Trophic Modes Research Articles

Plant and soil health in organic strawberry farms – Greater importance of fungal trophic modes and networks than α-diversity of the mycobiome

The mycobiome composition and health status of host plants are closely related. These relationships should be studied and recognized, as they may form the basis of future sustainable agriculture. The aim of this study was to select relevant biological indicators for monitoring soil microbial diversity by revealing characteristic differences between the mycobiomes of various soil compartments (bulk and rhizosphere) and plant niches (roots and shoots) from 13 healthy and diseased organic strawberry farms. The results of this study show that α-diversity of the mycobiome is less important in shaping plant health than fungal trophic mode composition. Healthy soil niches and roots contain less core taxa, but more differentially abundant taxa, than unhealthy ones. The results also suggest that plant health was shaped by more than just the most abundant fungal taxa, indicating that rare taxa should not be neglected in the analysis of mycobiome structure. We also demonstrate that fungal communities in the soil and plant niches from healthy strawberry farms create more stable and steady networks as compared to those from unhealthy farms. Finally, we show that the mycobiome roots-shoot axis is an important trait to consider in unhealthy plants from strawberry farms.

Exploration of Soil Microbial Diversity and Community Structure along Mid-Subtropical Elevation Gradients in Southeast China

Climate change is altering the abundance and distributions of natural communities in mountainous ecosystems, but the variations of soil microbial communities and their driving factors along elevation gradients at high altitudinal mid-subtropical zones have received limited attention. Such information is needed for a comprehensive understanding of the ecosystem’s response to intensifying climate changes. In this study, using Illumina sequencing, we investigated the shift in soil microbial diversity and community composition at eight evergreen broadleaf forest sites, which ranged from a low of 550 to a high of 1038 m above sea level (m a.s.l.) on Wuyi Mountain in Southeast China. Significant (p < 0.05) differences were observed only in the community structure of bacteria and fungi between the low and high elevation levels of forests, but not in their alpha-diversity indices. Soil bacterial diversity was significantly correlated with plant Shannon index. Likewise, plant richness and diversity modified soil bacterial community structures along the two elevations and were the best predictors. Soil pH was the main edaphic factor driving the fungal diversity across elevations, whereas inconsistency in the fungal trophic mode did not allow the identification of a determinant factor for soil fungal community structure. The variations of the predominant fungal trophic guilds, such as the symbiotrophs and pathotrophs, along elevation gradients were due to the plant richness and diversity prevailing at the low and high elevation levels of forest sites. The findings of this study reveal the soil microbial community dynamics and the local regulators across elevations on Wuyi mountain.

Metabolomic exploration of the physiological regulatory mechanism of the growth and metabolism characteristics of Chlorella vulgaris under photoautotrophic, mixotrophic, and heterotrophic cultivation conditions

Microalgae have various trophic modes such as photoautotrophy, mixotrophy, and heterotrophy, and the physiological and metabolic processes of algal cells in different trophic modes are different. To explore the mechanism underlying trophic mode-mediated regulation of the physiological metabolism of microalgae, Chlorella vulgaris 31 was cultivated under photoautotrophic, mixotrophic, and heterotrophic conditions. Mixotrophic and heterotrophic cultivation significantly promoted the growth, biomass, and lipid and saccharide biosynthesis of C. vulgaris, while higher photosynthetic pigment and protein content could be obtained under autotrophic conditions. Flow cytometry analysis revealed that light periodically and significantly regulated agal cell growth under the photoautotrophic condition, but a weakened effect was observed under mixotrophic and heterotrophic conditions. The mitochondrial structure was affected by enhanced aerobic respiration under mixotrophic and heterotrophic modes. Moreover, the accumulation of starch grains and lipid droplets was significantly higher than that in the photoautotrophic control; however, no significant changes were observed in the chloroplast and nucleus. Intracellular metabolites in mixotrophic and heterotrophic modes varied markedly, mainly involving saccharides, organic acids, fatty acids, and amino acids. Metabolic pathway analysis indicated that mixotrophy and heterotrophy could significantly enhance glycolysis, the tricarboxylic acid cycle, and the pentose phosphate pathway on the 3rd day of cultivation, while higher acetyl-CoA levels were available for fatty acid synthesis in the stationary phase. This finding clarified the mechanism of mixotrophic and heterotrophic growth of C. vulgaris for biomass and biomolecule production.

Speleomycology of Air in Stopića Cave (Serbia).

Fungi can colonize organic matter present in subterranean sites and have a significant role as dwellers in different microniches of cave habitats. In order to analyze the content of airborne fungal propagules in different parts of "Stopića Cave," a touristic site in Serbia, air sampling was carried out in three seasons during 2020, prior to and during the onset of COVID-19 pandemic. Culturable mycobiota was identified using both microscopic techniques and ITS region/BenA gene barcoding, while multivariate analyses were employed to establish the link between fungal taxa and different environmental factors. The maximal measured fungal propagule concentrations were recorded during spring sampling which were based on fungal propagule concentration categories; the cave environment matches the category V. A total of 29 fungal isolates were identified, while Aspergillus, Cladosporium, Fusarium, Lecanicillium, Mucor, and Penicillium were the most diverse genera. According to the trophic mode, most of the isolated fungal species were pathotrophs (75.86%), but when regarding ecological guilds, the most dominant were undefined saprobes and animal pathogens (41.38% for each). Show caves are especially vulnerable to human impacts, and the fungal propagules' concentration within the caves could be good indices for the level of ecological disturbance.

Bacterial and fungal diversities examined through high-throughput sequencing in response to lead contamination of tea garden soil.

Several studies have indicated that the heavy-metal content in tea is increasing gradually. Researchers examining the soil of more than 100 tea gardens in China have observed that lead content was higher in some soils. The effect of lead contamination on soil microorganisms in tea gardens was studied to determine the effect of lead on the essential functions of microorganisms in a tea garden soil ecosystem. Previous studies on pot experiments adopted the method of adding a single instance of pollution, which failed to comprehensively simulate the characteristics of the slow accumulation of heavy metals in soil. This study designed with two pollution modes (multistage and single instance) determined the content of soil lead in different forms according to the European Community Bureau of Reference extraction procedure. The community structure, species diversity and functional abundance of soil bacteria and fungi were examined by high-throughput sequencing. We observed that the content of four forms of lead was higher in the multistage contamination mode than in the single instance contamination mode. The effects of lead contamination on bacteria differed significantly (p < 0.05), and the abundance and diversity of bacteria were higher in the multistage contamination mode than in the single instance contamination mode. The community structure of fungi was more affected by lead than was that of bacteria. The content of each lead form was the environmental factor most strongly affecting soil bacteria and fungi. The predicted main function of the bacterial community was amino acid transport and metabolism, and the trophic mode of the fungal community was mainly pathotroph-saprotroph. This study revealed changes in soil microorganisms caused by different forms of lead and contamination methods in tea garden soil and provide a theoretical basis for examining the effects of lead contamination on soil microorganisms.

Metabolic flexibility during a trophic transition reveals the phenotypic plasticity of greater duckweed (Spirodela polyrhiza 7498).

The greater duckweed (Spirodela polyrhiza 7498) exhibits trophic diversity (photoautotrophic, heterotrophic, photoheterotrophic, and mixotrophic growth) depending on the availability of exogenous organic carbon sources and light. Here, we show that the ability to transition between various trophic growth conditions is an advantageous trait, providing great phenotypic plasticity and metabolic flexibility in S. polyrhiza 7498. By comparing S. polyrhiza 7498 growth characteristics, metabolic acclimation, and cellular ultrastructure across these trophic modes, we show that mixotrophy decreases photosynthetic performance and relieves the CO2 limitation of photosynthesis by enhancing the CO2 supply through the active respiration pathway. Proteomic and metabolomic analyses corroborated that S. polyrhiza 7498 increases its intracellular CO2 and decreases reactive oxygen species under mixotrophic and heterotrophic conditions, which substantially suppressed the wasteful photorespiration and oxidative-damage pathways. As a consequence, mixotrophy resulted in a higher biomass yield than the sum of photoautotrophy and heterotrophy. Our work provides a basis for using trophic transitions in S. polyrhiza 7498 for the enhanced accumulation of value-added products.

Carbon and nitrogen uptake through photosynthesis and feeding by photosymbiotic Acantharia

Background: Mixotrophy, combining phagotrophy and photoautotrophy in order to acquire nutrients and energy, is a widespread trophic mode in marine protist plankton. Acantharia (Radiolaria) are ubiquitous, but still uncultured oceanic protists. Many of them are mixoplanktic by endosymbiotic relations with microalgae. Here we aimed at quantitatively assessing phototrophy (inorganic nutrients) and phagotrophy (organic nutrients) of photosymbiotic Acantharia, to understand their physiology, and thereby improve integrations of mixotrophy into ecological models of oceanic ecosystems. Methods: Freshly collected Acantharia were incubated with stable isotopes of inorganic carbon and nitrogen to determine photosynthetic uptake rates. Grazing experiments (prey disappearance) were done with different algal cultures as potential food organisms to measure the contribution of prey ingestion to the acantharian metabolism. Fluorescently (and isotopically) labelled prey was used to verify prey uptake, qualitatively. Results/Conclusions: Carbon uptake rates were unaffected by the nitrogen source (i.e., nitrate or ammonium). Total carbon inorganic uptake rate was 1112±82 pgC h-1 Acantharia‑1, 22.3±1.6 pgC h-1 symbiont cell-1assuming 50 symbionts per Acantharia, at ~155-μmol photons m−2 s−1 irradiance. The Acantharia studied could use both inorganic ammonium and nitrate, but ammonium was taken up at a ~5 times higher rate. Prey ingestion of the haptophyte, Isochrysis galbana, was detected using labelled algae. Significant grazing by Acantharia could only be established on the dinoflagellate Effrenium voratum, with a grazing rate of 728 prey Acantharia‑1 hour-1 (i.e., ~56.3 ngC h-1, 46% of total holobiont carbon content) at a ratio of 1.06x104 prey predator-1. Daily photosynthetic carbon uptake rates made up ~14.5% of the total holobiont carbon content (0.9% hourly). The extent to which photosynthates are used and assimilated by the acantharian cell and/or if it is used for catabolic processes to obtain energy is still to be studied. Isotopic ratios further suggests seasonal differences in the usage of each trophic mode.

Beyond the limits of the unassigned protist microbiome: inferring large-scale spatio-temporal patterns of Syndiniales marine parasites

Marine protists are major components of the oceanic microbiome that remain largely unrepresented in culture collections and genomic reference databases. The exploration of this uncharted protist diversity in oceanic communities relies essentially on studying genetic markers from the environment as taxonomic barcodes. Here we report that across 6 large scale spatio-temporal planktonic surveys, half of the genetic barcodes remain taxonomically unassigned at the genus level, preventing a fine ecological understanding for numerous protist lineages. Among them, parasitic Syndiniales (Dinoflagellata) appear as the least described protist group. We have developed a computational workflow, integrating diverse 18S rDNA gene metabarcoding datasets, in order to infer large-scale ecological patterns at 100% similarity of the genetic marker, overcoming the limitation of taxonomic assignment. From a spatial perspective, we identified 2171 unassigned clusters, i.e., Syndiniales sequences with 100% similarity, exclusively shared between the Tropical/Subtropical Ocean and the Mediterranean Sea among all Syndiniales orders and 25 ubiquitous clusters shared within all the studied marine regions. From a temporal perspective, over 3 time-series, we highlighted 39 unassigned clusters that follow rhythmic patterns of recurrence and are the best indicators of parasite community’s variation. These clusters withhold potential as ecosystem change indicators, mirroring their associated host community responses. Our results underline the importance of Syndiniales in structuring planktonic communities through space and time, raising questions regarding host-parasite association specificity and the trophic mode of persistent Syndiniales, while providing an innovative framework for prioritizing unassigned protist taxa for further description.

Ingestion kinetics of mixotrophic and heterotrophic flagellates

AbstractIn sunlit waters, significant predation is performed by unicellular, phagotrophic mixotrophs, that is, predators that also possess plastids. The success of a mixotrophic lifestyle will depend in part on how well mixotrophs acquire prey relative to specialized heterotrophs. Likewise, consequences of mixotrophy for productivity and element cycling will depend on the rate and efficiency at which mixotrophs consume prey biomass relative to heterotrophs. However, trait differences between mixotrophs and heterotrophs are not well characterized. In addition, cell size of mixotrophs varies widely, and constitutive mixotrophs include small flagellates deriving from diverse taxa, while larger species are primarily dinoflagellates. To determine whether similar constraints apply to phagotrophs across this broad range of size and taxa, we compiled 83 measurements of flagellate functional responses and compared maximum clearance rates (Cmax) and maximum ingestion rates (Imax) between trophic modes. We found that the average mixotroph has a 3.7‐fold lower Cmax and 7.8‐fold lower Imax than the average heterotroph, after controlling for cell size. The smaller penalty for Cmax suggests that relative fitness of mixotrophs will be enhanced under dilute prey concentrations that are common in pelagic ecosystems. We also find that growth efficiency is greater for mixotrophs and for flagellates with lower Cmax, indicating a spectrum of trophic strategies that may be driven by phototrophy vs. phagotrophy allocation as well as fast vs. slow metabolic variation. Allometric scaling shows that Imax is constrained by a common relationship among dinoflagellates and other taxa, but dinoflagellates achieve a greater volume‐specific Cmax. These results should aid in interpreting protistan communities and modeling mixotrophy.

Under-Ice Development of Silica-Scaled Chrysophytes with Different Trophic Mode in Two Ultraoligotrophic Lakes of Yakutia

Silica-scaled chrysophytes are a widespread group of microeukaryotes, an important component of aquatic habitats. They belong to different evolutionary lineages and they are characterized by the presence of siliceous scales, but differ in trophic mode. We studied the diversity of these organisms in different months of the ice cover period in two subarctic lakes of Yakutia, Labynkyr and Vorota. Silica-scaled chrysophytes, due to various trophic modes, have a competitive advantage in conditions of a long period of ice cover. Statistical analysis has shown the relationship between the relative abundance of mixotrophic and photoautotrophic representatives of silica-scaled chrysophytes with the thickness of the snow cover and the transparency of the ice. An increase in snow cover thickness and the process of melting ice with a decrease in its transparency reduce the relative abundance of photoautotrophic and mixotrophic species. Photoautotrophic representatives of silica-scaled chrysophytes begin to develop already in April, when a thick, solid, and transparent layer of ice and a small layer of snow were observed. During the research period, from April to June, the relative abundance of colorless heterotrophic silica-scaled chrysophytes genera Paraphysomonas and Lepidochromonas was more or less stable. A new species of Spiniferomonas heterospina sp. nov. has been discovered in Lake Labynkyr.

Exploring the role of Sichuan Baoning vinegar microbiota and the association with volatile flavor compounds at different fermentation depths.

Cereal vinegar is usually produced through solid-state fermentation, and the microbial community plays an important role in fermentation. In this study, the composition and function of Sichuan Baoning vinegar microbiota at different fermentation depths were evaluated by high-throughput sequencing combined with PICRUSt and FUNGuild analysis, and variations in volatile flavor compounds were also determined. The results revealed that no significant differences (p > 0.05) were found in both total acid content and pH of vinegar Pei collected on the same day with different depths. There were significant differences between the bacterial community of samples from the same day with different depths at both phylum and genus levels (p < 0.05), however, no obvious difference (p > 0.05) was observed in the fungal community. PICRUSt analysis indicated that fermentation depth affected the function of microbiota, meanwhile, FUNGuild analysis showed that there were variations in the abundance of trophic mode. Additionally, differences in volatile flavor compounds were observed in samples from the same day with different depths, and significant correlations between microbial community and volatile flavor compounds were observed. The present study provides insights into the composition and function of microbiota at different depths in cereal vinegar fermentation and quality control of vinegar products.

Functional insights into succession in a phyllospheric microbial community across a full period of aquatic plant litter decomposition

Phyllosphere microbes are essential in the mediation of plant–soil biogeochemical recycling during the decomposition of plant litter in wetland ecosystems. However, there are few studies into microbial community succession in phyllosphere microbial communities in wetlands, and their functional attributes across a full period of wetland plant litter decomposition remain unclear. Here, we collected leaf samples of Typha latifolia var. orientalis (C. Presl.) Rohrb., an emergent wetland plant, during various stages of decomposition (growing, standing, lodging, and submerging stages) to investigate fungal and bacterial assemblage succession in the phyllosphere. We then parsed these assemblages into specific fungal trophic modes and bacterial phenotypes. Over the litter decomposition period, both fungal and bacterial assemblages underwent distinct succession, with generally increasing alpha diversity, and the proportion of litter microbes originating from sediments increased with decomposition. Saprotrophic and pathotrophic fungi dominated the fungal assemblage in the early stages of decomposition, but their dominance was replaced by undefined fungi as decomposition progressed. Relative abundances of both pathotrophic fungi and potentially pathogenic bacteria increased from the growing to the standing stage, implying that there was a turning point in assemblage composition shortly after plant leaf death. Gram-positive and gram-negative bacteria had opposite trends in their relative abundances over successive decomposition stages. When plant litter entered the water, bacteria tolerant of oxidative stress gradually decreased in abundance, but anaerobic bacteria abundance increased. We also aimed to determine the relationships between predicted microbial functional traits and leaf litter physicochemical attributes. Lignin and N content were the predominant predictors of decomposer fungal trophic modes and bacterial phenotypes. These findings provide evidence that the complex litter decomposition seen in wetlands is accompanied by a dynamic cross-kingdom succession of phyllospheric microbial communities, coupled with distinct changes in the phenotypes of the microbes present. Insights into phyllospheric microbial functional traits have implications for better elucidating the plant litter cycle for wetland plants.

Root Endophyte Shift and Key Genera Discovery in Rice under Barnyardgrass Stress

Despite increasing knowledge of barnyardgrass (Echinochloa crus-galli) interference with rice, relatively little is known how endophytes improve the ability of rice against barnyardgrass stress. Here, we provided a detailed temporal characterization of rice root-associated microbiomes during co-cultivation with barnyardgrass and a comparison with the microbiomes of weed-free rice plants. Alpha diversity analysis indicated that barnyardgrass had the opposite effects on endophytic bacteria and fungi in rice roots, in terms of the community diversity, richness and coverage at the rice seedling stage. Principal coordinate analysis showed that barnyardgrass had only a minor effect on the community composition of endophytes in rice roots at the rice seedling stage, but showed a significant and maximum interference at the heading stage. Rice recruited many endophytes to resist biotic stress from barnyardgrass, especially for fungi. PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states) predictive analysis indicated that 23 metabolic pathways of bacteria were overrepresented in rice. In addition, the main trophic mode of fungi was pathotroph according to FUNGuild analysis. A positive correlation between bacteria and fungi in rice roots was found via network analysis. Anaeromyxobacter, Azospira and Pseudolabrys were the vital bacteria, Phaeosphaeria and Funneliformis were the dominant fungi in maintaining the stability of the ecological network. These results provided data and a theoretical basis for the in-depth understanding of what role endophytes play in rice resistance to barnyardgrass stress and will have implications on improving the resistance of rice against biotic stress using root microbiota.

Effect of incorporation of broccoli residues into soil on occurrence of verticillium wilt of spring-sowing-cotton and on rhizosphere microbial communities structure and function.

Cotton verticillium wilt (CVW) represented a typical plant soil-borne disease and resulted in widespread economic losses in cotton production. However, the effect of broccoli residues (BR) on verticillium wilt of spring-sowing-cotton was not clear. We investigated the effects of BR on CVW, microbial communities structure and function in rhizosphere of two cotton cultivars with different CVW resistance using amplicon sequencing methods. Results showed that control effects of BR on CVW of susceptible cultivar (cv. EJ-1) and resistant cultivar (cv. J863) were 58.49% and 85.96%, and the populations of V. dahliae decreased by 14.31% and 34.19%, respectively. The bacterial diversity indices significantly increased in BR treatment, while fungal diversity indices significantly decreased. In terms of microbial community composition, the abilities to recruit bacteria and fungi were enhanced in BR treatment, including RB41, Gemmatimonas, Pontibacter, Streptomyces, Blastococcus, Massilia, Bacillus, and Gibberella, Plectosphaerella, Neocosmospora, Aspergillus and Preussia. However, the relative abundances of Sphingomonas, Nocardioides, Haliangium, Lysobacter, Penicillium, Mortierella and Chaetomidium were opposite tendency between cultivars in BR treatment. According to PICRUSt analysis, functional profiles prediction showed that significant shifts in metabolic functions impacting KEGG pathways of BR treatment were related to metabolism and biosynthesis. FUNGuild analysis indicated that BR treatment altered the relative abundances of fungal trophic modes. The results of this study demonstrated that BR treatment decreased the populations of V. dahliae in soil, increased bacterial diversity, decreased fungal diversity, changed the microbial community structure and function, and increased the abundances of beneficial microorganisms.

Amino acid profile and protein bioaccessibility of two Galdieria sulphuraria strains cultivated autotrophically and mixotrophically in pilot-scale photobioreactors

Galdieria sulphuraria is considered one of the most promising microalgae for food applications. In this study, we compared two strains of G. sulphuraria cultivated autotrophically and mixotrophically over 35 days in pilot-scale photobioreactors under nonsterile conditions. The low pH (<1.9) used for cultivation successfully prevented microbial contamination. The two strains had similar autotrophic and mixotrophic biomass productivities, the latter being 2.3 times higher than autotrophic productivity. Comparing the two strains, G. sulphuraria SAG 108.79 and ACUF 064 had 51% and 64% (w/w) protein and 4% and 9% (w/w) C-phycocyanin content, respectively. Interestingly, G. sulphuraria SAG 108.79 showed a protein bioaccessibility of 62%, in line with other microalgal species, whereas G. sulphuraria ACUF 064 had a protein bioaccessibility of only 14%. No differences in the amino acid profile were found between the two strains or between trophic modes. Stable and well-balanced protein profiles are encouraging results for future applications of this species. Industrial relevanceThe main focus of this study was the production of single-cell proteins using two strains of the polyextremophilic microalgae Galdieria sulphuraria. The acidic cultivation condition was sufficient to guarantee axenic production in not sterile conditions, even in the presence of glucose. Both strains were rich in proteins with a similar amino acid profile rich in all of the essential amino acids. Interestingly, there was a 4.4-fold difference in protein bioaccessibility between the two strains. Simple production of axenic microalgal biomass rich in protein is an encouraging result for future food applications of this species.

Fungal diversity dominates the response of multifunctionality to the conversion of pure plantations into two-aged mixed plantations

Plantation forests are essential in driving global biogeochemical cycling and mitigating climate change. Biodiversity and environmental factors can shape multiple forest ecosystem functions simultaneously (i.e., multifunctionality). However, their effect on multifunctionality when pure plantations are converted into two-aged plantations remains underexplored. Therefore, we assessed above- and below-ground biodiversity and environmental factors and 11 ecosystem functions in different plantation types in subtropical China. The two-aged mixed plantations exhibited higher multifunctionality than did a pure plantation, primarily due to soil fungal diversity and secondarily due to tree diversity, based on the coefficient of variation for tree diameter at breast height (CVD) and community-weighted specific leaf area (CWMSLA). Further analysis revealed saprotrophy as the key soil fungal trophic mode in maintaining multifunctionality. Moreover, structural equation modeling confirmed that soil environmental factors, namely the soil water content and pH, had no direct association with multifunctionality, but were indirectly related to multifunctionality via elevated CVD and CWMSLA, respectively. Our results indicate that the tree and soil fungal diversity, as well as soil environmental factors, resulting from the conversion of pure plantations to two-aged mixed plantations, can enhance multifunctionality, and provide a better comprehensive understanding of the driving mechanisms of multifunctionality, leading to the sustainable management of subtropical plantation forest ecosystems.

Mycoparasites, Gut Dwellers, and Saprotrophs: Phylogenomic Reconstructions and Comparative Analyses of Kickxellomycotina Fungi.

Improved sequencing technologies have profoundly altered global views of fungal diversity and evolution. High-throughput sequencing methods are critical for studying fungi due to the cryptic, symbiotic nature of many species, particularly those that are difficult to culture. However, the low coverage genome sequencing (LCGS) approach to phylogenomic inference has not been widely applied to fungi. Here we analyzed 171 Kickxellomycotina fungi using LCGS methods to obtain hundreds of marker genes for robust phylogenomic reconstruction. Additionally, we mined our LCGS data for a set of nine rDNA and protein coding genes to enable analyses across species for which no LCGS data were obtained. The main goals of this study were to: 1) evaluate the quality and utility of LCGS data for both phylogenetic reconstruction and functional annotation, 2) test relationships among clades of Kickxellomycotina, and 3) perform comparative functional analyses between clades to gain insight into putative trophic modes. In opposition to previous studies, our nine-gene analyses support two clades of arthropod gut dwelling species and suggest a possible single evolutionary event leading to this symbiotic lifestyle. Furthermore, we resolve the mycoparasitic Dimargaritales as the earliest diverging clade in the subphylum and find four major clades of Coemansia species. Finally, functional analyses illustrate clear variation in predicted carbohydrate active enzymes and secondary metabolites (SM) based on ecology, that is biotroph versus saprotroph. Saprotrophic Kickxellales broadly lack many known pectinase families compared with saprotrophic Mucoromycota and are depauperate for SM but have similar numbers of predicted chitinases as mycoparasitic.

Effect of disease severity on the structure and diversity of the phyllosphere microbial community in tobacco.

Tobacco target spot is a serious fungal disease and it is important to study the similarities and differences between fungal and bacterial community under different disease severities to provide guidance for the biological control of tobacco target spot. In this study, tobacco leaves at disease severity level of 1, 5, 7 and 9 (S1, S5, S7, and S9) were collected, both healthy and diseased leaf tissues for each level were sampled. The community structure and diversity of fungi and bacteria in tobacco leaves with different disease severities were compared using high-throughput sequencing technology. The results indicated that there was a significant differences in the community structure of fungi and bacteria for both healthy and diseased samples depending on the disease severity. In both healthy and diseased tobacco leaves for all four different disease severities, the most dominant fungal phylum was Basidiomycota with a high prevalence of genus Thanatephorus. The relative abundance of Thanatephorus was most found at S9 diseased samples. Proteobacteria represent the most prominent bacterial phylum, with Pseudomonas as predominant genus, followed by Pantoea. The relative abundance of Pseudomonas was most found at S7 healthy samples. In fungal community, the Alpha-diversity of healthy samples was higher than that of diseased samples. In contrast, in bacterial community, the Alpha-diversity of healthy samples was lower than that of diseased samples. LEfSe analysis showed that the most enrich fungal biomarker was Thanatephorus cucumeris in diseased samples. Clostridium disporicum and Ralstonia pickettii were the most enrich bacterial biomarker in healthy samples. FUNGuild analysis showed that the pathotroph mode was the most abundant trophic modes. The relative abundance of pathotroph mode in diseased samples changes insignificantly, but a peak at S5 was observed for healthy samples. PICRUSt analysis showed that most bacterial gene sequences seem to be independent of the disease severity. The results of this study provide scientific references for future studies on tobacco phyllosphere microecology aiming at prevention and control of tobacco target spot.

Soil nutrients shape the composition and function of fungal communities in abandoned ancient rice terraces

In recent decades, terraces abandonment has been prevalent in the hilly areas of China. Soil fungi play an important role in clarifying soil ecosystematic feedback after ancient rice terraces abandonment, but how their community composition and function shift remains unclear. Soil profiles of 0–120 cm were excavated in ancient rice terraces, dry land, and forest land (formed from ancient rice terraces abandonment), respectively. The 13C NMR and high-throughput sequencing were used to determine soil organic carbon chemical groups and fungal community, respectively, and FUNGuild was used to predict functional groups. The results showed that the soil fungal community changed from Ascomycota to Basidiomycota after ancient rice terraces abandonment. The trophic modes of dry land and forest land were transformed into pathotrophic fungi and symbiotrophic fungi, respectively. The number of nodes and edges of fungal co-occurrence networks increased by 83.8% and 644.1% in dry land, and 81.3% and 431.2% in forest land, respectively. Moreover, soil nutrients (especially DOC, TN, and TP) can more affected the variation of fungal community composition and function than soil organic carbon chemical groups. These findings indicate that soil fungal community shifts in different directions in response to ancient rice terraces abandonment, which is related to the adaptive strategies for environmental changes and may be more conducive to the acquisition and turnover of soil nutrients.

Effects of environmental factors on mycoplankton diversity and trophic modes in coastal surface water

Mycoplankton play a key role in aquatic microbial food webs and nutrient cycling. However, the environmental factors that affect their composition and trophic modes in coastal water remain unclear. In this study, we used fungal metabarcoding to characterize seasonal mycoplanktonic communities in the surface water of the Maowei Sea. Dothideomycetes and Sordariomycetes were the dominant classes in the Maowei Sea. Random forest modeling analyses suggested that Ochroconis, Rhodotorula, Perenniporia and Derxomyces were the best seasonal bioindicators of environmental changes. Spearman’s correlation analysis showed that TOC (total organic carbon) is the main factor affecting mycoplanktonic bioindicators. Through FUNGuild analysis, we classified mycoplankton in the Maowei Sea into eight trophic modes and found that saprotrophs were the most abundant. Random forest analysis and Spearman’s correlation indicated that the mycoplankton trophic modes could reflect environmental changes in the Maowei Sea and were mainly influenced by dissolved inorganic phosphorus (DIP), dissolved oxygen (DO), and total organic carbon (TOC). Mycoplanktonic alpha and beta diversities significantly varied in different seasons (p < 0.05). Spearman rank’s test, Mantel test, and partial Mantel test indicated that TOC was the key environmental factor that affected the mycoplanktonic alpha and beta diversities. Variation partition analysis revealed that mycoplankton community structure was affected more due to nutrient variability than water quality (18 % vs 7 %). Overall, this study enhanced our understanding of the key controlling environmental factors affecting mycoplanktonic diversities and trophic modes in the coastal environment.