Relative Abundance Of Fungi Research Articles

Ectomycorrhizal fungi and the nitrogen economy of Nothofagus in southern Patagonia.

Subantarctic Nothofagus forests are the southernmost forests in the world, with negligible atmospheric nitrogen (N) deposition. Most paradigms about the role of ectomycorrhizal (ECM) fungi in N cycling and plant N uptake at high latitudes have been tested in boreal coniferous forests, while in the southern hemisphere, ECM hosts are primarily angiosperms. Using ITS1 meta-barcoding, we characterized ECM and saprotrophic fungal communities in evergreen and deciduous Nothofagus forests forming monodominant and mixed stands in the archipelago of Tierra del Fuego (Chile and Argentina). We assessed the N economy of Nothofagus by correlating host species with fungal relative abundances, edaphic variables, net N mineralization, microbial biomass N and the activity of eight extracellular soil enzymes activities. The N economy of deciduous N. pumilio forests was strikingly similar to boreal coniferous forests, with the lowest inorganic N availability and net N mineralization, in correlation to higher relative abundances of ECM fungi with enzymatic capacity for organic N mobilization (genus Cortinarius). In contrast, the N economy of evergreen N. betuloides forests was predominantly inorganic and correlated with ECM lineages from the family Clavulinaceae, in acidic soils with poor drainage. Grassy understory vegetation in deciduous N. antarctica forests likely promoted saprotrophic fungi (i.e., genus Mortierella) in correlation with higher activities of carbon-degrading enzymes. Differences between Nothofagus hosts did not persist in mixed forests, illustrating the range of soil fertility of these ECM angiosperms and the underlying effects of soil and climate on Nothofagus distribution and N cycling in southern Patagonia.

Vaginal fungi are associated with treatment-induced shifts in the vaginal microbiota and with a distinct genital immune profile.

Vaginal colonization by fungi may elicit genital inflammation and enhance the risk of adverse reproductive health outcomes, such as HIV acquisition. Cross-sectional studies have linked fungi with an absence of bacterial vaginosis (BV), but it is unclear whether shifts in vaginal bacteria alter the abundance of vaginal fungi. Vaginal swabs collected following topical metronidazole treatment for BV during the phase 2b, placebo-controlled trial of LACTIN-V, a Lactobacillus crispatus-based live biotherapeutic, were assayed with semi-quantitative PCR for the relative quantitation of fungi and key bacterial species and multiplex immunoassay for immune factors. Vaginal fungi increased immediately following metronidazole treatment for BV (adjusted P = 0.0006), with most of this increase attributable to Candida albicans. Vaginal fungi were independently linked to elevated levels of the proinflammatory cytokine interleukin (IL) 17A, although this association did not remain significant after correcting for multiple comparisons. Fungal relative abundance by semi-quantitative PCR returned to baseline levels within 1 month of metronidazole treatment and was not affected by LACTIN-V or placebo administration. Fungal abundance was positively associated with Lactobacillus species, negatively associated with BV-associated bacteria, and positively associated with a variety of proinflammatory cytokines and chemokines, including IL-17A, during and after study product administration. Antibiotic treatment for BV resulted in a transient expanded abundance of vaginal fungi in a subset of women which was unaffected by subsequent administration of LACTIN-V. Vaginal fungi were positively associated with Lactobacillus species and IL-17A and negatively associated with BV-associated bacteria; these associations were most pronounced in the longer-term outcomes.IMPORTANCEVaginal colonization by fungi can enhance the risk of adverse reproductive health outcomes and HIV acquisition, potentially by eliciting genital mucosal inflammation. We show that standard antibiotic treatment for bacterial vaginosis (BV) results in a transient increase in the absolute abundance of vaginal fungi, most of which was identified as Candida albicans. Vaginal fungi were positively associated with proinflammatory immune factors and negatively associated with BV-associated bacteria. These findings improve our understanding of how shifts in the bacterial composition of the vaginal microbiota may enhance proliferation by proinflammatory vaginal fungi, which may have important implications for risk of adverse reproductive health outcomes among women.

Long-Term Organic Cultivation in Greenhouses Enhances Vegetable Yield and Soil Carbon Accumulation through the Promotion of Soil Aggregation

The long-term use of fertilizers and pesticides in conventional cultivation has resulted in a decrease in soil productivity and vegetable yields in greenhouses. However, there is little research exploring the changes in soil organic carbon and the microbial community mediated by soil aggregates, or their impacts on soil productivity. This study investigated the properties of soil aggregates, including the levels of organic carbon fractions, microbial community, and enzyme activity with the three aggregate classes: microaggregates (<0.25 mm), small macroaggregates (2–0.25 mm) and large macroaggregates (>2 mm) under conventional cultivation (CC), integrated cultivation (IC), and organic cultivation (OC) in greenhouses. The results showed that (1) OC and IC promoted the formation of small macroaggregates and enhanced aggregate stability compared to CC; (2) SOC in the three size fractions of OC increased by 92.06–98.99% compared to CC; EOC increased by 98.47–117.59%; POC increased by 138.59–208.70%; MBC increased by 104.71–230.61%; and DOC increased by 21.93–40.90%, respectively; (3) organic cultivation significantly increased enzyme activity in all three particle-size aggregates and increased the relative abundance of bacteria in microaggregates as well as the relative abundance of fungi in small macroaggregates. Structural equation model (SEM) analysis revealed that organic farming practices fostered the development of smaller macroaggregates, elevated microbial and enzyme activities within soil aggregates, and facilitated the conversion of soil nutrients and carbon sequestration. Therefore, long-term organic cultivation increases soil carbon content and vegetable yield in greenhouses by increasing the proportion of small aggregates. In conclusion, long-term organic cultivation in greenhouses improves soil structure, increase soil fertility and vegetable yield, and has a positive impact on the environment. Organic cultivation increases soil fertility and contributes to maintaining ecological balance and protecting the environment in greenhouses.

Characteristics of the Soil Microbial Community Structure under Long-Term Chemical Fertilizer Application in Yellow Soil Paddy Fields

To compare the differences in the soil microbial community structure in yellow soil paddy fields after the long-term application of chemical fertilizer, the role and mechanism of chemical fertilizer in maintaining soil microbial diversity were analyzed, and a theoretical basis for fertilization management in farmlands was provided. In this study, long-term experiments were conducted at the Scientific Observation and Experimental Station of the Arable Land Conservation and Agricultural Environment (Guizhou), Ministry of Agriculture and Rural Affairs. Soil samples were collected from five treatments: fertilizer N, P, and K (NPK); fertilizer P and K (PK); fertilizer N and K (NK); fertilizer N and P (NP); and no fertilizer (CK). High-throughput sequencing technology was used to analyze the microbial composition and diversity of the colonies, and the influencing factors are discussed. An analysis of the soil bacterial α diversity indices under the different fertilization treatments revealed that the long-term application of NPK fertilizers had less of an effect on the soil bacterial α diversity indices than did the CK. The long-term application of chemical fertilizers significantly reduced the soil bacterial Chao1, Shannon, and Simpson indices, while there was no significant difference in the bacterial Pielou e index among the treatments. The long-term application of chemical fertilizers significantly increased the soil fungal Chao1 index, but the effects on the other indices were not significant (p < 0.05). An analysis of the bacterial and fungal species under different fertilization treatments showed found that compared with CK, the long-term application of chemical fertilizer increased the relative abundance of Proteobacteria to varying degrees while reducing the relative abundance of Chloroflexi. The impact of other phyla was relatively small, and the difference in the relative abundance of fungi was not significant (p < 0.05). Principal component analysis revealed that, at the genus level, the bacterial and fungal community structures in the CK and NK treatments were relatively independent, while those in the NPK, PK, and NP treatments were similar. Random forest analysis revealed that OM, TP, and TK are the dominant factors that affect soil bacteria α diversity. The dominant factors affecting fungi α diversity are pH, OM, and AK. Redundancy analysis indicated that AK and TP were the main factors affecting bacterial community structure, while AP, AK, and pH were the main factors affecting fungal community structure. The conclusion drawn from this study is that the long-term application of nitrogen, phosphorus, and potassium fertilizer; phosphorus and potassium fertilizer; and nitrogen and phosphorus fertilizer can improve soil fertility, alter the soil environment, enhance microbial diversity, and improve the microbial community structure in yellow soil paddy fields, promoting soil ecosystem stability and health.

Niche partitioning association of fungal genera correlated with lower Fusarium and fumonisin-B1 levels in maize

Through partitioning of ecological niches, several fungi are able to coexist on the same host crop. In (partial) absence of niche partitioning, competitive exclusion among fungi can occur. Competitive exclusion is one of the bases for biocontrol. We investigated fungal correlations, in terms of relative abundance of the fungi, in pre-harvest maize, as a natural ecosystem model. Internal mycobiome fungal relative abundance of maize was used to establish correlations. The maize had been harvested from dry and wet agro-ecological zones of Zambia. The relative abundances of the fungal genera were determined using DNA amplicon sequencing. For this study, positive or absence of correlations between fungal genera signified good niche partitioning (co-existence), whereas negative correlations signified poor niche partitioning and potential for competitive exclusion. When species compete within one niche (competitive exclusion), we may expect to detect higher levels of mycotoxins—since mycotoxins are considered antagonistic agents aimed at defending or invading an ecological niche. To estimate the importance of mycotoxins in competitive exclusion, we measured the influence of the fungal correlations on levels of fumonisin-B1 (FB1) in the maize. FB1 data were derived from a previous study on the maize, determined by HPLC. Results showed that Sarocladium and Stenocarpella had the strongest significant negative correlation with Fusarium, suggesting poor niche partitioning and potential for antagonism of these genera with Fusarium. Furthermore, higher levels of Stenocarpella resonated with lower levels of FB1 and vice versa. It was also observed that, when Sarocladium was in low abundance (< 10%), the frequency of detection of higher levels of FB1 (> 100 µg kg−1) in the pre-harvest maize was highest.

Effects of Garlic Oil and Cinnamaldehyde on Sheep Rumen Fermentation and Microbial Populations in Rusitec Fermenters in Two Different Sampling Periods.

Garlic oil (GO) and cinnamaldehyde (CIN) have shown potential to modify rumen fermentation. The aim of this study was to assess the effects of GO and CIN on rumen fermentation, microbial protein synthesis (MPS), and microbial populations in Rusitec fermenters fed a mixed diet (50:50 forage/concentrate), as well as whether these effects were maintained over time. Six fermenters were used in two 15-day incubation runs. Within each run, two fermenters received no additive, 180 mg/L of GO, or 180 mg/L of CIN. Rumen fermentation parameters were assessed in two periods (P1 and P2), and microbial populations were studied after each of these periods. Garlic oil reduced the acetate/propionate ratio and methane production (p < 0.001) in P1 and P2 and decreased protozoal DNA concentration and the relative abundance of fungi and archaea after P1 (p < 0.05). Cinnamaldehyde increased bacterial diversity (p < 0.01) and modified the structure of bacterial communities after P1, decreased bacterial DNA concentration after P2 (p < 0.05), and increased MPS (p < 0.001). The results of this study indicate that 180 mg/L of GO and CIN promoted a more efficient rumen fermentation and increased the protein supply to the animal, respectively, although an apparent adaptive response of microbial populations to GO was observed.

Root microbiota analysis of Oryza rufipogon and Oryza sativa reveals an orientation selection during the domestication process.

The root-associated microbiota has a close relation to the life activities of plants, and its composition is affected by the rhizospheric environment and plant genotypes. Rice (Oryza sativa) was domesticated from the ancestor species Oryza rufipogon. Many important agricultural traits and adversity resistance of rice have changed during a long time of natural domestication and artificial selection. However, the influence of rice genotypes on root microbiota in important agricultural traits remains to be explained. In this study, we performed 16S rRNA and internal transcribed spacer (ITS) gene amplicon sequencing to generate bacterial and fungal community profiles of O. rufipogon and O. sativa, both of which were planted in a farm in Guangzhou and had reached the reproductive stage. We compared their root microbiota in detail by alpha diversity, beta diversity, different species, core microbiota, and correlation analyses. We found that the relative abundance of bacteria was significantly higher in the cultivated rice than in the common wild rice, while the relative abundance of fungi was the opposite. Significant differences in agricultural traits between O. rufipogon and O. sativa showed a high correlation with core microorganisms in the two Oryza species, which only existed in either or had obviously different abundance in both two species, indicating that rice genotype/phenotype had a strong influence on recruiting specific microorganisms. Our study provides a theoretical basis for the in-depth understanding of rice root microbiota and the improvement of rice breeding from the perspective of the interaction between root microorganisms and plants.IMPORTANCEPlant root microorganisms play a vital role not only in plant growth and development but also in responding the biotic and abiotic stresses. Oryza sativa is domesticated from Oryza rufipogon which has many excellent agricultural traits especially containing resistance to biotic and abiotic stresses. To improve the yield and resistance of cultivated rice, it is particularly important to deeply research on differences between O. sativa and O. rufipogon and find beneficial microorganisms to remodel the root microbiome of O. sativa.

Responses of bulk and rhizosphere soil microbiomes to different cover crop inputs and their connection and contribution to soil fertility and plant growth

Bulk and rhizosphere soil microbiomes may be naturally linked and exhibit unique responses to different cover crop inputs during the early decomposition process. However, their relationship and contribution to soil carbon and nitrogen levels and plant growth during the decomposition process remain unclear. Herein, we performed a pot-based experiment to investigate the interactive effects of cover crops (rye, hairy vetch [HV], and a mixture of rye and HV [mix]) and soil microbial habitats (bulk and rhizosphere soils) on the microbial community. Additionally, we identified the hub taxa and evaluated their contributions to the microbial community, soil fertility, and plant growth. Lettuce was grown in soil exposed to control, rye, HV, or mixed cover crops. Bacterial 16S rRNA) and fungal (ITS) community structures were characterized in bulk and rhizosphere soils of lettuce plants using a DNA-based molecular approach. The results showed that cover crops and soil microbial habitats independently affected microbial community structures; the relative abundances of fungi and bacteria, known as decomposers in bulk soil and plant growth-promoting bacteria in rhizosphere soil, increased. The hub taxa under each treatment represented specific groups that connect bulk and rhizosphere microbiomes. Based on Mantel statistical analysis, hub taxa may maintain the bulk soil microbiome, within which the bacterial community in HV and mix treatments may contribute to the nitrogen supply from cover crop residues. Additionally, the bacterial community in rhizosphere soil in HV and mix treatments may contribute to nitrogen absorption by lettuce plants. These results add to the understanding of the early process of sustainable agriculture using cover crops.

Simultaneous Analysis of Bacterial and Fungal Communities in Oral Samples from Intubated Patients in Intensive Care Unit.

Intubated patients in intensive care units (ICUs) too frequently contract ventilator-associated pneumonia or Candida infections. Oropharyngeal microbes are believed to play an important etiologic role. This study was undertaken to determine whether next-generation sequencing (NGS) can be used to simultaneously analyze bacterial and fungal communities. Buccal samples were collected from intubated ICU patients. Primers targeting the V1-V2 region of bacterial 16S rRNA and the internal transcribed spacer 2 (ITS2) region of fungal 18S rRNA were used. V1-V2, ITS2, or mixed V1-V2/ITS2 primers were used to prepare an NGS library. Bacterial and fungal relative abundances were comparable for V1-V2, ITS2, or mixed V1-V2/ITS2 primers, respectively. A standard microbial community was used to adjust the relative abundances to theoretical abundance, and NGS and RT-PCR-adjusted relative abundances showed a high correlation. Using mixed V1-V2/ITS2 primers, bacterial and fungal abundances were simultaneously determined. The constructed microbiome network revealed novel interkingdom and intrakingdom interactions, and the simultaneous detection of bacterial and fungal communities using mixed V1-V2/ITS2 primers enabled analysis across two kingdoms. This study provides a novel approach to simultaneously determining bacterial and fungal communities using mixed V1-V2/ITS2 primers.

Detritivores and exogenous nitrogen influence litter microbial communities in coastal salt marshes

Saprotrophic fungal communities and animal detritivores are known to regulate litter decomposition, yet their interaction has seldom been examined in coastal salt marshes. Such studies are important because salt marshes have some of the highest carbon storage rates of any ecosystem, and litter plays an important role in carbon cycling. Furthermore, it is currently unknown how species loss and nitrogen (N) pollution will impact the detritivore-fungi or detritivore-algae interactions that occur on litter. To test for changes in the microbial community of decaying Spartina alterniflora Loisel litter, we factorially altered the N concentrations of sediment surrounding the litter as well as the densities of Melampus bidentatus Say, 1822, an abundant but declining detritivorous snail that increases fungal abundance and litter decomposition rates. In each of 36 experimental plots, we analyzed the fungal and algal community composition of litter bundles (collected after 50 and 100 d, respectively) along with detritivore densities, plant traits, sediment and litter N, sediment chemistry, and microclimate. Notably, the densities of snails and isopods were associated with changes in the evenness and relative abundances of fungi in the litter, while amphipods influenced both fungal and algal communities. N additions further altered fungal community structure and increased the dominant saprotroph Natantispora retorquens at both timepoints. In sum, our novel field study revealed that N pollution and the loss of key detritivores, both of which are expected to increase in the future, will likely impact salt marsh fungi. Therefore, global change may impact the animal-microbial dynamics that influence above-ground carbon cycling.

Linking soil microbial community with the changes in soil physicochemical properties in response to long-term agricultural land use change of different chronosequences and depth layers

Agricultural land use changes are essential in addressing global urbanization demands. The improper management of agricultural land may lead to the alteration of the microbial ecosystem, which ultimately affects soil quality. Here, we assessed how soil microbial diversity, communities, and physicochemical properties in three layers of soil; upper (0–15 cm), middle (15–30 cm), and lower (30–45 cm), responded to a long-term land use change from paddy land (PL) to dry land of different chronosequences; PD3 (3 years), PD5 (5 years), and PD10 (10 years). We found PL conversion into dry lands increased soil pH, soil 3 phase R-value, bulk density (BD), organic matter (OM), total phosphorus (TP), total nitrogen (TN), and decreased electrical conductivity (EC), water holding capacity (WHC), and moisture content (MC) in all three layers. The land use change from PL to dry lands initially (PD3) decreased (11–25 %) bacterial diversity, while it significantly increased in PD5 (0.1–16 %), and PD10 (1–14 %) in all three layers. Unlike bacterial diversity, fungal diversity was high in PD5 in the upper layer, while the middle and lower layer was the least affected. We also found the conversion of PL to dry land altered relative abundance (RA) of bacteria on the upper layer, while RA of fungi was reshaped in all three layers. The Pearson’s correlation coefficient showed that MC, OM, pH, R-value, TN, TP, and WHC were important physicochemical factors, which significantly (P < 0.05) influenced Nitrospirae, Chloroflexi, Proteobacteria, and Basidiomycota composition. Briefly, our study show that land use change initially (3 years) caused huge changes in the microbiome, which improved somehow in further years (5 and 10 years), and we conclude that land use changes impact positively on functional biodiversity and biological quality of the soil.

Mycoflora Associated with Barely Grains (Hordeum vulgare L.) in the Eastern Parts of Libya

During the harvest season (2019-2020), local variety of barley seeds (Hordeum vulgare L.) were collected from three different locations, Almerj, Gerdina, and Sultan; situated in the eastern part of Libya. The present experiment was performed to identify, and compare natural mycoflora associated with barley seeds among these locations, also to evaluate sodium hypochlorite’s application, as seed disinfectants against fungal contaminators. Barley seeds were surface disinfected with a 4% sodium hypochlorite for two minutes or washed only with deionized water (control) before plating on potato dextrose agar (PDA) medium. The following parameters were recorded and calculated: seed survival (G %), fungal frequency (F), isolation frequency (IF) and fungal relative abundance (RD). Four fungal species were identified as Aspergillus niger van Tiegh, A. flavus Link (ascomycetes), Rhizopus stolonifera (Ehrenb. :Fr.) Vuill (zygomycetes), and Bipolaris australiensis (Bugnicourt) (ascomycetes). The most predominant recovered species was A. niger followed by B. australiensis, R. stolonifera, and A. flavus, (18.5%), (9.67%) (2.84%), (4.65%), respectively. Results also showed Sultan had the highest seed germination, followed by Almerj and Gerdina, 64.5 %, 44.5%, and 20.5 %, respectively. Moreover, seed’s pretreatment with sodium hypochlorite and seed’s origin had no significant effect on frequency and relative abundance of fungi.

Habitat Significantly Affect CWD Decomposition but No Home-Field Advantage of the Decomposition Found in a Subtropical Forest, China

The home-field advantage (HFA) effect has been reported to occur in coarse woody debris (CWD) and litter. It is thought that the HFA effect may be due to the specialization of decomposers in their original habitats. However, the relative contribution of microorganisms, particularly fungi and bacteria, to deadwood decomposition is unclear because of differences in their functional at-tributes and carbon requirements, and the microorganisms that drive the HFA effect of deadwood are also unclear. Here, we analysed a dataset of microbial PLFA and substrate properties collected from the soil and CWD of two subtropical trees, Cryptomeria japonica and Platycarya strobilacea, from forests dominated by one or the other of the two species, with both species present in the forests. Our results showed that habitat and tree types all significantly affected CWD respiration rates, the CWD respiration rates were significantly higher in the deciduous broadleaf forests (DBF) than in the coniferous forest (CF) regardless of tree types, but no a large HFA of CWD decomposition found (HFA index was 4.75). Most biomarkers indicated bacteria and fungi were more abundant in the DBF than in the CF, and the concentration of microbial PLFAs was higher in Platycarya strobilacea than in Cryptomeria japonica. In addition, the relative abundance of fungi and soil B/F were remarkably positively correlated with CWD respiration, indicating that fungi may be the primary decomposers of CWD. In conclusion, our work highlights the importance of interactions between the three primary drivers (environment, substrate quality and microbes) on CWD decomposition.

Inside old reclaimed mine tailings in Northern Ontario, Canada: A microbial perspective

Large areas of metal–contaminated tailings have been revegetated in Northern Ontario (Canada). The specific objective of the present study is to determine if variations in vegetation, and soil physico-chemistry in sulfide tailings is associated with microbial biomass, abundance and diversity. Microbial biomass was determined using Phospholipid fatty acid analysis (PLFA). Amplicon based analysis of the soil bacterial and fungal microbiota was assessed by high throughput sequencing of 16S rRNA gene for bacteria and internal transcribed spacer (ITS) region for fungi. Significant differences in soil pH, organic matter content, and total metals (Cu, Fe, Ni, and Zn) were observed among sites. There were significant variations in microbial biomass among the tailing sites with areas covered with white birch showing the highest level of bacterial and fungal biomass compared to areas vegetated by pines species or pine-white birch mixture. Proteobacteria was the most dominant bacterial phylum while Basidiomycota was the predominant fungal phylum. The most abundant bacterial genus was Mucilaginibacter , followed by Acidobacterium , Acidisphaera , Burkholderia , and Steroidobacter . Site-specific bacterial and fungal genera were identified. However, there were no significant differences for # of OTUs, Chao 1, Simpson index, Shannon index, and species richness among the bacterial populations from different soil tailing areas despite differences in plant populations and soil physico-chemistry. The relative abundance of fungi was associated with the variation in ecology of specific areas. Chao 1, # of OTUs, Simpson index, Shannon index, and species richess were significantly lower at Vale 3 compared to Vale 1 and Vale 5.

Synthetic community improves crop performance and alters rhizosphere microbial communities

AbstractIntroductionHarnessing synthetic communities (SynCom) of plant growth‐promoting (PGP) microorganisms is considered a promising approach to improve crop fitness and productivity. However, biotic mechanisms that underpin improved plant performance and the effects of delivery mode of synthetic community are poorly understood. These are critical knowledge gaps that constrain field efficacy of SynCom and hence large‐scale adoption by the farming community.Material &amp; MethodsIn this study, a SynCom of four PGP microbial species was constructed and applied to either as seed dressing (treatment T1, applied at the time of sowing) or to soil (treatment T2, applied in soil at true leaf stage) across five different cotton (Gossypium hirsutum) cultivars. The impact of SynCom on plant growth, rhizosphere microbiome and soil nutrient availability, and how this was modified by plant variety and mode of applications, was assessed.ResultsResults showed that the seed application of SynCom had the strongest positive impact on overall plant fitness, resulting in higher germination (14.3%), increased plant height (7.4%) and shoot biomass (5.4%). A significant increase in the number of flowers (10.4%) and yield (8.5%) was also observed in T1. The soil nitrate availability was enhanced by 28% and 55% under T1 and T2, respectively. Results further suggested that SynCom applications triggered enrichment of members from bacterial phyla Actinobacteria, Firmicutes and Cyanobacteria in the rhizosphere. A shift in fungal communities was also observed, with a significant increase in the relative abundance of fungi from phyla Chytridiomycota and Basidiomycota in SynCom treatments. A structural equation model suggested that SynCom directly increased crop productivity but also indirectly via impacting the alpha diversity of bacteria.ConclusionOverall, this study provides mechanistic evidence that SynCom applications can shift rhizosphere microbial communities and improve soil fertility, plant growth, and crop productivity, suggesting that their use could contribute toward sustainable increase in farm productivity.

Estimating soil fungal abundance and diversity at a macroecological scale with deep learning spectrotransfer functions

Abstract. Soil fungi play important roles in the functioning of ecosystems, but they are challenging to measure. Using a continental-scale dataset, we developed and evaluated a new method to estimate the relative abundance of the dominant phyla and diversity of fungi in Australian soil. The method relies on the development of spectrotransfer functions with state-of-the-art machine learning and uses publicly available data on soil and environmental proxies for edaphic, climatic, biotic and topographic factors, and visible–near infrared (vis–NIR) wavelengths, to estimate the relative abundances of Ascomycota, Basidiomycota, Glomeromycota, Mortierellomycota and Mucoromycota and community diversity measured with the abundance-based coverage estimator (ACE) index. The algorithms tested were partial least squares regression (PLSR), random forest (RF), Cubist, support vector machines (SVM), Gaussian process regression (GPR), extreme gradient boosting (XGBoost) and one-dimensional convolutional neural networks (1D-CNNs). The spectrotransfer functions were validated with a 10-fold cross-validation (n=577). The 1D-CNNs outperformed the other algorithms and could explain between 45 % and 73 % of fungal relative abundance and diversity. The models were interpretable, and showed that soil nutrients, pH, bulk density, ecosystem water balance (a proxy for aridity) and net primary productivity were important predictors, as were specific vis–NIR wavelengths that correspond to organic functional groups, iron oxide and clay minerals. Estimates of the relative abundance for Mortierellomycota and Mucoromycota produced R2≥0.60, while estimates of the abundance of the Ascomycota and Basidiomycota produced R2 values of 0.5 and 0.58 respectively. The spectrotransfer functions for the Glomeromycota and diversity were the poorest with R2 values of 0.48 and 0.45 respectively. There is no doubt that the method provides estimates that are less accurate than more direct measurements with conventional molecular approaches. However, once the spectrotransfer functions are developed, they can be used with very little cost, and could serve to supplement the more expensive and laborious molecular approaches for a better understanding of soil fungal abundance and diversity under different agronomic and ecological settings.

Metagenomic and physicochemical analyses reveal microbial community and functional differences between three types of low-temperature Daqu

Complex microbes of different types of low-temperature Daqu (LTD) play an important role in the formation of flavors and qualities of light-flavor Baijiu during fermentation. However, characterizing the taxonomic and functional diversity of microbiota in three types of LTD (Houhuo, Hongxin, Qingcha) remains a major challenge. The present study combined metagenomic sequencing with culture-based methods and physicochemical analysis to compare the three LTD microbiota and elucidate their function in LFB brewing. The results revealed a high diversity of microbes in LTD, with 1286 genera and 4157 species detected across all studied samples. Bacteria and fungi were the main microbes in LTD, with a bacterial to fungal relative abundance ratio of above 4:1. Bacillus (21.18%) and Bacillus licheniformis (17.45%) were the most abundant microbes in the LTD microbiota at the genus and species levels, respectively. Culture-dependent analysis found the highest abundances of bacteria, fungi, and lactic acid bacteria in Houhuo, while the metagenomic-based microbiota found that the relative abundance of bacteria and fungi were highest in Houhuo and Hongxin among the three types of LTD, respectively. The different production temperatures of LTD had little effect on its microbial variety, but obviously impacted the microbiota structure and metagenomic function of LTD. Although the microbiota of the three types of LTD shared a high commonality, each had specific microbiota and functional metagenomic features, suggesting their different but complementary roles in the LFB fermentation process. The representative dominant microbes in Houhuo were mostly involved in metabolic pathways associated with the production of flavor substances in liquor. In contrast, the enriched microbes in Qingcha and Hongxin were not only capable of producing specific flavor substances but also had a strong ability to degrade macromolecular substances in raw materials, promoting microbial growth. This study has greatly enriched our knowledge of the effect of LTD fermentation temperature on its quality, providing practical and interesting information for future improvement of LTD and light-flavor Baijiu products.

New Insights into the Fungal Diversity of Cranberry Fruit Rot in Québec Farms Through a Large-Scale Molecular Analysis.

Cranberry fruit rot (CFR) pathogens are widely reported in the literature, but performing large-scale analysis of their presence inside fruit has always been challenging. In this study, a new molecular diagnostic tool, capable of identifying simultaneously 12 potential fungal species causing CFR, was used to better define the impact of CFR across cranberry fields in Québec. For this purpose, 126 fields and 7,825 fruits were sampled in three cranberry farms distributed throughout the province and subjected to comparative analyses of fungal presence and abundance according to cultural practices, sampling times, and cranberry cultivars. All 12 pathogens were detected throughout the study, but as a first major finding, the analyses revealed that four species, Godronia cassandrae, Colletotrichum fructivorum, Allantophomopsis cytisporea, and Coleophoma empetri, were consistently predominant regardless of the parameters studied. Comparison of conventional and organic productions showed a significant reduction in fungal richness and relative abundance. Interestingly, Monilinia oxycocci was found almost exclusively in organic productions, indicating that fungicides had a strong and persistent effect on its population. Surprisingly, there were no significant differences in fungal relative abundance or species richness between fruit sampled at harvest or in storage, suggesting that there may not exist a clear distinction between field and storage rot, as was previously thought. Comparative analysis of fungal species found on eight different cranberry cultivars indicated that they were all infected by the same fungi but could not rule out differences in genetic resistance. This large-scale analysis allows us to draw an exhaustive picture of CFR in Québec and provides new information with respect to its management.

Phyllospheric Microbial Composition and Diversity of the Tobacco Leaves Infected by Didymella segeticola.

A Myriad of biotic and abiotic factors inevitably affects the growth and production of tobacco (Nicotiana tabacum L.), which is a model crop and sought-after worldwide for its foliage. Among the various impacts the level of disease severity poses on plants, the influence on the dynamics of phyllospheric microbial diversity is of utmost importance. In China, recurring reports of a phyto-pathogen, Didymella segeticola, a causal agent of tobacco leaf spot, accentuate the need for its in-depth investigation. Here, a high-throughput sequencing technique, IonS5TMXL was employed to analyze tobacco leaves infected by D. segeticola at different disease severity levels, ranging from T1G (least disease index) to T4G (highest disease index), in an attempt to explore the composition and diversity of phyllospheric microbiota. In all healthy and diseased tobacco leaves, the most dominant fungal phylum was Ascomycota with a high prevalence of genus Didymella, followed by Boeremia, Meyerozyma and Alternaria, whereas in the case of bacterial phyla, Proteobacteria was prominent with Pseudomonas being a predominant genus, followed by Pantoea. The relative abundance of fungi, i.e., Didymella and Boeremia (Ascomycota) and bacteria, i.e., Pseudomonas and Pantoea (Proteobacteria) were higher in diseased groups compared to healthy groups. Healthy tissues exhibited relatively rich and diverse fungal communities in contrast with diseased groups. The infection of D. segeticola had a complex and significant effect on fungal as well as bacterial alpha diversity. FUNGuild analysis indicated that the relative abundance of pathotrophs and saprotrophs in diseased tissues proportionally increased with disease severity. PICRUSt analysis of diseased tissues indicated that the relative abundance of bacterial cell motility and membrane transport-related gene sequences elevated with an increase in disease severity from T1G to T3G and then tended to decrease at T4G. Conclusively, the current study shows the typical characteristics of the tobacco leaf microbiome and provides insights into the distinct microbiome shifts on tobacco leaves infected by D. segeticola.

Gut Microbial Alterations in Diarrheal Baer's Pochards (Aythya baeri).

The structure and composition of gut microbiota correlate with the occurrence and development of host health and disease. Diarrhea can cause alterations in gut microbiota in animals, and the changes in the gut microbial structure and composition may affect the development of diarrhea. However, there is a scarcity of information on the effects of diarrhea on gut fungal composition and structure, particularly in Baer's pochard (Aythya baeri). The current study was performed for high-throughput sequencing of the fungal-specific internal transcribed spacer 1 (ITS-1) to detect the differences of gut mycobiota in healthy and diarrheal Baer's pochard. Results showed that the gut mycobiota not only decreased significantly in diversity but also in structure and composition. Statistical analysis between two groups revealed a significant decrease in the abundance of phylum Rozellomycota, Zoopagomycota, Mortierellomycota, and Kickxellomycota in diarrheal Baer's pochard. At the genus levels, fungal relative abundance changed significantly in 95 genera, with 56 fungal genera, such as Wickerhamomyces, Alternaria, Penicillium, Cystofilobasidium, and Filobasidium, increasing significantly in the gut of the diarrheal Baer's pochard. In conclusion, the current study revealed the discrepancy in the gut fungal diversity and community composition between the healthy and diarrheal Baer's pochard, laying the basis for elucidating the relationship between diarrhea and the gut mycobiota in Baer's pochard.