributed. There was higher spatial variability in the absence of ploughing, with fungal taxa distributed according to a small-scale pattern, corresponding to micro-niches that probably remained undisturbed and heterogeneously distributed. Many differentially represented OTUs in all the conditions investigated were unidentified species or OTUs matching at high taxa level (i.e., phylum, class, order). Among the fungi with key roles in all the investigated conditions, there were several yeast species known to have pronounced endemism in soil and are also largely unidentified. In addition to yeasts, other fungal species emerged as either indicator of a kind of management or as strongly associated with a specific condition. Plant residues played a substantial role in defining the assortment of species.

Patterns of yeast diversity distribution and its drivers in rhizosphere soil of Hami melon orchards in different regions of Xinjiang

BACKGROUND

The unique climatic conditions of the Xinjiang region nurture rich melon and fruit resources, the melon and fruit sugar sources provide sufficient nutrients for the survival of yeast, and the diverse habitats accompanied by extreme climatic conditions promote the production of yeast diversity and strain resources. However, the relationship between yeast species and their relationship with environmental factors in the soil of Xinjiang specialty cash crop Hami melon is not clear. Here, we aimed to characterize the diversity, community structure, and relationship between yeast species and environmental factors in Hami melon orchards soils in different regions of Xinjiang, China.

RESULTS

Based on Illumina MiSeq high-throughput sequencing analysis of the D1 domain of the LSU rRNA genes, the community richness of yeast in the soil of Northern Xinjiang was higher than in the Southern and Eastern Xinjiang, but the community diversity was significantly lower in the Northern Xinjiang than in the Southern and Eastern Xinjiang. A total of 86 OTUs were classified into 59 genera and 86 species. Most OTUs (90.4%) belonged to the Basidiomycota; only a few (9.6%) belonged to Ascomycota. The most dominant species in the Southern, Eastern and Northern Xinjiang were Filobasidium magnum (17.90%), Solicoccozyma aeria (35.83%) and Filobasidium magnum (75.36%), respectively. Principal coordinates analysis (PCoA) showed that the yeast community composition in the soils of the three regions were obviously different, with the Southern and Eastern Xinjiang having more similar yeast community. Redundancy analysis (RDA) showed that soil factors such as conductivity (CO), total phosphorus (TP) and Total potassium (TK) and climate factors such as average annual precipitation (PRCP), relative humidity (RH) and net solar radiation intensity (SWGNT) were significantly correlated with yeast communities (P < 0.05).

CONCLUSION

There are abundant yeast resources in the rhizosphere soil of Hami melon orchard in Xinjiang, and there are obvious differences in the diversity and community structure of yeast in the three regions of Xinjiang. Differences in climatic factors related to precipitation, humidity and solar radiation intensity and soil factors related to conductivity, total phosphorus and total potassium are key factors driving yeast diversity and community structure.

Application of soil biofertilizers to a clayey soil contaminated with Sclerotium rolfsii can promote production, protection and nutritive status of Phaseolus vulgaris

Sclerotium rolfsii is a soil-borne fungus that causes big losses in productivity of various plant species including Phaseolus vulgaris L. The objectives of this study were to (1) evaluate the impacts of Sclerotium rolfsii on growth and production of common bean plants, (2) determine the effects of Sclerotium rolfsii on nutritive contents of beans, and (3) test the efficacy of bio-inoculants on suppressing plant infection with Sclerotium rolfsii. To fulfill these objectives, we used a coupled pot and field experimental approaches during two growing seasons. Common beans were inoculated with either arbuscular mycorrhizal fungi (Claroideoglomus etunicatum), Saccharomyces cerevisiae, or Trichoderma viride solely or in different combinations. Non-inoculated plants and fungicide treated ones were considered as reference treatments. Throughout these experiments, minimal amounts of rock phosphate were added during soil preparation for bio-inoculated treatments, while the non-inoculated reference treatments received a full dose of P as calcium superphosphate. Results revealed that all tested bioinoculants significantly raised the activities of plant defense enzymes i.e. chitinase, peroxidase and polyphenoloxidase as compared to non-inoculated control. Likewise, pre-, post- and plant survival percentages significantly increased due to these bio-inoculations. Increased survival percentages were attributed to the concurrent increases in uptake of N, P and Zn nutrients by plants treated with bioinoculants. In this concern, plant nutrients uptake was higher in combined than single bio-inoculant treatments. Moreover, the uptake values of plant nutrients owing to the combined bio-inoculants were higher than the corresponding ones achieved due to fungicide treatment. In conclusion, application of the tested bio-inoculants, especially the combined ones can be considered an eco-friendly approach that not only enhances plants resistance against infection with Sclerotium rolfsii but also improves plant nutritive status.

Tremellomycetes Yeasts in Kernel Ecological Niche: Early Indicators of Enhanced Competitiveness of Endophytic and Mycoparasitic Symbionts against Wheat Pathobiota

Tremellomycetes rDNA sequences previously detected in wheat kernels by MiSeq were not reliably assigned to a genus or clade. From comparisons of ribosomal internal transcribed spacer region (ITS) and subsequent phylogenetic analyses, the following three basidiomycetous yeasts were resolved and identified: Vishniacozymavictoriae, V. tephrensis, and an undescribed Vishniacozyma rDNA variant. The Vishniacozyma variant’s clade is evolutionarily close to, but phylogenetically distinct from, the V. carnescens clade. These three yeasts were discovered in wheat kernel samples from the Canadian prairies. Variations in relative Vishniacozyma species abundances coincided with altered wheat kernel weight, as well as host resistance to chemibiotrophic Tilletia (Common bunt—CB) and necrotrophic Fusarium (Fusarium head blight—FHB) pathogens. Wheat kernel weight was influenced by the coexistence of Vishniacozyma with endophytic plant growth-promoting and mycoparasitic biocontrol fungi that were acquired by plants. Kernels were coated with beneficial Penicillium endophyte and Sphaerodes mycoparasite, each of which had different influences on the wild yeast population. Its integral role in the kernel microbiome renders Vishniacozyma a measurable indicator of the microbiome–plant interaction. The ability of NGS technology to detect specific endophytic DNA variants and early changes in dynamics among symbionts within the kernel ecological niche enables the prediction of crop disease emergence, suggesting that advanced microbiological testing may be a potentially useful tool for both phytoprotection and more efficient wheat breeding programs.

Photoprotective compounds and radioresistance in pigmented and non-pigmented yeasts

Ultraviolet radiation, continuously reaching our planet's surface, is a type of electromagnetic energy within the wavelength range of 10 to 400 nm. Despite essential for all life on Earth, ultraviolet radiation may have severe adverse cellular effects, including DNA dimerization and production of reactive oxygen species. Radioresistant microorganisms can survive under high doses of ultraviolet radiation, enduring the direct and indirect effects on nucleic acids and other biomolecules. The synthesis and accumulation of photoprotective compounds are among the main strategies employed by radioresistant yeast species to bear the harmful effects of ultraviolet radiation. A correlation between pigments and resistance to ultraviolet radiation has been widely recognized in these microorganisms; however, there is still some debate on this topic, with non-pigmented strains sometimes being more resistant than their pigmented counterparts. In this review, we explore the role of photoprotective compounds-specifically, melanin, carotenoids, and mycosporines-and compare the differences found in resistance between pigmented and non-pigmented yeasts. We also discuss the biotechnological potential of these photoprotective compounds, with special emphasis on those produced by non-pigmented yeast strains, such as phytoene and phytofluene. The use of "-omics" approaches should further unveil the radioresistance mechanisms of non-pigmented yeasts, opening new opportunities for both research and commercial applications. KEY POINTS: • Updated knowledge on photoprotective compounds from radioresistant yeasts. • Differences on radioresistance between pigmented and non-pigmented yeasts. • Future prospects over the study of non-pigmented photoprotective compounds.

Culturable Yeasts as Biofertilizers and Biopesticides for a Sustainable Agriculture: A Comprehensive Review

The extensive use of synthetic fertilizers and pesticides has negative consequences in terms of soil microbial biodiversity and environmental contamination. Faced with this growing concern, a proposed alternative agricultural method is the use of microorganisms as biofertilizers. Many works have been focused on bacteria, but the limited literature on yeasts and their potential ability to safely promote plant growth is gaining particular attention in recent years. Thus, the objective of this review is to highlight the application of yeasts as biological agents in different sectors of sustainable agricultural practices through direct or indirect mechanisms of action. Direct mechanisms include the ability of yeasts to provide soluble nutrients to plants, produce organic acids and phytohormones (indole-3-acetic acid). Indirect mechanisms involve the ability for yeasts to act as biocontrol agents through their high antifungal activity and lower insecticidal and herbicidal activity, and as soil bioremediating agents. They also act as protective agents against extreme environmental factors by activating defense mechanisms. It is evident that all the aspects that yeasts offer could be useful in the creation of quality biofertilizers and biopesticides. Hence, extensive research on yeasts could be promising and potentially provide an environmentally friendly solution to the increased crop production that will be required with a growing population.

A review on metal-based nanoparticles and their toxicity to beneficial soil bacteria and fungi

The unregulated deposition of metal-based nanoparticles in terrestrial ecosystems particularly in agricultural systems has alarmingly threatened the sustainability of the environment and diversity of beneficial microbial populations such as soil bacteria and fungi. This occurs due to the poor treatment of biosolids during wastewater treatment and their application in agricultural fields to enhance the fertility of soils. Continuous deposition, low biodegradability, and longer persistence of metal nanoparticles in soils adversely impact the population of soil beneficial bacteria and fungi. The current literature suggests the toxic outcome of nanoparticle-fungi and nanoparticle-bacteria interactions based on various toxicity endpoints. Therefore, due to the extreme importance of beneficial soil bacteria and fungi for soil fertility and plant growth, this review summarizes the production, application, release of metal nanoparticles in the soil system and their impact on various soil microbes specifically plant growth-promoting rhizobacteria, cellular toxicity and impact of nanoparticles on bioactive molecule production by microbes, destructive nanoparticle impact on unicellular, mycorrhizal, and cellulose/lignin degrading fungi. This review also highlights the molecular alterations in fungi and bacteria-induced by nanoparticles and suggests a plausible toxicity mechanism. This review advances the understanding of the nano-toxicity aspect as a common outcome of nanoparticles and fungi/bacteria interactions.

Moniliella spathulata, an oil-degrading yeast, which promotes growth of barley in oil-polluted soil

The yeast strain Moniliella spathulata SBUG-Y 2180 was isolated from oil-contaminated soil at the Tengiz oil field in the Atyrau region of Kazakhstan on the basis of its unique ability to use crude oil and its components as the sole carbon and energy source. This yeast used a large number of hydrocarbons as substrates (more than 150), including n-alkanes with chain lengths ranging from C10 to C32, monomethyl- and monoethyl-substituted alkanes (C9-C23), and n-alkylcyclo alkanes with alkyl chain lengths from 3 to 24 carbon atoms as well as substituted monoaromatic and diaromatic hydrocarbons. Metabolism of this huge range of hydrocarbon substrates produced a very large number of aliphatic, alicyclic, and aromatic acids. Fifty-one of these were identified by GC/MS analyses. This is the first report of the degradation and formation of such a large number of compounds by a yeast. Inoculation of barley seeds with M. spathulata SBUG-Y 2180 had a positive effect on shoot and root development of plants grown in oil-contaminated sand, pointing toward potential applications of the yeast in bioremediation of polluted soils. KEY POINTS: • Moniliella spathulata an oil-degrading yeast • Increase of the growth of barley.

Mrakia panshiensis sp. nov. a new member of the Cystofilobasidiales from soil in China, and description of the teleomorphic-stage of M. arctica

In a study on the fungal diversity in Northeast China, twelve yeast isolates were obtained from soils collected in three provinces, Helongjiang, Jilin and Liaoning. Morphological assessment and phylogenetic analyses of the nuc rDNA internal transcribed spacer (ITS) region and the D1/D2 domains of the nuc 28S rDNA (nuc 28S) gene of the 12 cultures placed them in the genus Mrakia, namely Mrakiaaquatica, Mrakiaarctica, Mrakiafrigida, Mrakiagelida and Mrakiarobertii. A total of three isolates represented a hitherto undescribed species, which is described here as M.panshiensissp. nov. (MB 834813). The species M.panshiensissp. nov. shares several morphological characters with M.niccombsii, M.aquatica, M.fibulata and M.hoshinonis. These species can be distinguished based on physiological traits and pairwise rDNA sequence similarities. The study also describes for the first time the formation of teliospores by previously described M.arctica.

Unconventional Yeasts Are Tolerant to Common Antifungals, and Aureobasidium pullulans Has Low Baseline Sensitivity to Captan, Cyprodinil, and Difenoconazole

Many yeasts have demonstrated intrinsic insensitivity to certain antifungal agents. Unlike the fungicide resistance of medically relevant yeasts, which is highly undesirable, intrinsic insensitivity to fungicides in antagonistic yeasts intended for use as biocontrol agents may be of great value. Understanding how frequently tolerance exists in naturally occurring yeasts and their underlying molecular mechanisms is important for exploring the potential of biocontrol yeasts and fungicide combinations for plant protection. Here, yeasts were isolated from various environmental samples in the presence of different fungicides (or without fungicide as a control) and identified by sequencing the internal transcribed spacer (ITS) region or through matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Among 376 isolates, 47 taxa were identified, and Aureobasidium pullulans was the most frequently isolated yeast. The baseline sensitivity of this yeast was established for 30 isolates from different environmental samples in vitro to captan, cyprodinil, and difenoconazole. For these isolates, the baseline minimum inhibitory concentration (MIC₅₀) values for all the fungicides were higher than the concentrations used for the control of plant pathogenic fungi. For some isolates, there was no growth inhibition at concentrations as high as 300 µg/mL for captan and 128 µg/mL for cyprodinil. This information provides insight into the presence of resistance among naturally occurring yeasts and allows the choice of strains for further mechanistic analyses and the assessment of A. pullulans for novel applications in combination with chemical agents and as part of integrated plant-protection strategies.