Volatile-mediated antagonism of soil bacterial communities against fungi

Rotation with other crops slow down the fungal process in tobacco-growing soil

Continuous cultivation of tobacco could cause serious soil health problems, which could cause bacterial soil to change to fungal soil. In order to study the diversity and richness of fungal community in tobacco-growing soil under different crop rotation, three treatments were set up in this study: CK (tobacco continuous cropping); B (barley-tobacco rotation cropping) and R (oilseed rape-tobacco rotation cropping). The results of this study showed that rotation with other crops significantly decreased the soil fungal OTUs, and also decreased the community richness, evenness, diversity and coverage of fungal communities. Among them, B decreased the most. In the analysis of the composition and structure of the fungal community, it was found that the proportion of plant pathogens Nectriaceae decreased from 19.67% in CK to 5.63% in B, which greatly reduced the possibility of soil-borne diseases. In the analysis of the correlation between soil environmental factors and fungal communities, it was found that Filobasidiaceae had a strong correlation with TP and AP, and Erysiphaceae had a strong correlation with TK and AK. NO3--N and NH4+-N were the two environmental factors with the strongest correlation with fungal communities. The results of this study showed that rotation with other crops slowed down the process of soil fungi in tobacco-growing soil and changed the dominant species of soil fungi community. At the same time, crop rotation changed the diversity and richness of soil fungal community by changing the physical and chemical properties of soil.

Volatilome: Smells like microbial spirit

In recent years, the study of volatile compounds has sparked interest due to their implications in signaling and the enormous variety of bioactive properties attributed to them. Despite the absence of analysis methods standardization, there are a multitude of tools and databases that allow the identification and quantification of volatile compounds. These compounds are chemically heterogeneous and their diverse properties are exploited by various fields such as cosmetics, the food industry, agriculture and medicine, some of which will be discussed here. In virtue of volatile compounds being ubiquitous and fast chemical messengers, these molecules mediate a large number of interspecific and intraspecific interactions, which are key at an ecological level to maintaining the balance and correct functioning of ecosystems. This review briefly summarized the role of volatile compounds in inter- and intra-specific relationships as well as industrial applications associated with the use of these compounds that is emerging as a promising field of study.

The Changes, Aggregation Processes, and Driving Factors for Soil Fungal Communities during Tropical Forest Restoration

Soil fungal communities play crucial roles in mediating the functional associations between above- and belowground components during forest restoration. Forest restoration shapes the alterations in plant and soil environments, which exerts a crucial effect on soil fungal assemblages. However, the changes, assembly processes, and driving factors of soil fungi communities during tropical forest restoration are still uncertain. We used Illumina high-throughput sequencing to identify the changes of soil fungal communities across a tropical secondary forest succession chronosequence (i.e., 12-, 42-, and 53-yr stages) in Xishuangbanna. During forest restoration, the dominant taxa of soil fungi communities shifted from r- to K-strategists. The relative abundance of Ascomycota (r-strategists) decreased by 10.0% and that of Basidiomycota (K-strategists) increased by 4.9% at the 53-yr restoration stage compared with the 12-yr stage. From the 12-yr to 53-yr stage, the operational taxonomic unit (OTU), abundance-based coverage estimator (ACE), Chao1, and Shannon index of fungal communities declined by 14.5-57.4%. Although the stochastic processes were relatively important in determining fungal assemblages at the late stage, the fungal community assembly was dominated by deterministic processes rather than stochastic processes. The shifts in soil properties resulting from tropical forest restoration exerted significant effects on fungal composition and diversity. The positive effects of microbial biomass carbon, readily oxidizable carbon, and soil water content explained 11.5%, 9.6%, and 9.1% of the variations in fungal community composition, respectively. In contrast, microbial biomass carbon (40.0%), readily oxidizable carbon (14.0%), and total nitrogen (13.6%) negatively contributed to the variations in fungal community diversity. Our data suggested that the changes in fungal composition and diversity during tropical forest restoration were primarily mediated by the positive or negative impacts of soil carbon and nitrogen pools.

Microbiological status of natural and anthropogenic soils of the Taganrog Bay coast at different levels of combined pollution with heavy metals and PAHs

The effect of heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) pollution on the microbiological status of soils on the coast of the Taganrog Bay and adjacent areas was studied. The content of total and exchangeable forms of HMs, the content of 16 priority PAHs and the abundance of several groups of culturable microorganisms was determined, namely copiotrophic, prototrophic, aerobic spore-forming bacteria, actinomycetes, molds and yeasts. The content of total and exchangeable forms of HMs in urban coastal soils in industrial zone significantly exceeded that in non-urban soils. The maximum concentrations of total forms of Mn, Cr, Ni, Cu, Zn, Pb and Cd are 1821, 871, 143, 89, 1390, 317 and 10 mg/kg, respectively. The median value of the total content of 16 PAHs in urban soils is 3 times higher than in the soils of natural areas and reached 4309 ng/g. The lowest numbers of copiotrophic bacteria, prototrophic bacteria and aerobic spore-forming bacteria were found in the soils of industrial zone: 6.8, 13.8 and 0.63 million CFU g-1 dry soil, respectively. The largest numbers of copiotrophic bacteria, prototrophic bacteria and aerobic spore-forming bacteria were recorded in the soils of natural areas-72.5, 136 and 5.73 million CFU g-1 dry soil, respectively. It was found that the abundance of copiotrophs, prototrophs, and aerobic spore-forming bacteria is more affected by the urbanization of coastal soils including the pollution of HMs and PAHs. Other groups of microorganisms (actinomycetes, molds and yeasts) turned out to be more resistant to anthropogenic factors.

Soil labile organic carbon fractions mediate microbial community assembly processes during long-term vegetation succession in a semiarid region

Conceptual diagram for the labile organic carbon (OC) fractions mediating microbial assembly processes during long-term vegetation succession.

Antifungal mechanism of volatile compounds emitted by Actinomycetota Paenarthrobacter ureafaciens from a disease-suppressive soil on Saccharomyces cerevisiae

Increasing evidence suggests that in disease-suppressive soils, microbial volatile compounds (mVCs) released from bacteria may inhibit the growth of plant-pathogenic fungi. However, the antifungal activities and molecular responses of fungi to different mVCs remain largely undescribed. In this study, we first evaluated the responses of pathogenic fungi to treatment with mVCs from Paenarthrobacter ureafaciens. Then, we utilized the well-characterized fungal model organism Saccharomyces cerevisiae to study the potential mechanistic effects of the mVCs. Our data showed that exposure to P. ureafaciens mVCs leads to reduced growth of several pathogenic fungi, and in yeast cells, mVC exposure prompts the accumulation of reactive oxygen species. Further experiments with S. cerevisiae deletion mutants indicated that Slt2/Mpk1 and Hog1 MAPKs play major roles in the yeast response to P. ureafaciens mVCs. Transcriptomic analysis revealed that exposure to mVCs was associated with 1,030 differentially expressed genes (DEGs) in yeast. According to gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses, many of these DEGs are involved in mitochondrial dysfunction, cell integrity, mitophagy, cellular metabolism, and iron uptake. Genes encoding antimicrobial proteins were also significantly altered in the yeast after exposure to mVCs. These findings suggest that oxidative damage and mitochondrial dysfunction are major contributors to the fungal toxicity of mVCs. Furthermore, our data showed that cell wall, antioxidant, and antimicrobial defenses are induced in yeast exposed to mVCs. Thus, our findings expand upon previous research by delineating the transcriptional responses of the fungal model. IMPORTANCE Since the use of bacteria-emitted volatile compounds in phytopathogen control is of considerable interest, it is important to understand the molecular mechanisms by which fungi may adapt to microbial volatile compounds (mVCs). Paenarthrobacter ureafaciens is an isolated bacterium from disease-suppressive soil that belongs to the Actinomycetota phylum. P. ureafaciens mVCs showed a potent antifungal effect on phytopathogens, which may contribute to disease suppression in soil. However, our knowledge about the antifungal mechanism of mVCs is limited. This study has proven that mVCs are toxic to fungi due to oxidative stress and mitochondrial dysfunction. To deal with mVC toxicity, antioxidants and physical defenses are required. Furthermore, iron uptake and CAP proteins are required for antimicrobial defense, which is necessary for fungi to deal with the thread from mVCs. This study provides essential foundational knowledge regarding the molecular responses of fungi to inhibitory mVCs.

The Exploitation of Microbial Antagonists against Postharvest Plant Pathogens

Postharvest disease management is vital to increase the quality and productivity of crops. As part of crop disease protection, people used different agrochemicals and agricultural practices to manage postharvest diseases. However, the widespread use of agrochemicals in pest and disease control has detrimental effects on consumer health, the environment, and fruit quality. To date, different approaches are being used to manage postharvest diseases. The use of microorganisms to control postharvest disease is becoming an eco-friendly and environmentally sounds approach. There are many known and reported biocontrol agents, including bacteria, fungi, and actinomycetes. Nevertheless, despite the abundance of publications on biocontrol agents, the use of biocontrol in sustainable agriculture requires substantial research, effective adoption, and comprehension of the interactions between plants, pathogens, and the environment. To accomplish this, this review made an effort to locate and summarize earlier publications on the function of microbial biocontrol agents against postharvest crop diseases. Additionally, this review aims to investigate biocontrol mechanisms, their modes of operation, potential future applications for bioagents, as well as difficulties encountered during the commercialization process.

The Golden Goal of Soil Management: Disease-Suppressive Soils

Disease-suppressive soils encompass specific plant-pathogen-microbial interactions and represent a rare example of an agroecosystem where soil conditions and microbiome together prevent the pathogen from causing disease. Such soils have the potential to serve as a model for characterizing soil pathogen-related aspects of soil health, but the mechanisms driving the establishment of suppressive soils vary and are often poorly characterized. Yet, they can serve as a resource for identifying markers for beneficial activities of soil microorganisms concerning pathogen prevention. Many recent studies have focused on the nature of disease-suppressive soils, but it has remained difficult to predict where and when they will occur. This review outlines current knowledge on the distribution of these soils, soil manipulations leading to pathogen suppression, and markers including bacterial and fungal diversity, enzymes, and secondary metabolites. The importance to consider soil legacy in research on the principles that define suppressive soils is also highlighted. The goal is to extend the context in which we understand, study, and use disease-suppressive soils by evaluating the relationships in which they occur and function. Finally, we suggest that disease-suppressive soils are critical not only for the development of indicators of soil health, but also for the exploration of general ecological principles about the surrounding landscape, effects of deeper layers of the soil profile, little studied soil organisms, and their interactions for future use in modern agriculture.

Plant growth promotion and differential expression of defense genes in chilli pepper against Colletotrichum truncatum induced by Trichoderma asperellum and T. harzianum

BACKGROUND

Trichoderma asperellum and T. harzianum were assessed in this study as a potential biological control against Colletotrichum truncatum. C. truncatum is a hemibiotrophic fungus that causes anthracnose disease in chilli thereby affecting plant growth and fruit yield. Scanning electron microscope (SEM) technique showed the beneficial interaction between chilli root-Trichoderma spp. inducing the plant growth promotion, mechanical barrier, and defense network under C. truncatum challenged conditions.

METHODS

Seeds bio-primed with T. asperellum, T. harzianum, and T. asperellum + T. harzianum promoted the plant growth parameters and strengthening of physical barrier via lignification on the wall of vascular tissues. Seed primed with bioagents were used for exploring the molecular mechanism of defense response in pepper against anthracnose to assess the temporal expression of six defense genes in the Surajmukhi variety of Capsicum annuum. QRT-PCR demonstrated induction of defense responsive genes in chilli pepper bioprimed with Trichoderma spp. such as plant defensin 1.2 (CaPDF1.2), superoxide dismutase (SOD), ascorbate peroxidase (APx), guaiacol peroxidase (GPx), pathogenesis related proteins PR-2 and PR-5.

RESULTS

The results showed that bioprimed seeds were assessed for T. asperellum, T. harzianum, and T. asperellum + T. harzianum-chilli root colonization interaction under in vivo conditions. The results of the scanning electron microscope revealed that T. asperellum, T. harzianum and T. asperellum + T. harzianum interact with chilli roots directly via the development of plant-Trichoderma interaction system. Seeds bio-primed with bioagents promoted the plant growth parameters, fresh and dry weight of shoot and root, plant height, leaf area index, number of leaves, stem diameter and strengthening of physical barrier via lignification on the wall of vascular tissues and expression of six defense related genes in pepper against anthracnose.

CONCLUSIONS

Application of T. asperellum and T. harzianum and in combination of treatments enhanced the plant growth. Further, as seeds bioprimed with T. asperellum, T. harzianum and in combination with treatment of T. asperellum + T. harzianum induced the strengthening of the cell wall by lignification and expression of six defense related genes CaPDF1.2, SOD, APx, GPx, PR-2 and PR-5 in pepper against C. truncatum. Our study contributed for better disease management through biopriming with T. asperellum, T. harzianum and T. asperellum + T. harzianum. The biopriming possess enormous potential to promote plant growth, modulate the physical barrier, and induced the defense related genes in chilli pepper against anthracnose.

Biotic interactions contribute more than environmental factors and geographic distance to biogeographic patterns of soil prokaryotic and fungal communities

Recent studies have shown distinct soil microbial assembly patterns across taxonomic types, habitat types and regions, but little is known about which factors play a dominant role in soil microbial communities. To bridge this gap, we compared the differences in microbial diversity and community composition across two taxonomic types (prokaryotes and fungi), two habitat types (Artemisia and Poaceae) and three geographic regions in the arid ecosystem of northwest China. To determine the main driving factors shaping the prokaryotic and fungal community assembly, we carried out diverse analyses including null model, partial mantel test and variance partitioning analysis etc. The findings suggested that the processes of community assembly were more diverse among taxonomic categories in comparison to habitats or geographical regions. The predominant driving factor of soil microbial community assembly in arid ecosystem was biotic interactions between microorganisms, followed by environmental filtering and dispersal limitation. Network vertex, positive cohesion and negative cohesion showed the most significant correlations with prokaryotic and fungal diversity and community dissimilarity. Salinity was the major environmental variable structuring the prokaryotic community. Although prokaryotic and fungal communities were jointly regulated by the three factors, the effects of biotic interactions and environmental variables (both are deterministic processes) on the community structure of prokaryotes were stronger than that of fungi. The null model revealed that prokaryotic community assembly was more deterministic, whereas fungal community assembly was structured by stochastic processes. Taken together, these findings unravel the predominant drivers governing microbial community assembly across taxonomic types, habitat types and geographic regions and highlight the impacts of biotic interactions on disentangling soil microbial assembly mechanisms.

Linking bacterial and fungal assemblages to soil nutrient cycling within different aggregate sizes in agroecosystem

Soil aggregates provide spatially heterogeneous microhabitats that support the coexistence of soil microbes. However, there remains a lack of detailed assessment of the mechanism underlying aggregate-microbiome formation and impact on soil function. Here, the microbial assemblages within four different aggregate sizes and their correlation with microbial activities related to nutrient cycling were studied in rice fields in Southern China. The results show that deterministic and stochastic processes govern bacterial and fungal assemblages in agricultural soil, respectively. The contribution of determinism to bacterial assemblage improved as aggregate size decreased. In contrast, the importance of stochasticity to fungal assemblage was higher in macroaggregates (>0.25 mm in diameter) than in microaggregates (<0.25 mm). The association between microbial assemblages and nutrient cycling was aggregate-specific. Compared with microaggregates, the impacts of bacterial and fungal assemblages on carbon, nitrogen, and phosphorus cycling within macroaggregates were more easily regulated by soil properties (i.e., soil organic carbon and total phosphorus). Additionally, soil nutrient cycling was positively correlated with deterministic bacterial assemblage but negatively correlated with stochastic fungal assemblage in microaggregates, implying that bacterial community may accelerate soil functions when deterministic selection increases. Overall, our study illustrates the ecological mechanisms underlying the association between microbial assemblages and soil functions in aggregates and highlights that the assembly of aggregate microbes should be explicitly considered for revealing the ecological interactions between agricultural soil and microbial communities.

Dormancy and germination of microsclerotia of Verticillium longisporum are regulated by soil bacteria and soil moisture levels but not by nutrients

The soil-borne pathogen Verticillium longisporum infects roots of its host plant, oilseed rape, and systemically colonizes stems where it finally forms microsclerotia at crop maturity. Once returned to the soil after harvest, microsclerotia undergo a stage of dormancy, in which they may survive for several years. Since there is neither efficient chemical control nor effective resistance in oilseed rape cultivars to control the disease, alternative control strategies may consist in regulating the germination and dormancy of microsclerotia in the soil. Therefore, a series of experiments were conducted to explore the effects of nutrients, soil moisture, and the soil microbiome on germination of dormant microsclerotia. Experiments with microsclerotia exposed in vitro to different nutrients indicated that under sterile conditions the stimulating effect of nutrients on microsclerotia germination was not enhanced as compared to water. Moreover, further assays revealed a strong inhibitory effect of unsterile soil on microsclerotia germination. Accordingly, oilseed rape plants inoculated with microsclerotia of V. longisporum showed severe infection with V. longisporum when grown in autoclaved soil, in contrast to plants grown in unsterile soil. These experiments indicate a crucial role of soil fungistasis and thus the soil microbiome on microsclerotia germination. Further bioassays demonstrated that viable soil bacteria obtained from the rhizosphere of oilseed rape plants and bulk field soil effectively inhibited microsclerotia germination, whereas dead bacteria and bacterial culture filtrates hardly suppressed germination. A putative inhibitory role of volatile organic compounds (VOCs) produced by soil bacteria was confirmed in two-compartment Petri dishes, where microsclerotia germination and colony growth were significantly inhibited. Bacterial VOCs were collected and analyzed by GC–MS. In total, 45 VOCs were identified, among which two acid and two alcohol compounds were emitted by all tested bacteria. A bioassay, conducted with corresponding pure chemicals in two-compartment Petri dishes, indicated that all acidic volatile compounds, including 3-methylbutanoic acid, 2-methylbutanoic acid, hexanoic acid, and 2-methylpropionic acid, induced strong inhibitory effects on microsclerotia. We conclude that bacterial acidic volatiles play a key role in the fungistatic effect on microsclerotia of V. longisporum in the soil and could thus be targeted for development of novel strategies to control this pathogen by artificially regulating dormancy of microsclerotia in soil.

Synthetic microbial consortia derived from rhizosphere soil protect wheat against a soilborne fungal pathogen

Synthetic microbial communities (SynComs) could potentially enhance some functions of the plant microbiome and emerge as a promising inoculant for improving crop performance. Here, we characterized a collection of bacteria, previously isolated from the wheat rhizosphere, for their antifungal activity against soilborne fungal pathogens. Ten SynComs with different compositions from 14 bacterial strains were created. Seven SynComs protected wheat from Rhizoctonia solani AG8 infection, although SynComs were not more effective than single strains in reducing wheat root rot disease. Further, the mechanisms of interaction of the tested bacteria with each other and plants were explored. We found that nine bacteria and nine SynComs impacted the root growth of Arabidopsis. Nine bacteria and four SynComs significantly inhibited the growth of AG8 by producing volatiles. The cell-free supernatants from six bacteria inhibited the growth of AG8. Together, this study provided the potential for improving crop resilience by creating SynComs.

Effects of soil protists on the antibiotic resistome under long term fertilization

Soil protists are key in regulating soil microbial communities. However, our understanding on the role of soil protists in shaping antibiotic resistome is limited. Here, we considered the diversity and composition of bacteria, fungi and protists in arable soils collected from a long-term field experiment with multiple fertilization treatments. We explored the effects of soil protists on antibiotic resistome using high-throughput qPCR. Our results showed that long term fertilization had stronger effect on the composition of protists than those of bacteria and fungi. The detected number and relative abundance of antibiotic resistance genes (ARGs) were elevated in soils amended with organic fertilizer. Co-occurrence network analysis revealed that changes in protists may contribute to the changes in ARGs composition, and the application of different fertilizers altered the communities of protistan consumers, suggesting that effects of protistan communities on ARGs might be altered by the top-down impact on bacterial composition. This study demonstrates soil protists as promising agents in monitoring and regulating ecological risk of antibiotic resistome associated with organic fertilizers.

Priming of rhizobial nodulation signaling in the mycosphere accelerates nodulation of legume hosts

The simultaneous symbiosis of leguminous plants with two root mutualists, endophytic fungi and rhizobia is common in nature, yet how two mutualists interact and co-exist before infecting plants and the concomitant effects on nodulation are less understood. Using a combination of metabolic analysis, fungal deletion mutants and comparative transcriptomics, we demonstrated that Bradyrhizobium and a facultatively biotrophic fungus, Phomopsis liquidambaris, interacted to stimulate fungal flavonoid production, and thereby primed Bradyrhizobial nodulation signaling, enhancing Bradyrhizobial responses to root exudates and leading to early nodulation of peanut (Arachis hypogaea), and such effects were compromised when disturbing fungal flavonoid biosynthesis. Stress sensitivity assays and reactive oxygen species (ROS) determination revealed that flavonoid production acted as a strategy to alleviate hyphal oxidative stress during P. liquidambaris-Bradyrhizobial interactions. By investigating the interactions between P. liquidambaris and a collection of 38 rhizobacteria, from distinct bacterial genera, we additionally showed that the flavonoid-ROS module contributed to the maintenance of fungal and bacterial co-existence, and fungal niche colonization under soil conditions. Our results demonstrate for the first time that rhizobial nodulation signaling can be primed by fungi before symbiosis with host plants and highlight the importance of flavonoid in tripartite interactions between legumes, beneficial fungi and rhizobia.

Cross-kingdom co-occurrence networks in the plant microbiome: Importance and ecological interpretations

Microbial co-occurrence network analysis is being widely used for data exploration in plant microbiome research. Still, challenges lie in how well these microbial networks represent natural microbial communities and how well we can interpret and extract eco-evolutionary insights from the networks. Although many technical solutions have been proposed, in this perspective, we touch on the grave problem of kingdom-level bias in network representation and interpretation. We underscore the eco-evolutionary significance of using cross-kingdom (bacterial-fungal) co-occurrence networks to increase the network’s representability of natural communities. To do so, we demonstrate how ecosystem-level interpretation of plant microbiome evolution changes with and without multi-kingdom analysis. Then, to overcome oversimplified interpretation of the networks stemming from the stereotypical dichotomy between bacteria and fungi, we recommend three avenues for ecological interpretation: (1) understanding dynamics and mechanisms of co-occurrence networks through generalized Lotka-Volterra and consumer-resource models, (2) finding alternative ecological explanations for individual negative and positive fungal-bacterial edges, and (3) connecting cross-kingdom networks to abiotic and biotic (host) environments.

Novel culture chamber to evaluate in vitro plant-microbe volatile interactions: Effects of Trichoderma harzianum volatiles on wheat plantlets

The field of plant-microbe interactions mediated by Biogenic Volatile Organic Compounds (BVOCs) still faces several limitations due to the lack of reliable equipment. We present a novel device designed to evaluate in vitro plant-microbe volatile interactions, the plant-microbe VOC Chamber. It was tested by evaluating the effects exerted on wheat development by volatiles from three Trichoderma harzianum strains, a wild type and two genetically modified strains; one expressing the tri5 gene, which leads to the synthesis and emission of the volatile trichodiene, and the other by silencing the erg1 gene, impairing ergosterol production. The wild type and the erg1-silenced strain enhanced fresh weight and length of the aerial part, but reduced root dry weight. Interestingly, no differences were found between them. Conversely, the tri5-transformant strain reduced root and aerial growth compared to the control and the other strains. No differences were observed regarding chlorophyll fluorescence quantum yield and leaf chlorophyll content, suggesting that the released BVOCs do not interfere with photosynthesis. The plant-microbe VOC Chamber proved to be a simple and reliable method to evaluate the in vitro effects of microbial BVOCs on plant development, perfect for the screening of microorganisms with interesting volatile traits.

Indigenous microorganisms offset the benefits of growth and nutrition regulated by inoculated arbuscular mycorrhizal fungi for four pioneer herbs in karst soil

Arbuscular mycorrhizal (AM) fungi, as beneficial soil microorganisms, inevitably interact with indigenous microorganisms, regulating plant growth and nutrient utilization in natural habitats. However, how indigenous microorganisms affect the benefits of growth and nutrition regulated by inoculated AM fungi for plants in karst ecosystem habitats remains unclear today. In this experiment, the Gramineae species Setaria viridis vs. Arthraxon hispidus and the Compositae species Bidens pilosa vs. Bidens tripartita exist in the initial succession stage of the karst ecosystem. These plant species were planted into different soil microbial conditions, including AM fungi soil (AMF), AM fungi interacting with indigenous microorganisms soil (AMI), and a control soil without AM fungi and indigenous microorganisms (CK). The plant biomass, nitrogen (N), and phosphorus (P) were measured; the effect size of different treatments on these variables of plant biomass and N and P were simultaneously calculated to assess plant responses. The results showed that AMF treatment differently enhanced plant biomass accumulation, N, and P absorption in all species but reduced the N/P ratio. The AMI treatment also significantly increased plant biomass, N and P, except for the S. viridis seedlings. However, regarding the effect size, the AM fungi effect on plant growth and nutrition was greater than the interactive effect of AM fungi with indigenous microorganisms. It indicates that the indigenous microorganisms offset the AM benefits for the host plant. In conclusion, we suggest that the indigenous microorganisms offset the benefits of inoculated AM fungi in biomass and nutrient accumulation for pioneer plants in the karst habitat.

Linking soil fungi to bacterial community assembly in arid ecosystems

Revealing the roles of biotic factors in driving community assembly, which is crucial for the understanding of biodiversity and ecosystem functions, is a fundamental but infrequently investigated subject in microbial ecology. Here, combining a cross-biome observational study with an experimental microcosm study, we provided evidence to reveal the major roles of biotic factors (i.e., soil fungi and cross-kingdom species associations) in determining soil bacterial biogeography and community assembly in complex terrestrial ecosystems of the arid regions of northwest China. The results showed that the soil fungal richness mediates the balance of assembly processes of bacterial communities, and stochastic assembly processes decreased with increasing fungal richness. Our results further suggest that the predicted increase in aridity conditions due to climate change will reduce bacterial α-diversity, particularly in desert soils and subsurface layer, and induce more negative species associations. Together, our study represents a significant advance in linking soil fungi to the mechanisms underlying bacterial biogeographic patterns and community assembly in arid ecosystems under climate aridity and land-use change scenarios.

Air Ambulance: Antimicrobial Power of Bacterial Volatiles

We are currently facing an antimicrobial resistance crisis, which means that a lot of bacterial pathogens have developed resistance to common antibiotics. Hence, novel and innovative solutions are urgently needed to combat resistant human pathogens. A new source of antimicrobial compounds could be bacterial volatiles. Volatiles are ubiquitous produced, chemically divers and playing essential roles in intra- and interspecies interactions like communication and antimicrobial defense. In the last years, an increasing number of studies showed bioactivities of bacterial volatiles, including antibacterial, antifungal and anti-oomycete activities, indicating bacterial volatiles as an exciting source for novel antimicrobial compounds. In this review we introduce the chemical diversity of bacterial volatiles, their antimicrobial activities and methods for testing this activity. Concluding, we discuss the possibility of using antimicrobial volatiles to antagonize the antimicrobial resistance crisis.

The Endophytic Strain Trichoderma asperellum 6S-2: An Efficient Biocontrol Agent against Apple Replant Disease in China and a Potential Plant-Growth-Promoting Fungus

A study was conducted for endophytic antagonistic fungi obtained from the roots of healthy apple trees growing in nine replanted orchards in Shandong Province, China. The fungi were assessed for their ability to inhibit Fusarium proliferatum f. sp. malus domestica MR5, a fungal strain associated with apple replant disease (ARD). An effective endophyte, designated as strain 6S-2, was isolated and identified as Trichoderma asperellum. Strain 6S-2 demonstrated protease, amylase, cellulase, and laccase activities, which are important for the parasitic and antagonistic functions of pathogenic fungi. The inhibition rate of 6S-2 against Fusarium proliferatum f. sp. malus domestica MR5 was 52.41%. Strain 6S-2 also secreted iron carriers, auxin, ammonia and was able to solubilize phosphorus. Its fermentation extract and volatile substances inhibited the growth of MR5, causing its hyphae to twist, shrink, swell, and rupture. The antifungal activity of the 6S-2 fermentation extract increased with increasing concentrations. It promoted the production and elongation of Arabidopsis thaliana lateral roots, and the strongest effects were seen at a concentration of 50 mg/mL. A GC-MS analysis of the 6S-2 fermentation extract and volatile substances showed that they comprised mainly alkanes, alcohols, and furanones, as well as the specific volatile substance 6-PP. The application of 6S-2 spore suspension to replanted apple orchard soils reduced plant oxidative damage and promoted plant growth in a pot experiment. Therefore, the endophytic strain T. asperellum 6S-2 has the potential to serve as an effective biocontrol fungus for the prevention of ARD in China, and appears to promote plant growth.

Removal of Toxic Volatile Compounds in Batch Culture Prolongs Stationary Phase and Delays Death of Escherichia coli

The mechanisms controlling entry into and exit from the death phase in the bacterial life cycle remain unclear. Although bacterial growth studies in batch cultures traditionally focus on the first three phases during incubation, two additional phases, the death phase and the long-term stationary phase, are less understood. Although there are a number of stressors that arise during long-term batch culture, including nutrient depletion and the accumulation of metabolic toxins such as reactive oxidative species, their roles in cell death are not well-defined. By manipulating the environmental conditions of Escherichia coli incubated in long-term batch culture through chemical and mechanical means, we investigated the role of volatile metabolic toxins in modulating the onset of the death phase. Here, we demonstrate that with the introduction of substrates with high binding affinities for volatile compounds, toxic by-products of normal cell metabolism, into the headspace of batch cultures, cells display a prolonged stationary phase and delayed entry into the death phase. The addition of these substrates allows cultures to maintain a high cell density for hours to days longer than cultures incubated under standard growth conditions. A similar effect is observed when the gaseous headspace in culture flasks is continuously replaced with sterile air, mechanically preventing the accumulation of metabolic by-products in batch cultures. We establish that toxic compound(s) are produced during the exponential phase, demonstrate that buildup of toxic by-products influence entry into the death phase, and present a novel tool for improving high-density growth in batch culture that may be used in future research or industrial or biotechnology applications. IMPORTANCE Bacteria, such as Escherichia coli, are routinely used in the production of biomaterials because of their efficient and sustainable capacity for synthesis of bioproducts. Industrial applications of microbial synthesis typically utilize cells in the stationary phase, when cultures have the greatest density of viable cells. By manipulating culture conditions to delay the transition from the stationary phase to the death phase, we can prolong the stationary phase on a scale of hours to days, thereby maintaining the maximum density of cells that would otherwise quickly decline. Characterization of the mechanisms that control entry into the death phase for the model organism E. coli not only deepens our understanding of the bacterial life cycle but also presents an opportunity to enhance current protocols for batch culture growth and explore similar effects in a variety of widely used bacterial strains.

Fungistatic Mechanism of Ammonia against Nematode-Trapping Fungus Arthrobotrys oligospora, and Strategy for This Fungus To Survive Ammonia

Soil fungistasis is a phenomenon in which the germination and growth of fungal propagules is widely inhibited in soils. Although fungistatic compounds are known to play important roles in the formation of soil fungistasis, how such compounds act on soil fungi is little studied. In this study, it was found that ammonia (NH₃) induced global protein misfolding marked by increased ubiquitination levels of proteins (ubiquitylome data and Western blot verification). The misfolded proteins should trigger the endoplasmic reticulum (ER) stress, which was indicated by electron microscope image and proteome data. Results from the mutants of BiP and proteasome subunit alpha 7 suggested that ER stress played a mechanistic role in inhibiting conidial germination. Results from proteome data indicated that, to survive ammonia fungistasis, conidia first activated the unfolded protein response (UPR) to decrease ER stress and restore ER protein homeostasis, and the function of UPR in surviving ammonia was confirmed by using mutant strains. Second, ammonia toxicity could be reduced by upregulating carbon metabolism-related proteins, which benefited ammonia fixation. The results that metabolites (especially glutamate) could relieve the ammonia fungistasis confirmed this indirectly. Finally, results from gene knockout mutants also suggested that the fungistatic mechanism of ammonia is common for soil fungistasis. This study increased our knowledge regarding the mechanism of soil fungistasis and provided potential new strategies for manipulating soil fungistasis. IMPORTANCE Soil fungistasis is a phenomenon in which the germination and growth of fungal propagules is widely inhibited in soil. Although fungistatic compounds are known to play important roles in the formation of soil fungistasis, how such compounds act on soil fungi remains little studied. This study revealed an endoplasmic reticulum stress-related fungistatic mechanism with which ammonia acts on Arthrobotrys oligospora and a survival strategy of conidia under ammonia inhibition. Our study provides the first mechanistic explanation of how ammonia impacts fungal spore germination, and the mechanism may be common for soil fungistasis. This study increases our knowledge regarding the mechanism of soil fungistasis in fungal spores and provides potential new strategies for manipulating soil fungistasis.

In vitro interactions between the ectomycorrhizal Pisolithus tinctorius and the saprotroph Hypholoma fasciculare fungi: morphological aspects and volatile production

Ectomycorrhizal fungi are crucial for forests sustainability. For Castanea sativa, ectomycorrhizal fungus Pisolithus tinctorius is an important mutualist partner. Saprotrophic fungi Hypholoma fasciculare, although used for biocontrol of Armillaria root disease, it negatively affected the interaction between the P. tinctorius and plant host roots, by compromise the formation of P. tinctorius-C. sativa mycorrhizae. In this work, fungal morphology during inhibition of H. fasciculare against P. tinctorius was elucidated. P. tinctorius growth was strongly affected by H. fasciculare, which was significantly reduced after six days of co-culture and become even more significant through time. During this period, P. tinctorius developed vesicles and calcium oxalate crystals, which were described as mechanisms to stress adaption by fungi. H. fasciculare produced different volatile organic compounds in co-cultures over time and differ between single or in dual-species. H. fasciculare highly produced sesquiterpenes (namely, α-muurolene) and nitrogen-containing compounds, which are recognised as having antimicrobial activity.

Endophytic Fungus Alleviates Soil Sickness in Peanut Crops by Improving the Carbon Metabolism and Rhizosphere Bacterial Diversity

Endophytic fungi can profoundly affect host productivity, but the underlying mechanisms of these effects are only partly understood. As the most important regulators of plant-soil feedback, root exudates can easily cause soil sickness in continuous monoculture systems by reducing certain microbes in the rhizosphere. In this study, exudates from roots colonized by the endophytic fungus Phomopsis liquidambaris significantly increased rhizosphere bacterial abundance, soil respiration, microbial biomass and enzyme activities in a long-term continuously cropped peanut soil. Further analysis revealed that P. liquidambaris-colonized root exudates clearly altered the carbon metabolism and rhizosphere bacterial diversity, which were closely correlated with changes in soil chemical properties caused by the exudates from the colonized roots. Finally, a synthetic root exudate experiment further confirmed that the root exudates derived from P. liquidambaris colonization can indeed play an important role in promoting peanut growth. Therefore, these results show that this endophytic fungus could improve the carbon metabolism and rhizosphere bacterial community in long-term monoculture soils via exudates from colonized roots, which contribute to the alleviation of soil sickness.

Methylglyoxal Has Different Impacts on the Fungistatic Roles of Ammonia and Benzaldehyde, and Lactoylglutathione Lyase Is Necessary for the Resistance of Arthrobotrys oligospora to Soil Fungistasis

Biocontrol of root-knot nematode has attracted increasing attention over the past two decades. The inconsistent field performance of biocontrol agents, which is caused by soil fungistasis, often restricts their commercial application. There is still a lack of research on the genes involved in biocontrol fungi response to soil fungistasis, which is important for optimizing practical applications of biocontrol fungi. In this study, the lactoylglutathione lyase-encoding AOL_s00004g335 in the nematophagous fungi Arthrobotrys oligospora was knocked out, and three mutant strains were obtained. The hyphal growth of mutants on the three media was almost the same as that of the wild-type strain, but mutants had slightly higher resistance to NaCl, SDS, and H₂O₂. Methylglyoxal (MG) significantly increased the resistance of A. oligospora to ammonia, but decreased the resistance to benzaldehyde. Furthermore, the resistance of the mutants to soil fungistasis was largely weakened and MG could not increase the resistance of A. oligospora to soil fungistasis. Our results revealed that MG has different effects on the fungistatic roles of ammonia and benzaldehyde and that lactoylglutathione lyase is very important for A. oligospora to resist soil fungistasis.

Volatile Organic Compound Chamber: A Novel Technology for Microbiological Volatile Interaction Assays

The interest in the study of microbiological interactions mediated by volatile organic compounds (VOCs) has steadily increased in the last few years. Nevertheless, most assays still rely on the use of non-specific materials. We present a new tool, the volatile organic compound chamber (VOC chamber), specifically designed to perform these experiments. The novel devices were tested using four Trichoderma strains against Fusarium oxysporum and Rhizoctonia solani. We demonstrate that VOC chambers provide higher sensitivity and selectivity between treatments and higher homogeneity of results than the traditional method. VOC chambers are also able to test both vented and non-vented conditions. We prove that ventilation plays a very important role regarding volatile interactions, up to the point that some growth-inhibitory effects observed in closed environments switch to promoting ones when tested in vented conditions. This promoting activity seems to be related to the accumulation of squalene by T. harzianum. The VOC chambers proved to be an easy, homogeneous, flexible, and repeatable method, able to better select microorganisms with high biocontrol activity and to guide the future identification of new bioactive VOCs and their role in microbial interactions.

Linking Bacterial-Fungal Relationships to Microbial Diversity and Soil Nutrient Cycling

Biodiversity is important for supporting ecosystem functioning. To evaluate the factors contributing to the strength of microbial diversity-function relationships in complex terrestrial ecosystems, we conducted a soil survey over different habitats, including an agricultural field, forest, wetland, grassland, and desert. Soil microbial multidiversity was estimated by the combination of bacterial and fungal diversity. Soil ecosystem functions were evaluated using a multinutrient cycling index (MNC) in relation to carbon, nitrate, phosphorus, and potassium cycling. Significant positive relationships between soil multidiversity and multinutrient cycling were observed in all habitats, except the grassland and desert. Specifically, community compositions showed stronger correlations with multinutrient cycling than α-diversity, indicating the crucial role of microbial community composition differences on soil nutrient cycling. Importantly, we revealed that changes in both the neutral processes (Sloan neutral modeling) and the proportion of negative bacterial-fungal associations were linked to the magnitude and direction of the diversity-MNC relationships. The habitats less governed by neutral processes and dominated by negative bacterial-fungal associations exhibited stronger negative microbial α-diversity-MNC relationships. Our findings suggested that the balance between positive and negative bacterial-fungal associations was connected to the link between soil biodiversity and ecosystem function in complex terrestrial ecosystems. This study elucidates the potential factors influencing diversity-function relationships, thereby enabling future studies to forecast the effects of belowground biodiversity on ecosystem function.IMPORTANCE The relationships between soil biodiversity and ecosystem functions are an important yet poorly understood topic in microbial ecology. This study presents an exploratory effort to gain predictive understanding of the factors driving the relationships between microbial diversity and potential soil nutrient cycling in complex terrestrial ecosystems. Our structural equation modeling and random forest analysis revealed that the balance between positive and negative bacterial-fungal associations was clearly linked to the strength of the relationships between soil microbial diversity and multiple nutrients cycling across different habitats. This study revealed the potential factors underpinning diversity-function relationships in terrestrial ecosystems and thus helps us to manage soil microbial communities for better provisioning of key ecosystem services.

Pathogen Infection and Host-Resistance Interactively Affect Root-Associated Fungal Communities in Watermelon

Interactions of pathogen infection, host plant resistance, and fungal communities are poorly understood. Although the use of resistant watermelon cultivars is an effective control measure of watermelon wilt disease, fungal communities may also have significant effects on the development of the soil-borne pathogen complexes. We characterized the root and rhizosphere fungal communities associated with healthy and diseased watermelons of three different cultivars with different susceptibilities toward wilt disease by paired-end Illumina MiSeq sequencing. Thirty watermelon plants including highly wilt-resistant, moderately resistant, and susceptible cultivars were collected from a greenhouse, half of which showing clear wilt symptoms and the other half with no symptoms. Patterns of watermelon wilt disease and the response of the fungal communities varied among the three cultivars. The amount of the pathogen Fusarium oxysporum f. sp. niveum was higher in diseased root and rhizosphere samples, particularly in the susceptible cultivar, and was significantly positively correlated with the disease index of Fusarium wilt. Plant health had significant effects on root-associated fungal communities, whereas only the highly resistant cultivar had significant effects only on the rhizosphere fungal communities. Co-occurrence networks revealed a higher complexity of fungal communities in the symptom-free roots compared to diseased roots. In addition, networks from roots of the highly resistant plants showing symptoms had a higher complexity compared to the susceptible cultivars. Keystone species were identified for the plants with different symptom severity and the different cultivars in the root and rhizosphere, such as Fusarium oxysporum, Monosporascus cannonballus, and Mortierella alpina. Overall, the most important factor determining fungal communities in the roots was plant symptom severity, whereas in the rhizosphere, plant genotype was the most important factor determining fungal communities.

Underlying Mechanism of Wild Radix pseudostellariae in Tolerance to Disease Under the Natural Forest Cover

Replanting disease caused by negative plant-soil feedback in continuous monoculture of Radix pseudostellariae is a critical factor restricting the development of this common and popular Chinese medicine, although wild R. pseudostellariae plants were shown to grow well without occurrence of disease in the same site for multiple years. Therefore, we aimed to identify the changes in microbial community composition in the rhizosphere soil of wild R. pseudostellariae thus providing a potential method for controlling soil-borne diseases. We analyzed differences in soil physicochemical properties, changes in soil microbial community structure, and root exudates of wild R. pseudostellariae under different biotopes. And then, simple sequence repeats amplification was used to isolate and collect significantly different formae speciales of Fusarium oxysporum. Finally, we analyzed the pathogenicity testing and influence of root exudates on the growth of F. oxysporum. We found that the different biotopes of R. pseudostellariae had significant effects on the soil microbial diversity. The soil fungal and bacterial abundances were significantly higher and the abundance of F. oxysporum was significantly lower under the rhizosphere environment of wild R. pseudostellariae than under consecutive monoculture. The relative abundances of most genera were Penicillium, Aspergillus, Fusarium, Nitrobacter, Nitrospira, Streptomyces, Actinoplanes, and Pseudomonas. Venn diagram and LEfSe analyses indicated numerously specific microbiome across all the samples, and the numbers of specific fungi were higher than the shared ones in the four biotopes. Eight types of phenolic acids were identified across all the rhizosphere soils. Mixed phenolic acids and most of the examined single phenolic acids had negative effects on the growth of isolated pathogenic F. oxysporum strains and promoted the growth of non-pathogenic strains. Similarly, correlation analysis suggested that most of the identified phenolic acids were positively associated with beneficial Pseudomonas, Nitrobacter, Nitrospira, Streptomyces, and Bacillus. This study suggested that wild R. pseudostellariae was able to resist or tolerate disease by increasing soil microbial diversity, and reducing the accumulation of soil-borne pathogens.