Outdoor climate drives diversity patterns of dominant microbial taxa in caves worldwide.

The cave microbiota is assumed to be shaped by indoor microclimate, biotic and abiotic factors, which are largely dependent from outside environmental conditions; however, this knowledge is available at local or regional scales only. To address this knowledge gap, we reanalyzed over 1050 bacterial and fungal communities of caves worldwide, and found that outdoor temperature and rainfall play a critical role in explaining differences in microbial diversity patterns of global caves, selecting specific dominant taxa across gradients of growing aridity conditions with arid climate leading to a reduction in total cave microbial diversity. Moreover, we found that fungal (from 186 to 1908 taxa) and bacterial (from 467 to 1619 taxa) diversity increased under temperate-tropical and temperate-continental climatic regions, respectively, highlighting an opposite preference for the two microbial compartments. We hypothesized that outdoor geographical, climatic variables and lithology are critical epistatic drivers in assembling microbial communities and their dominant taxa, whose ecological responses could be useful to predict the fate of these subterranean environments in the context of climate change. Our work elucidates the intimate connection between caves microbiota and surface ecosystems highlighting the sensitivity of cave microbial communities to climatic changes and environmental degradation. This work also provides a natural benchmark for the biogeographic information for caves globally and for protection strategies aiming at conservation of underground environments.

Fungal community dynamics on limestone at the Chichén Itzá archaeological site in Mexico driven by protective treatments.

Microorganisms naturally colonize rock-based materials in outdoor environments, thereby contributing to their degradation. Fungi, especially in tropical environments with abundant water and favorable temperatures, play a significant role in biodegradation. However, many aspects of the microorganism-stone interaction, including fungal colonization dynamics and the impact of treatment applications, remain unclear. This study conducted a four-year in-situ evaluation of fungal community dynamics on limestone surfaces in the Temple of the Warriors at the Chichén Itzá archaeological site in Mexico, focusing on cleaning and treatment using nanoparticles (NPs). These NPs included zinc oxide (ZnO) and CaZn2(OH)6·2H2O (CZ)-based NPs synthesized via sol-gel (CZ-SG) and mechanochemical methods (CZ-MC), as well as CZ/Ca(OH)2-based products (CZ:Ca-SG). The microbial colonization cover was assessed using colorimetric measurements, and the surface was sampled for fungal community isolation and identification. The results demonstrated significant impacts of cleaning and nanomaterial applications on cultivable fungal communities (melanized filamentous, hyaline, and microcolonial fungi), altering composition, dynamics, and stone surface coloration. In particular, ZnO NPs caused 50 % decline in fungal species and individuals, whereas CZ:Ca-SG NPs displaced most species, indicating effective inhibition of the cultivable fungal community. Microcolonial fungi (MCF), known for their tolerance to withstand harsh environmental conditions, were the only fungal group found in the CZ:Ca-SG treatment. In contrast, CZ-SG and CZ-MC increased the abundance of melanized species, resulting in darkening and reduced color intensity. This study highlights the importance of microcolonial fungi that are tolerant to cleaning and coating procedures in the preservation of stone cultural heritage. These findings enhance our understanding of fungal colonization dynamics following treatment and provide valuable insights into the challenges associated with preserving stone materials in tropical environments.

Different long-term fertilization regimes affect soil protists and their top-down control on bacterial and fungal communities in Mollisols.

Soil protists represent a vastly diverse component of soil microbial communities and significantly contribute to biogeochemical cycling. However, how different fertilization regimes impact the protistan communities and their top-down control on bacteria and fungi remain largely unknown. Here, using high-throughput sequencing, we investigated the differences in protist communities and their relationships with bacterial and fungal communities in Mollisols of Northeast China that were subjected to chemical and organic fertilization over 30 years. The results showed that manure addition rather than chemical fertilization significantly increased protistan alpha diversity and changed protistan community structure. Manure amendments markedly increased the relative abundances of protistan consumers (such as Cercozoa) and reduced the proportion of phototrophic protists (such as Chlorophyta). Soil pH was the most influential factor driving microbial communities, and protists were less sensitive to environmental disturbances than bacteria and fungi. Protistan communities exhibited more stronger relationships with bacterial communities than fungal communities, and Chlorococcum was the most important contributor in regulation of microbial taxa and functional genes. Furthermore, manure addition slightly simplified the microbial network, and chemical plus manure fertilization improved network stability with the highest robustness. Manure addition specifically mitigated the negative interactions between protists and bacteria while reinforced the positive interactions between protists and fungi. This study advanced our knowledge about the roles of protistan groups in regulating microbial communities and ecosystem functions associated with chemical and organic fertilization.

Arbuscular mycorrhizal fungi alter rhizosphere fungal community characteristics of Acorus calamus to improve Cr resistance.

To investigate changes in fungal community characteristics under different Cr(VI) concentration stresses and the advantages of adding arbuscular mycorrhizal fungi (AMF), we used high throughput sequencing to characterize the fungal communities. Cr(VI) stress reduced rhizosphere soil SOM (soil organic matter) content and AMF addition improved this stress phenomenon. There were significant differences in fungal community changes under different Cr(VI) concentrations. The fungal community characteristics changed through inhibition of fungal metabolic ability, as fungal abundance increased after AMF addition, and the fungal diversity increased under high Cr(VI) concentration. The dominant phyla were members of the Ascomycota, Basidiomycota, Mortierellomycota, and Rozellomycota. Dominant groups relevant to Cr resistance were Ascomycota and Basidiomycota fungi. Moreover, Fungal community characteristics were analyzed using high-throughput sequencing of the cytochrome c metabolic pathway, NADH dehydrogenase, and NADH: ubiquinone reductase and all these functions were enhanced after AMF addition. Therefore, Cr(VI) stress significantly affects fungal community structure, while AMF addition could increase its SOM content, and metabolic capacity, and improve fungal community tolerance to Cr stress. This study contributed to the understanding response of rhizosphere fungal community in AMF-assisted wetland phytoremediation under Cr stress.

Analysis of fungal microbiota of ambient air in an intensive care unit in Rio Branco, Acre, Western Amazon, Brazil.

Fungi exhibit three adverse effects on human health: inflammatory, allergic and toxic effects, these implications affect mainly immunodepressed patients. The objective of this work was to analyze the fungal microbiota of the ambient air of an Intensive Care Unit. Three collections were carried out in an Intensive Care Unit in the city of Rio Branco, Acre, Western Amazon, Brazil from March to May 2017. 126 Petri dishes were exposed with the culture medium Agar Sabouraud with chloramphenicol and Agar Mycosel, considering the distribution of the 21 air conditioners, split residential model. The plates were incubated for seven days at room temperature and the growth of Colony Forming Units was observed. Colony counting and isolation for the morphological characterization of the granted fungi was performed. After quantification, the concentration of fungi per cubic meters of air (CFU.m-3) was settled. The third collection had a larger number of colony forming units with 48.6%. In the total of the analyzed samples, filamentous fungi (85.5%) and yeasts (14.5%) were isolated. Thirteen genera of fungi were identified, with the most frequent filaments being Cladosporium spp. 33.0%, Aspergillus spp. 30.4% and Penicillium spp. 19.6%, and yeasts Candida spp. 52.6%, Trichosporon spp. 36.9%. The colony-forming unit per cubic meter (CFU.m-3) did not shown any difference between the Cores in the same collection period, however in the 1st and 3rd collection, Core 1 had the highest average. The fungal microbiota of this Unit presented thirteen different genera potentially pathogenic, revealing the need for monitoring microorganisms and prevention actions.

[Effects of Aeration Methods on Microbial Diversity and Community Structure in Rice Rhizosphere].

To explore the effects of different aeration methods on the abundance of microorganisms and microorganism community structure in rice rhizosphere soil, two rice varieties, Miyang 46(MY) and Zhenshan 97B(ZS), were used with three aeration treatments:alternate wetting and drying(AWD), continuous flooding and aeration(CFA), and continuous flooding(CF). The diversity of bacterial and fungal communities in rice rhizosphere soil was analyzed using Illumina MiSeq high-throughput sequencing. Soil physical and chemical factors were also analyzed. The results showed that the dominant bacterial communities in rice rhizosphere soil were Chloroflexi, Actinobaciota, Acidobacteria, Proteobacteria, and Firmicutes, and the dominant fungal communities were Ascomycota and Basidiomycota in rice rhizosphere soil. At each growth stage, the relative abundance of Chloroflexi and Acidobacteria was higher in the AWD treatment than in the other treatments, and the relative abundance of Actinobaciota was higher in the CFA treatment than in the other treatments. The relative abundance of Firmicutes was lower in the AWD treatment than in the other treatments. Aeration methods affected the diversity and richness of rhizosphere microbial species. For example, the diversity of bacterial species was higher, and the richness of bacterial species was lower in the AWD treatment than that in the other treatments. The diversity and richness of fungal species were higher in the AWD and CFA treatments than those in the CF treatment. The physical and chemical properties of rhizosphere soil were also affected by aeration method. The soil redox potential(Eh) was the highest in AWD, followed by that in CFA and CF, and significant differences were observed among treatments. The NO3--N content was significantly higher, and the NH4+-N content was significantly lower in the AWD and CFA treatments than in the CF treatment in rhizosphere soil at all growth stages. Correlation analysis showed that the pH and Eh of rhizosphere soil were positively correlated with the diversity of bacterial species, negatively correlated with the richness of bacterial species, and positively correlated with the diversity and richness of fungal species. Redundancy analysis indicated that the relative abundance of Chloroflexi was positively correlated with the pH and NH4+-N content at each period, positively correlated with the Eh and NO3--N content at the tillering and heading stages, and negatively correlated with Eh and NO3--N content at the maturity stage. At each growth stage, the pH and Eh were positively correlated with the relative abundance of Acidobacteria, Proteobacteria, and Basidiomycota and negatively correlated with the relative abundance of Firmicutes and Ascomycota. During the entire growth period, the relative abundance of Ascomycota was negatively correlated with the NO3--N content and positively correlated with the NH4+-N content, and the opposite patterns were observed for the relative abundance of Basidiomycota. In summary, rhizosphere oxygenation enhanced the soil oxygen environment, altered soil physical and chemical properties, and affected microbial community diversity and richness to optimize microbial community structure.

Impact of storage time on non-volatile metabolites and fungal communities in Liupao tea using LC-MS based non-targeted metabolomics and high-throughput sequencing.

Long-term storage of Liupao tea (LPT) is usually believed to enhance its quality and commercial value. The non-volatile metabolites variations and the fungal succession play a key role for organoleptic qualities during the storage procedure. To gain in-depth understanding the impact of storage time on the quality of LPT, two different brands of LPT with different storage time, including Maosheng LPTs (MS) with 0, 5, 10 and 15 years and Tianyu LPTs (TY) with 0, 3, 5, 8 and 10 years, were resorted to investigate the changes of non-volatile metabolites and fungi as well as their correlation by multi-omics. A total of 154 and 119 differential metabolites were identified in these two different brands of MS and TY, respectively, with the aid of high-performance liquid chromatography with quadrupole-time-of-flight mass spectrometry. In both categories of LPTs, the transformation of differential metabolites in the various stages referred to the formation of alkaloids, increase of organic acids, biosynthesis of terpenoids as well as glycosylation and methylation of flavonoids. Thereinto, glycosylation and methylation of flavonoids were the critical stages for distinguishing MS and TY, which were discovered in MS and TY stored for about 10 and 8 years, respectively. Moreover, the results of high-throughput sequencing showed that the key fungal genera in the storage of LPTs consisted of Eurotium, Aspergillus, Blastobotrys, Talaromyces, Thermomyces and Trichomonascus. It was confirmed on the basis of multivariate analysis that the specific fungal genera promoted the transformation of metabolites, affecting the tea quality to some extent. Therefore, this study provided a theoretical basis for the process optimization of LPT storage.

Composition, functional, and niche differentiation of fungal communities in the rhizosphere and root endosphere of Cinnamomum migao in southwestern China.

AIMS: Roots are key parts of plant material circulation and energy flow, creating two distinct niches for the plant microbiome, such as the rhizosphere and root endosphere, which interact to maintain plant growth and health. In this study, two niches of plant rhizosphere and root endosphere were selected to study the composition and differences of fungi communities in order to better understand how differences in the structure and function of plant fungi communities affect plant health. METHODS AND RESULTS: The community structure, diversity, and ecological function of fungi in the rhizosphere and root endosphere of Cinnamomum migao were studied using high-throughput sequencing techniques, traditional culture methods, and the FUNGuild database. The results of the analysis of alpha diversity showed that the diversity of rhizosphere fungal communities in C. migao was much higher than that of root endosphere communities. Some similarities and differences were noted between the two niche fungal communities, and some fungi had niche preferences. Functional prediction results demonstrated that fungi in the rhizosphere and root endosphere adopt multiple trophic modes, mostly saprophytic fungi. CONCLUSIONS: This study provided a basis for an in-depth understanding of the structural variation, niche differentiation, and function of plant root-related fungal microbiota. We believe that it could provide guidance on the subsequent development of beneficial fungi.

Effect of Aspergillus flavus contamination on the fungal community succession, mycotoxin production and storage quality of maize kernels at various temperatures.

Aspergillus flavus, a notorious saprobe and opportunistic plant pathogen, alters mycotoxin contamination and biochemical components in maize kernels during processing and storage, thereby reducing the possibilities of maize end use and compromising food safety. This study explored changes in mycotoxin production, fungal community succession and biochemical components in maize kernels stored at 20, 25 and 30 °C, exposed to A. flavus. Results showed that aflatoxin B1 concentration increased over time, reaching 4.88 µg/kg at 20 °C, 167.23 µg/kg at 25 °C and 349.64 µg/kg at 30 °C after 15 days of storage, whereas the zearalenone production was characterized by an increase followed by a decrease. Correspondingly, the number of molds gradually increased and reached a stable stage after 10 days. High-throughput sequencing of the internal transcribed spacer (ITS) revealed that Eurotium dominated the fungal communities, with A. flavus reaching maximum abundance in maize kernels stored at 30 °C for 15 days. Correlation analysis indicated that the relative abundance of A. flavus was significantly negatively correlated with the content of zein and moisture (P < 0.05). Moreover, the wet milling process of maize effectively eliminated the concentration of aflatoxin B1 and zearalenone from the starch. Pasting temperature and setback value of starch decreased while peak viscosity, final viscosity and breakdown value increased with storage. These findings indicate that interactions between the epiphytic fungal community and A. flavus at elevated storage temperatures aggravate both maize quality deterioration and mycotoxin contamination. Furthermore, they have a discernible impact on the pasting properties of starch. This insight informs strategies to control fungal infections during maize processing and storage.

Cold adapted and closely related mucoraceae species colonise dry-aged beef (DAB).

The dry ageing is a historically relevant method of meat preservation, now used as a way to produce the dry-aged beef (DAB) known for its pronounced flavour. Partially responsible for the taste of the DAB may be various microorganisms that grow on the surface of the meat. Historically, the fungal species colonising the DAB were described as members of the genera Thamnidium and Mucor. In this study we used both culture based approach as well as ITS2 rDNA metabarcoding analysis to investigate the fungal community of the DAB, with special emphasis on the mucoralean taxa. Isolated fungi were members of 6 different species from the family Mucoraceae, belonging to the genera Mucor and Helicostylum. Metabarcoding data provided supplementary information regarding the presence of other fungi including those from the Thamnidium genus. In both approaches used in this study isolates closely related to the Mucor flavus strain CBS 992.68 dominated.

Beyond the surface: exploring the mycobiome of Norway spruce under drought stress and with Heterobasidion parviporum.

The mycobiome, comprising fungi inhabiting plants, potentially plays a crucial role in tree health and survival amidst environmental stressors like climate change and pathogenic fungi. Understanding the intricate relationships between trees and their microbial communities is essential for developing effective strategies to bolster the resilience and well-being of forest ecosystems as we adopt more sustainable forest management practices. The mycobiome can be considered an integral aspect of a tree's biology, closely linked to its genotype. To explore the influence of host genetics and environmental factors on fungal composition, we examined the mycobiome associated with phloem and roots of Norway spruce (Picea abies (L.) Karst.) cuttings under varying watering conditions. To test the "mycobiome-associated-fitness" hypothesis, we compared seedlings artificially inoculated with Heterobasidion parviporum and control plants to evaluate mycobiome interaction on necrosis development. We aimed to 1) identify specific mycobiome species for the Norway spruce genotypes/families within the phloem and root tissues and their interactions with H. parviporum and 2) assess stability in the mycobiome species composition under abiotic disturbances (reduced water availability). The mycobiome was analyzed by sequencing the ribosomal ITS2 region. Our results revealed significant variations in the diversity and prevalence of the phloem mycobiome among different Norway spruce genotypes, highlighting the considerable impact of genetic variation on the composition and diversity of the phloem mycobiome. Additionally, specific mycobiome genera in the phloem showed variations in response to water availability, indicating the influence of environmental conditions on the relative proportion of certain fungal genera in Norway spruce trees. In the root mycobiome, key fungi such as Phialocephala fortinii and Paraphaeosphaeria neglecta were identified as conferring inhibitory effects against H. parviporum growth in Norway spruce genotypes. Furthermore, certain endophytes demonstrated greater stability in root ecosystems under low water conditions than ectomycorrhizal fungi. This knowledge can contribute to developing sustainable forest management practices that enhance the well-being of trees and their ecosystems, ultimately bolstering forest resilience.

Fungal community characteristics and driving factors in Bothriochloa ischaemum litter in a copper mining area.

Among influencing biotic and abiotic factors, microorganisms predominate litter decomposition, playing an important role in maintaining the ecosystem material cycle. Bothriochloa ischaemum was the dominant plant species in China's Eighteen River tailings dam, and it was selected as the research object. We explored the dynamic of fungal community characteristics in B. ischaemum litter during different decomposition stages and investigated relevant driving factors affecting associative dynamic changes. Results showed that Ascomycetes and Basidiomycetes were the dominant phyla during litter decomposition. At a class level, the relative abundance of Dothideomycetes gradually decreased as litter decomposition progressed while Sordariomycetes gradually increased, ultimately becoming the dominant class. The community structure of the fungal community was mainly affected by litter pH, total carbon (TC), and copper (Cu) content. The fungal community's network structure was the most complex compared to other decomposition stages after 200 days of litter decomposition. Additionally, the fungal community's modularity gradually increased, while the degree of functional differentiation also increased, strengthening fungal community stability during litter decomposition. This study clarifies fungal community structure during litter decomposition in this copper tailings area, and provides a scientific basis for further improving soil fertility and nutrient cycling in mining areas.

Characterizations of the multi-kingdom gut microbiota in Chinese patients with gouty arthritis.

OBJECTIVE: The gut microbial composition has been linked to metabolic and autoimmune diseases, including arthritis. However, there is a dearth of knowledge on the gut bacteriome, mycobiome, and virome in patients with gouty arthritis (GA). METHODS: We conducted a comprehensive analysis of the multi-kingdom gut microbiome of 26 GA patients and 28 healthy controls, using whole-metagenome shotgun sequencing of their stool samples. RESULTS: Profound alterations were observed in the gut bacteriome, mycobiome, and virome of GA patients. We identified 1,117 differentially abundant bacterial species, 23 fungal species, and 4,115 viral operational taxonomic units (vOTUs). GA-enriched bacteria included Escherichia coli_D GENOME144544, Bifidobacterium infantis GENOME095938, Blautia_A wexlerae GENOME096067, and Klebsiella pneumoniae GENOME147598, while control-enriched bacteria comprised Faecalibacterium prausnitzii_G GENOME147678, Agathobacter rectalis GENOME143712, and Bacteroides_A plebeius_A GENOME239725. GA-enriched fungi included opportunistic pathogens like Cryptococcus neoformans GCA_011057565, Candida parapsilosis GCA_000182765, and Malassezia spp., while control-enriched fungi featured several Hortaea werneckii subclades and Aspergillus fumigatus GCA_000002655. GA-enriched vOTUs mainly attributed to Siphoviridae, Myoviridae, Podoviridae, and Microviridae, whereas control-enriched vOTUs spanned 13 families, including Siphoviridae, Myoviridae, Podoviridae, Quimbyviridae, Phycodnaviridae, and crAss-like. A co-abundance network revealed intricate interactions among these multi-kingdom signatures, signifying their collective influence on the disease. Furthermore, these microbial signatures demonstrated the potential to effectively discriminate between patients and controls, highlighting their diagnostic utility. CONCLUSIONS: This study yields crucial insights into the characteristics of the GA microbiota that may inform future mechanistic and therapeutic investigations.

Species composition of root-associated mycobiome of ruderal invasive Anthemis cotula L. varies with elevation in Kashmir Himalaya / La composición de especies del micobioma asociado a las raíces de la invasora ruderal Anthemis cotula L. varía con la elevación en Cachemira Himalaya

Investigating the microbial communities associated with invasive plant species can provide insights into how these species establish and thrive in new environments. Here, we explored the fungal species associated with the roots of the invasive species Anthemis cotula L. at 12 sites with varying elevations in the Kashmir Himalaya. Illumina MiSeq platform was used to identify the species composition, diversity, and guild structure of these root-associated fungi. The study found a total of 706 fungal operational taxonomic units (OTUs) belonging to 8 phyla, 20 classes, 53 orders, 109 families, and 160 genera associated with roots of A. cotula, with the most common genus being Funneliformis. Arbuscular mycorrhizal fungi (AMF) constituted the largest guild at higher elevations. The study also revealed that out of the 12 OTUs comprising the core mycobiome, 4 OTUs constituted the stable component while the remaining 8 OTUs comprised the dynamic component. While α-diversity did not vary across sites, significant variation was noted in β-diversity. The study confirmed the facilitative role of the microbiome through a greenhouse trial in which a significant effect of soil microbiome on height, shoot biomass, root biomass, number of flower heads, and internal CO2 concentration of the host plant was observed. The study indicates that diverse fungal mutualists get associated with this invasive alien species even in nutrient-rich ruderal habitats and may be contributing to its spread into higher elevations. This study highlights the importance of understanding the role of root-associated fungi in invasion dynamics and the potential use of mycobiome management strategies to control invasive species.(AU)

Effects of rotation and Bacillus on the changes of continuous cropping soil fungal communities in American ginseng.

The continuous cropping obstacle is the main factor in leading to difficulty in American ginseng replanting. The dormant microbiota in the soil may be the cause of American ginseng disease and eventually caused continuous cropping obstacles, but there are few studies on the dynamic changes of soil microenvironment after American ginseng planting. In this study, we tracked short-term variation in physicochemical properties, enzyme activities, and fungal communities over time-series in soils with continuous cropping obstacle under crop rotation and probiotic Bacillus treatments. Furthermore, we examined the relationships between the important fungal compositions and the soil properties. The results showed that sucrase, cellulase, urease and acid phosphatase activities were significantly increased, while catalase and dehydrogenase were decreased with treatments time. Rotation treatment significantly affected the diversity, dissimilarity degree and species distribution of soil fungal community with continuous cropping obstacle over a short-term. Moreover, beneficial fungal biomarkers such as Cladorrhinum, Oidiodendron, and Mariannaea were accumulated at 48 h under rotation treatments. Almost all fungal biomarkers were negatively correlated with hydrolases and positively correlated with oxidoreductases and acid phosphatase under crop rotation treatments. This study suggested that compared to probiotic Bacillus, crop rotation can significantly affect soil fungal community structure, especially the enrichment of specific potentially beneficial fungal species. Our findings provide a scientific basis for understanding the dynamic changes of fungal communities and soil properties with continuous cropping obstacle of American ginseng in initial stage of soil improvement.

A Sedentary Lifestyle Changes the Composition and Predicted Functions of the Gut Bacterial and Fungal Microbiota of Subjects from the Same Company.

A sedentary lifestyle affects the diversity and composition of the gut microbiota, but previous studies have mainly focused on bacteria instead of fungi. Here, we compared both the fecal bacterial and fungal microbiota compositions and functions in sedentary persons and controls. Subjects from the China Railway Corporation, including 99 inspectors and 88 officials, were enrolled in our study. Fecal microbiota communities were analyzed using 16S rRNA gene sequencing for bacteria and ITS sequencing for fungi. We found that the diversity of the gut microbiota of the sedentary group was significantly lower than that of the control group (P < 0.05). The sedentary group had a higher abundance of Firmicutes, a lower abundance of Actinobacteria and Proteobacteria and a higher abundance of Ascomycota, and a lower abundance of Basidiomycota. Furthermore, functional prediction analysis of the fungal microbiota revealed more L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde, more phospholipid remodeling (phosphatidylethanolamine, yeast), and more L-tyrosine degradation I, as well as less pentose phosphate pathway (non-oxidative branch), less adenosine nucleotide biosynthesis and less L-valine biosynthesis in the sedentary group (P < 0.05). Thus, a sedentary lifestyle changes the composition and function of the gut microbiota. It may change the pentose phosphate pathway (non-oxidative branch), nucleic acid and amino acid biosynthesis and phospholipid metabolism in fungi.

Succession of Fungal Communities and Their Functional Profiles in a Decaying Foundation Species.

Dead plant biomass from foundation plant species is fundamental for the survival of coastal salt marshes because dead biomass aids in the vertical accretion of the ecosystem. Fungi regulate the decomposition of dead biomass, and thus play an essential role for marsh survival. Despite their importance, little is known about the compositional and functional changes of fungal communities in plant matter throughout senescence and litter decomposition. Here, we analyzed how fungal communities and their functionality change in the foundation plant species Spartina patens, which builds vast amounts of dead plant biomass (thatch) on the soil surface. We analyzed the chemical and fungal properties of live biomass, standing dead biomass (dead biomass shortly after senescence), upper thatch (top layer of litter on the soil surface), and lower thatch (bottom layer of litter on the soil surface) during September and November of 2021. We found that the chemical and fungal properties of different S. patens biomass types followed a predictable litter decomposition pattern. Notably, live biomass, standing dead biomass, upper thatch, and lower thatch all hosted unique fungal communities and litter chemistry. Functional groups present in live biomass (pathogens, epiphytes, and mycoparasites) were lost during senescence and later replaced by diverse saprotrophs. The abundance of lignocellulose saprotrophs increased throughout decomposition, with the highest abundance occurring in lower thatch. These results suggest a predictable succession of fungal communities through the senescence and decomposition of the foundation species S. patens. Our study highlights the diversity of fungal communities in a disappearing foundation species.

The wild solitary bees Andrena vaga, Anthophora plumipes, Colletes cunicularius, and Osmia cornuta microbiota are host specific and dominated by endosymbionts and environmental microorganisms.

We characterized the microbial communities of the crop, midgut, hindgut, and ovaries of the wild solitary bees Andrena vaga, Anthophora plumipes, Colletes cunicularius, and Osmia cornuta through 16S rRNA gene and ITS2 amplicon sequencing and a large-scale isolation campaign. The bacterial communities of these bees were dominated by endosymbionts of the genera Wolbachia and Spiroplasma. Bacterial and yeast genera representing the remaining predominant taxa were linked to an environmental origin. While only a single sampling site was examined for Andrena vaga, Anthophora plumipes, and Colletes cunicularius, and two sampling sites for Osmia cornuta, the microbiota appeared to be host specific: bacterial, but not fungal, communities generally differed between the analyzed bee species, gut compartments and ovaries. This may suggest a selective process determined by floral and host traits. Many of the gut symbionts identified in the present study are characterized by metabolic versatility. Whether they exert similar functionalities within the bee gut and thus functional redundancy remains to be elucidated.

Composition of fungal communities upon multiple passaging of rhizosphere microbiome for salinity stress mitigation in Vigna radiata.

The top-down approach of microbiome-mediated rhizosphere engineering has emerged as an eco-friendly approach for mitigating stress and enhancing crop productivity. It has been established to mitigate salinity stress in Vigna radiata using multi-passaging approach. During the process of acclimatization under increasing levels of salinity stress, the structure of rhizospheric microbial community undergoes dynamic changes, while facilitating stress mitigation in plants. In this study, using ITS-based amplicon sequencing, the dynamics of rhizosphere fungal community was unravelled over successive passages under salinity stress in V. radiata. Clear shifts were evident among the fungal community members under stress and non-stress conditions, upon application of acclimatized rhizosphere microbiome in V. radiata across successive passages. These shifts correlated with enhanced plant biometrics and reduced stress marker levels in plant. Significant changes in the fungal community structure were witnessed in the rhizosphere across specific passaging cycles under salinity stress, which possibly facilitated stress mitigation in V. radiata.

Fungal microbiota isolated from native stingless bee species inhibited pathogens of Apis mellifera.

Social bees can establish interactions with microorganisms to keep their colonies free of pathogens and parasites by developing different protection strategies. We explored the fungal microbiota isolated from three species of stingless bees, Tetragonisca fiebrigi, Plebeias sp., and Scaptotrigona jujuyensis, and its potential ability to suppress pathogenic microorganisms of A. mellifera, namely Paenibacillus larvae, Ascosphaera apis and Aspergillus flavus, which were tested and evaluated. Six filamentous fungal strains, Trametes hirsuta, Alternaria alternata, Curvularia spicifera, Skeletocutis sp., Alternaria tenuissima, Monascus spp., as well as the yeast Wickerhamomyces anomalus, were selected for trials and isolated from the heads of foraging bees. The fungal strains were identified by macroscopic and microscopic taxonomic characteristics and by sequencing of the ITS1-5.8S-ITS2 region of ribosomal DNA. All fungal strains inhibited these pathogens of A. mellifera. We also evaluated the effect of the secondary metabolites extracted with and without ethanol. Both metabolites showed antimicrobial properties, and our results suggest that fungi isolated from stingless bees produce bioactive compounds with antibacterial and antifungal effects that could be used to treat Apis mellifera colony diseases and maintain colony health.