Volatile Organic Compounds Produced by Co-Culture of Burkholderia vietnamiensis B418 with Trichoderma harzianum T11-W Exhibits Improved Antagonistic Activities against Fungal Phytopathogens

Recently, there has been a growing interest in the biocontrol activity of volatile organic compounds (VOCs) produced by microorganisms. This study specifically focuses on the effects of VOCs produced by the co-culture of Burkholderia vietnamiensis B418 and Trichoderma harzianum T11-W for the control of two phytopathogenic fungi, Botrytis cinerea and Fusarium oxysporum f. sp. cucumerium Owen. The antagonistic activity of VOCs released in mono- and co-culture modes was evaluated by inhibition assays on a Petri dish and in detached fruit experiments, with the co-culture demonstrating significantly higher inhibitory effects on the phytopathogens on both the plates and fruits compared with the mono-cultures. Metabolomic profiles of VOCs were conducted using the solid-liquid microextraction technique, revealing 341 compounds with significant changes in their production during the co-culture. Among these compounds, linalool, dimethyl trisulfide, dimethyl disulfide, geranylacetone, 2-phenylethanol, and acetophenone were identified as having strong antagonistic activity through a standard inhibition assay. These key compounds were found to be related to the improved inhibitory effect of the B418 and T11-W co-culture. Overall, the results suggest that VOCs produced by the co-culture of B. vietnamiensis B418 and T. harzianum T11-W possess great potential in biological control.

Impact of cooperative or competitive dynamics between the yeast Saccharomyces cerevisiae and lactobacilli on the immune response of the host

Fungi and bacteria can be found coexisting in a wide variety of environments. The combination of their physical and molecular interactions can result in a broad range of outcomes for each partner, from competition to cooperative relationships. Most of these interactions can also be found in the human gastrointestinal tract. The gut microbiota is essential for humans, helping the assimilation of food components as well as the prevention of pathogen invasions through host immune system modulation and the production of beneficial metabolites such as short-chain fatty acids (SCFAs). Several factors, including changes in diet habits due to the progressive Westernization of the lifestyle, are linked to the onset of dysbiosis statuses that impair the correct balance of the gut environment. It is therefore crucial to explore the interactions between commensal and diet-derived microorganisms and their influence on host health. Investigating these interactions through co-cultures between human- and fermented food-derived lactobacilli and yeasts led us to understand how the strains' growth yield and their metabolic products rely on the nature and concentration of the species involved, producing either cooperative or competitive dynamics. Moreover, single cultures of yeasts and lactobacilli proved to be ideal candidates for developing immune-enhancing products, given their ability to induce trained immunity in blood-derived human monocytes in vitro. Conversely, co-cultures as well as mixtures of yeasts and lactobacilli have been shown to induce an anti-inflammatory response on the same immune cells in terms of cytokine profiles and activation surface markers, opening new possibilities in the design of probiotic and dietary therapies.

From Skin to Gut: Understanding Microbial Diversity in Rana amurensis and R. dybowskii

Amphibians face the threat of decline and extinction, and their health is crucially affected by the microbiota. Their health and ecological adaptability essentially depend on the diverse microbial communities that are shaped by unique host traits and environmental factors. However, there is still limited research on this topic. In this study, cutaneous (C) and gut (G) microbiota in Rana amurensis (A) and R. dybowskii (D) was analyzed through 16S amplicon sequencing. Groups AC and DC significantly differed in alpha diversity, while the gut groups (AG and DG) showed no such differences. Analyses of Bray-Curtis dissimilarity matrix and unweighted UniFrac distances showed significant differences in cutaneous microbiota between groups AC and DC, but not between groups AG and DG. Stochastic processes significantly influenced the assembly of cutaneous and gut microbiota in amphibians, with a notably higher species dispersal rate in the gut. The predominant phyla in the skin of R. amurensis and R. dybowskii were Bacteroidetes and Proteobacteria, respectively, with significant variations in Bacteroidota. Contrarily, the gut microbiota of both species was dominated by Firmicutes, Proteobacteria, and Bacteroidetes, without significant phylum-level differences. Linear discriminant analysis effect size (LEfSe) analysis identified distinct microbial enrichment in each group. Predictive analysis using phylogenetic investigation of communities by reconstruction of unobserved states 2 (PICRUSt2) revealed the significant functional pathways associated with the microbiota, which indicates their potential roles in immune system function, development, regeneration, and response to infectious diseases. This research underscores the critical impact of both host and environmental factors in shaping amphibian microbial ecosystems and emphasizes the need for further studies to explore these complex interactions for conservation efforts.

Disproof of the Structures and Biosynthesis of Ergoynes, Gs-Polyyne-l-Ergothioneine Cycloadducts from Gynuella sunshinyii YC6258

Some bacteria produce "bacterial polyynes" bearing a conjugated C≡C bond that starts with a terminal alkyne. Ergoynes A and B have been reported as sulfur-containing metabolites from Gynuella sunshinyii YC6258. These compounds were thought to be formed by cycloaddition between a bacterial polyyne (named Gs-polyyne) and l-ergothioneine. The biosynthetic gene clusters (BGCs), which may contribute to their synthesis, were present in the YC6258 genome. The biosynthetic origin of Gs-polyyne is interesting considering its rare 2-isopentyl fatty acyl skeleton. Here, the structures and biosynthesis of Gs-polyyne and ergoynes were verified by analytical, chemical, and genetic techniques. In the YC6258 extract, which was prepared considering their instability, Gs-polyyne was detected as a major LC peak, and ergoynes were not detected. The NMR data of the isolated Gs-polyyne contradicted the proposed structure and identified it as the previously reported protegenin A. The expression of Gs-polyyne BGC in Escherichia coli BL21(DE3) also yielded protegenin A. The cyclization between protegenin A and l-ergothioneine did not proceed during sample preparation; a base, such as potassium carbonate, was required. Overall, Gs-polyyne was identified as protegenin A, while ergoynes were determined to be artifacts. This cyclization may provide a derivatization to stabilize polyynes or create new chemical space.

Structures and Biosynthesis of Caryoynencins, Unstable Bacterial Polyynes from Pseudomonas protegens Recombinant Expressing the cayG Gene

Bacteria in certain genera can produce "bacterial polyynes" that contain a conjugated C≡C bond starting from a terminal alkyne. Protegenin A is a derivative of octadecanoic acid that contains an ene-tetrayne moiety. It was discovered in Pseudomonas protegens Cab57 and exhibits strong antioomycete and moderate antifungal activity. By introducing cayG, a cytochrome P450 gene from Burkholderia caryophylli, into P. protegens Cab57, protegenin A was converted into more complex polyynes, caryoynencins A-E. A purification method that minimized the degradation and isomerization of caryoynencins was established. For the first time, as far as we know, the 1H and 13C{1H} NMR signals of caryoynencins were completely assigned by analyzing the NMR data of the isolated compounds and protegenin A enriched with [1-13C]- or [2-13C]-acetate. Through the structural analysis of caryoynencins D/E and bioconversion experiments, we observed that CayG constructs the allyl alcohol moiety of caryoynencins A-C through sequential hydroxylation, dehydration, and hydroxylation. The recombinant strain exhibited a stronger antioomycete activity compared to the wild-type strain. This paper proposes a stable purification and structural determination method for various bacterial polyynes, and P. protegens Cab57 holds promise as an engineering host for the production of biologically active polyynes.

Microbiome Assembly in Fermented Foods

For thousands of years, humans have enjoyed the novel flavors, increased shelf-life, and nutritional benefits that microbes provide in fermented foods and beverages. Recent sequencing surveys of ferments have mapped patterns of microbial diversity across space, time, and production practices. But a mechanistic understanding of how fermented food microbiomes assemble has only recently begun to emerge. Using three foods as case studies (surface-ripened cheese, sourdough starters, and fermented vegetables), we use an ecological and evolutionary framework to identify how microbial communities assemble in ferments. By combining in situ sequencing surveys with in vitro models, we are beginning to understand how dispersal, selection, diversification, and drift generate the diversity of fermented food communities. Most food producers are unaware of the ecological processes occurring in their production environments, but the theory and models of ecology and evolution can provide new approaches for managing fermented food microbiomes, from farm to ferment.

Penicillium molds impact the transcriptome and evolution of the cheese bacterium Staphylococcus equorum

The observation that Penicillium molds can inhibit the growth of Staphylococcus was a catalyst for the antibiotic revolution. Considerable attention has been paid to purified Penicillium metabolites that inhibit bacteria, but little is known about how Penicillium species impact the ecology and evolution of bacteria in multispecies microbial communities. Here, we investigated how four different species of Penicillium can impact global transcription and evolution of a widespread Staphylococcus species (S. equorum) using the cheese rind model microbiome. Through RNA sequencing, we identified a core transcriptional response of S. equorum against all five tested Penicillium strains, including upregulation of thiamine biosynthesis, fatty acid degradation, and amino acid metabolism as well as downregulation of genes involved in the transport of siderophores. In a 12-week evolution experiment where we co-cultured S. equorum with the same Penicillium strains, we observed surprisingly few non-synonymous mutations across S. equorum populations evolved with the Penicillium species. A mutation in a putative DHH family phosphoesterase gene only occurred in populations evolved without Penicillium and decreased the fitness of S. equorum when co-cultured with an antagonistic Penicillium strain. Our results highlight the potential for conserved mechanisms of Staphylococcus-Penicillium interactions and demonstrate how fungal biotic environments may constrain the evolution of bacterial species.IMPORTANCEFungi and bacteria are commonly found co-occurring both in natural and synthetic microbiomes, but our understanding of fungal-bacterial interactions is limited to a handful of species. Conserved mechanisms of interactions and evolutionary consequences of fungal-bacterial interactions are largely unknown. Our RNA sequencing and experimental evolution data with Penicillium species and the bacterium S. equorum demonstrate that divergent fungal species can elicit conserved transcriptional and genomic responses in co-occurring bacteria. Penicillium molds are integral to the discovery of novel antibiotics and production of certain foods. By understanding how Penicillium species affect bacteria, our work can further efforts to design and manage Penicillium-dominated microbial communities in industry and food production.

AM fungal-bacterial relationships: what can they tell us about ecosystem sustainability and soil functioning?

Considering our growing population and our continuous degradation of soil environments, understanding the fundamental ecology of soil biota and plant microbiomes will be imperative to sustaining soil systems. Arbuscular mycorrhizal (AM) fungi extend their hyphae beyond plant root zones, creating microhabitats with bacterial symbionts for nutrient acquisition through a tripartite symbiotic relationship along with plants. Nonetheless, it is unclear what drives these AM fungal-bacterial relationships and how AM fungal functional traits contribute to these relationships. By delving into the literature, we look at the drivers and complexity behind AM fungal-bacterial relationships, describe the shift needed in AM fungal research towards the inclusion of interdisciplinary tools, and discuss the utilization of bacterial datasets to provide contextual evidence behind these complex relationships, bringing insights and new hypotheses to AM fungal functional traits. From this synthesis, we gather that interdependent microbial relationships are at the foundation of understanding microbiome functionality and deciphering microbial functional traits. We suggest using pattern-based inference tools along with machine learning to elucidate AM fungal-bacterial relationship trends, along with the utilization of synthetic communities, functional gene analyses, and metabolomics to understand how AM fungal and bacterial communities facilitate communication for the survival of host plant communities. These suggestions could result in improving microbial inocula and products, as well as a better understanding of complex relationships in terrestrial ecosystems that contribute to plant-soil feedbacks.

Co-responses of bacterial and fungal communities to fire management treatments in Mediterranean pyrophytic ecosystems

Cistus scrublands are pyrophytic ecosystems and occur widely across Mediterranean regions. Management of these scrublands is critical to prevent major disturbances, such as recurring wildfires. This is because management appears to compromise the synergies necessary for forest health and the provision of ecosystem services. Furthermore, it supports high microbial diversity, opening questions of how forest management practices impact belowground associated diversity as research related to this issue is scarce. This study aims to investigate the effects of different fire prevention treatments and site history on bacterial and fungi co-response and co-occurrence patterns over a fire-risky scrubland ecosystem. Two different site histories were studied by applying three different fire prevention treatments and samples were analyzed by amplification and sequencing of ITS2 and 16S rDNA for fungi and bacteria, respectively. The data revealed that site history, especially regarding fire occurrence, strongly influenced the microbial community. Young burnt areas tended to have a more homogeneous and lower microbial diversity, suggesting environmental filtering to a heat-resistant community. In comparison, young clearing history also showed a significant impact on the fungal community but not on the bacteria. Some bacteria genera were efficient predictors of fungal diversity and richness. For instance, Ktedonobacter and Desertibacter were a predictor of the presence of the edible mycorrhizal bolete Boletus edulis. These results demonstrate fungal and bacterial community co-response to fire prevention treatments and provide new tools for forecasting forest management impacts on microbial communities.

Marine Fungi Select and Transport Aerobic and Anaerobic Bacterial Populations from Polycyclic Aromatic Hydrocarbon-Contaminated Sediments

The organization of microbial communities in marine sediment relies on complex biotic and abiotic interactions. Among them, the interaction between fungi and bacteria plays a crucial role building specific microbial assemblages, resulting in metabolic networks adapted to environmental conditions. The fungal-bacterial interaction (FBI) includes bacterial translocation via fungal mycelia, allowing bacterial dispersion, and ecological niche colonization. In order to demonstrate that the translocation of bacteria through fungal mycelia involves bacterial selection, the mycelia of two fungi isolated from marine coastal sediment, Alternaria destruens F10.81 and Fusarium pseudonygamai F5.76, showing different strategies for uptake of polycyclic aromatic hydrocarbon (PAH), homogenous internalization and vacuole forming respectively, were used to translocate bacteria through hydrophobic hydrocarbon contaminated sediments. A. destruens F10.81 selected four specific bacteria, while bacterial selection by F. pseudonygamai F5.76 was not evident. Among the bacteria selected by A. destruens F10.81, Spirochaeta litoralis, known as strictly anaerobic bacterium, was identified, indicating that A. destruens F10.81 selects and transports both aerobic and anaerobic bacteria. Such a result is consistent with the observed formation of anoxic micro-niches in areas surrounding and affected by fungal hyphae. Our findings provide new insights on the selection and dispersion of bacterial communities by fungi, which are crucial for the organization of microbial communities and their functioning in coastal PAH-contaminated sediments. IMPORTANCE The study provides advances for understanding fungal-bacterial relationships, particularly on the selection and dispersion of bacterial communities by fungi, which are crucial for the organization of microbial communities and their functioning in coastal PAH-contaminated sediments. The transportation of bacteria via fungal hyphae (fungal highway) results in bacterial selection; in particular, fungal hyphae offer adequate conditions for the transport of both aerobic and anaerobic bacteria through hydrophobic patches for the colonization of novel niches.

Surface-enhanced Raman spectral characterization of antifungal activity of selenium and zinc based organometallic compounds

Surface-enhanced Raman spectroscopy (SERS) is used to identify the biochemical changes associated with the antifungal activities of selenium and zinc organometallic complexes against Aspergillus niger fungus. These biochemical changes identified in the form of SERS peaks can help to understand the mechanism of action of these antifungal agents which is important for development of new antifungal drugs. The SERS spectral changes indicate the denaturation and conformational changes of proteins and fungal cell wall decomposition in complex exposed fungal samples. The SERS spectra of these organometallic complexes exposed fungi are analyzed by using statistical tools like principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA). PCA is employed to differentiate the SERS spectra of fungal samples exposed to ligands and complexes. The PLS-DA discriminated different groups of spectra with 99.8% sensitivity, 100% specificity, 98% accuracy and 86 % area under receiver operating characteristic (AUROC) curve.

Toxin-Producing Endosymbionts Shield Pathogenic Fungus against Micropredators

The fungus Rhizopus microsporus harbors a bacterial endosymbiont (Mycetohabitans rhizoxinica) for the production of the antimitotic toxin rhizoxin. Although rhizoxin is the causative agent of rice seedling blight, the toxinogenic bacterial-fungal alliance is, not restricted to the plant disease. It has been detected in numerous environmental isolates from geographically distinct sites covering all five continents, thus raising questions regarding the ecological role of rhizoxin beyond rice seedling blight. Here, we show that rhizoxin serves the fungal host in fending off protozoan and metazoan predators. Fluorescence microscopy and coculture experiments with the fungivorous amoeba Protostelium aurantium revealed that ingestion of R. microsporus spores is toxic to P. aurantium. This amoebicidal effect is caused by the dominant bacterial rhizoxin congener rhizoxin S2, which is also lethal toward the model nematode Caenorhabditis elegans. By combining stereomicroscopy, automated image analysis, and quantification of nematode movement, we show that the fungivorous nematode Aphelenchus avenae actively feeds on R. microsporus that is lacking endosymbionts, whereas worms coincubated with symbiotic R. microsporus are significantly less lively. This study uncovers an unexpected ecological role of rhizoxin as shield against micropredators. This finding suggests that predators may function as an evolutionary driving force to maintain toxin-producing endosymbionts in nonpathogenic fungi.

Water stress and disruption of mycorrhizas induce parallel shifts in phyllosphere microbiome composition

Water and nutrient acquisition are key drivers of plant health and ecosystem function. These factors impact plant physiology directly as well as indirectly through soil- and root-associated microbial responses, but how they in turn affect aboveground plant-microbe interactions are not known. Through experimental manipulations in the field and growth chamber, we examine the interacting effects of water stress, soil fertility, and arbuscular mycorrhizal fungi on bacterial and fungal communities of the tomato (Solanum lycopersicum) phyllosphere. Both water stress and mycorrhizal disruption reduced leaf bacterial richness, homogenized bacterial community composition among plants, and reduced the relative abundance of dominant fungal taxa. We observed striking parallelism in the individual microbial taxa in the phyllosphere affected by irrigation and mycorrhizal associations. Our results show that soil conditions and belowground interactions can shape aboveground microbial communities, with important potential implications for plant health and sustainable agriculture.

Bacterial-fungal interactions under agricultural settings: from physical to chemical interactions

Bacteria and fungi are dominant members of environmental microbiomes. Various bacterial-fungal interactions (BFIs) and their mutual regulation are important factors for ecosystem functioning and health. Such interactions can be highly dynamic, and often require spatiotemporally resolved assessments to understand the interplay which ranges from antagonism to mutualism. Many of these interactions are still poorly understood, especially in terms of the underlying chemical and molecular interplay, which is crucial for inter-kingdom communication and interference. BFIs are highly relevant under agricultural settings; they can be determinative for crop health. Advancing our knowledge related to mechanisms underpinning the interactions between bacteria and fungi will provide an extended basis for biological control of pests and pathogens in agriculture. Moreover, it will facilitate a better understanding of complex microbial community networks that commonly occur in nature. This will allow us to determine factors that are crucial for community assembly under different environmental conditions and pave the way for constructing synthetic communities for various biotechnological applications. Here, we summarize the current advances in the field of BFIs with an emphasis on agriculture.

Contrasting effects of soil microbial interactions on growth-defence relationships between early- and mid-successional plant communities

Plants allocate resources to processes related to growth and enemy defence. Simultaneously, they interact with complex soil microbiomes that also affect plant performance. While the influence of individual microbial groups on single plants is increasingly studied, effects of microbial interactions on growth, defence and growth-defence relationships remain unknown, especially at the plant community level. We investigated how three microbial groups (bacteria, fungi, protists), alone and in full-factorial combinations, affect plant performance and potential growth-defence relationships by measuring phenolics composition in early- and mid-successional grass and forb communities in a glasshouse experiment. Microbial groups did not affect plant growth and only fungi increased defence compounds in early- and mid-successional forbs, while grasses were not affected. Shoot biomass-defence relationships were negatively correlated in most microbial treatments in early-successional forbs, but positively in several microbial treatments in mid-successional forbs. The growth-defence relationship was generally negative in early-successional but not in mid-successional grasses. The presence of different microbiomes commonly removed the observed growth-defence relationships. We conclude that soil microorganisms and their interactions can shift growth-defence relationships differentially for plant functional groups and the relationships vary between successional stages. Microbial interaction-induced growth-defence shifts might therefore underlie distinct plant strategies and fitness.

Biosynthesis of Antibacterial Iron-Chelating Tropolones in Aspergillus nidulans as Response to Glycopeptide-Producing Streptomycetes

The soil microbiome comprises numerous filamentous fungi and bacteria that mutually react and challenge each other by the production of bioactive secondary metabolites. Herein, we show in liquid co-cultures that the presence of filamentous Streptomycetes producing antifungal glycopeptide antibiotics induces the production of the antibacterial and iron-chelating tropolones anhydrosepedonin (1) and antibiotic C (2) in the mold Aspergillus nidulans. Additionally, the biosynthesis of the related polyketide tripyrnidone (5) was induced, whose novel tricyclic scaffold we elucidated by NMR and HRESIMS data. The corresponding biosynthetic polyketide synthase-encoding gene cluster responsible for the production of these compounds was identified. The tropolones as well as tripyrnidone (5) are produced by genes that belong to the broad reservoir of the fungal genome for the synthesis of different secondary metabolites, which are usually silenced under standard laboratory conditions. These molecules might be part of the bacterium-fungus competition in the complex soil environment, with the bacterial glycopeptide antibiotic as specific environmental trigger for fungal induction of this cluster.

Does a decrease in microbial biomass alter mycorrhizal attributes and soil quality indicators in coal mining areas under revegetation process?

Losses of microbial diversity in degraded ecosystems still have obscure consequences, especially when considering the interaction between arbuscular mycorrhizal fungi (AMF) and soil bacteria. This study investigates the effect of decreasing microbial biomass on mycorrhizal attributes and soil quality indicators. The dilution-to-extinction approach was applied in microcosms to search for associations among bacterial diversity, mycorrhizal attributes, and soil quality indicators. The experiment was conducted with four soil treatments (undiluted control 10⁰ = D0, 10^-3 = D3, 10^-6 = D6, and 10^-9 = D9) from a short-term (two years = 2Y) and a long-term (15 years = 15Y) coal mine revegetation area. Microcosms were inoculated with 300 spores of Acaulospora colombiana, Gigaspora albida, and Claroideoglomus etunicatum with millet as the host plant. Results included the total number of AMF spores, mycorrhizal colonization, soil aggregation, glomalin, fluorescein diacetate hydrolysis (FDA), basal soil respiration, microbial biomass, and soil bacterial microbiome. Larger differences were observed between areas than between dilution treatments within the sampling area. Attributes that presented differences in the dilutions compared to D0 2Y samples were mycorrhizal colonization (D0 = 85% and D9 = 43.3%), FDA (D0 = 77.2% and D9 = 55.5%), extractable glomalin-related soil protein (D0 = 0.09 and D9 = 0.11) and bacterial diversity (D0 = 7.3 and D6 = 5.3). D0 15Y samples presented differences in microbial biomass nitrogen (D0: 232.0) and bacterial diversity (D0: 7.9, D9: 5.6) compared to the dilutions. Bacterial microbiome present in the D0 samples formed distinct clusters as to other samples and correlated with soil aggregation and basal respiration attributes. Results suggest that AMF inoculation and dilution-to-extinction did not affect soil quality indicators preeminently, but the bacterial community is affected and can influence the process of environmental revegetation. A long-term revegetation period is substantial to improve quality indicators and establish the diversity of microorganisms and consequently revegetation in areas impacted by coal mining.

Overlapping Roles of Yeast Transporters Aqr1, Qdr2, and Qdr3 in Amino Acid Excretion and Cross-Feeding of Lactic Acid Bacteria

Microbial species occupying the same ecological niche or codeveloping during a fermentation process can exchange metabolites and mutualistically influence each other’s metabolic states. For instance, yeast can excrete amino acids, thereby cross-feeding lactic acid bacteria unable to grow without an external amino acid supply. The yeast membrane transporters involved in amino acid excretion remain poorly known. Using a yeast mutant overproducing and excreting threonine (Thr) and its precursor homoserine (Hom), we show that excretion of both amino acids involves the Aqr1, Qdr2, and Qdr3 proteins of the Drug H⁺-Antiporter Family (DHA1) family. We further investigated Aqr1 as a representative of these closely related amino acid exporters. In particular, structural modeling and molecular docking coupled to mutagenesis experiments and excretion assays enabled us to identify residues in the Aqr1 substrate-binding pocket that are crucial for Thr and/or Hom export. We then co-cultivated yeast and Lactobacillus fermentum in an amino-acid-free medium and found a yeast mutant lacking Aqr1, Qdr2, and Qdr3 to display a reduced ability to sustain the growth of this lactic acid bacterium, a phenotype not observed with strains lacking only one of these transporters. This study highlights the importance of yeast DHA1 transporters in amino acid excretion and mutualistic interaction with lactic acid bacteria.

Fungal social influencers: secondary metabolites as a platform for shaping the plant-associated community

Fungal secondary metabolites (FSMs) are capable of manipulating plant community dynamics by inhibiting or facilitating the establishment of co-habitating organisms. Although production of FSMs is not crucial for survival of the producer, their absence can indirectly impair growth and/or niche competition of these fungi on the plant. The presence of FSMs with no obvious consequence on the fitness of the producer leaves questions regarding ecological impact. This review investigates how fungi employ FSMs as a platform to mediate fungal-fungal, fungal-bacterial and fungal-animal interactions associated with the plant community. We discuss how the biological function of FSMs may indirectly benefit the producer by altering the dynamics of surrounding organisms. We introduce several instances where FSMs influence antagonistic- or alliance-driven interactions. Part of our aim is to decipher the meaning of the FSM 'language' as it is widely noted to impact the surrounding community. Here, we highlight the contribution of FSMs to plant-associated interaction networks that affect the host either broadly or in ways that may have previously been unclear.

Multimodal Molecular Imaging and Identification of Bacterial Toxins Causing Mushroom Soft Rot and Cavity Disease

Soft rot disease of edible mushrooms leads to rapid degeneration of fungal tissue and thus severely affects farming productivity worldwide. The bacterial mushroom pathogen Burkholderia gladioli pv. agaricicola has been identified as the cause. Yet, little is known about the molecular basis of the infection, the spatial distribution and the biological role of antifungal agents and toxins involved in this infectious disease. We combine genome mining, metabolic profiling, MALDI-Imaging and UV Raman spectroscopy, to detect, identify and visualize a complex of chemical mediators and toxins produced by the pathogen during the infection process, including toxoflavin, caryoynencin, and sinapigladioside. Furthermore, targeted gene knockouts and in vitro assays link antifungal agents to prevalent symptoms of soft rot, mushroom browning, and impaired mycelium growth. Comparisons of related pathogenic, mutualistic and environmental Burkholderia spp. indicate that the arsenal of antifungal agents may have paved the way for ancestral bacteria to colonize niches where frequent, antagonistic interactions with fungi occur. Our findings not only demonstrate the power of label-free, in vivo detection of polyyne virulence factors by Raman imaging, but may also inspire new approaches to disease control.

Improving Fungal Cultivability for Natural Products Discovery

The pool of fungal secondary metabolites can be extended by activating silent gene clusters of cultured strains or by using sensitive biological assays that detect metabolites missed by analytical methods. Alternatively, or in parallel with the first approach, one can increase the diversity of existing culture collections to improve the access to new natural products. This review focuses on the latter approach of screening previously uncultured fungi for chemodiversity. Both strategies have been practiced since the early days of fungal biodiscovery, yet relatively little has been done to overcome the challenge of cultivability of as-yet-uncultivated fungi. Whereas earlier cultivability studies using media formulations and biological assays to scrutinize fungal growth and associated factors were actively conducted, the application of modern omics methods remains limited to test how to culture the fungal dark matter and recalcitrant groups of described fungi. This review discusses the development of techniques to increase the cultivability of filamentous fungi that include culture media formulations and the utilization of known chemical growth factors, in situ culturing and current synthetic biology approaches that build upon knowledge from sequenced genomes. We list more than 100 growth factors, i.e., molecules, biological or physical factors that have been demonstrated to induce spore germination as well as tens of inducers of mycelial growth. We review culturing conditions that can be successfully manipulated for growth of fungi and visit recent information from omics methods to discuss the metabolic basis of cultivability. Earlier work has demonstrated the power of co-culturing fungi with their host, other microorganisms or their exudates to increase their cultivability. Co-culturing of two or more organisms is also a strategy used today for increasing cultivability. However, fungi possess an increased risk for cross-contaminations between isolates in existing in situ or microfluidics culturing devices. Technological improvements for culturing fungi are discussed in the review. We emphasize that improving the cultivability of fungi remains a relevant strategy in drug discovery and underline the importance of ecological and taxonomic knowledge in culture-dependent drug discovery. Combining traditional and omics techniques such as single cell or metagenome sequencing opens up a new era in the study of growth factors of hundreds of thousands of fungal species with high drug discovery potential.

Elicitation of Streptomyces lunalinharesii secondary metabolism through co-cultivation with Rhizoctonia solani

The concern regarding the emergence of phytopathogens strains which are resistant to conventional agrochemicals has given support to the search for alternatives on the use of chemical pesticides in agriculture. In this context, microorganisms are considered as promising sources of useful natural compounds and actinobacteria are particularly relevant since they are known to produce several bioactive metabolites. The objective of this work was to investigate the production of secondary metabolites with antifungal activity by a strain of the actinobacteria Streptomyces lunalinharesii (A54A) under axenic conditions and in co-cultivation with the phytopathogen Rhizoctonia solani. Tests to evaluate antifungal activity of the extracts indicated the presence of diffusable molecules capable of inhibiting the growth of R. solani produced by S. lunalinharesii, especially when in the presence of the fungus during fermentation. Metabolomic analyzes allowed the putative annotation of the bioactive compounds desferrioxamine E and anisomycin, in addition to the evaluation of the metabolic profile of the isolate when grown in axenic mode and in co-cultivation, while statistical analyzes enabled the comparison of such profiles and the identification of metabolites produced in greater relative quantities in the elicitation condition. Such methodologies provided the selection of unknown features with high bioactive potential for dereplication, and several metabolites of S. lunalinharesii possibly represent novel compounds.

Potential use of fungal-bacterial co-cultures for the removal of organic pollutants

Fungi and bacteria coexist in a wide variety of natural and artificial environments which can lead to their association and interaction - ranging from antagonism to cooperation - that can affect the survival, colonization, spatial distribution and stress resistance of the interacting partners. The use of polymicrobial cultivation approaches has facilitated a more thorough understanding of microbial dynamics in mixed microbial communities, such as those composed of fungi and bacteria, and their influence on ecosystem functions. Mixed (multi-domain) microbial communities exhibit unique associations and interactions that could result in more efficient systems for the degradation and removal of organic pollutants. Several previous studies have reported enhanced biodegradation of certain pollutants when using combined fungal-bacterial treatments compared to pure cultures or communities of either fungi or bacteria (single domain systems). This article reviews: (i) the mechanisms of pollutant degradation that can occur in fungal-bacterial systems (e.g.: co-degradation, production of secondary metabolites, enhancement of degradative enzyme production, and transport of bacteria by fungal mycelia); (ii) case studies using fungal-bacterial co-cultures for the removal of various organic pollutants (synthetic dyes, polycyclic aromatic hydrocarbons, pesticides, and other trace or volatile organic compounds) in different environmental matrices (e.g. water, gas/vapors, soil); (iii) the key aspects of engineering artificial fungal-bacterial co-cultures, and (iv) the current challenges and future perspectives of using fungal-bacterial co-cultures for environmental remediation.

Identification of a New Antimicrobial, Desertomycin H, Utilizing a Modified Crowded Plate Technique

The antibiotic-resistant bacteria-associated infections are a major global healthcare threat. New classes of antimicrobial compounds are urgently needed as the frequency of infections caused by multidrug-resistant microbes continues to rise. Recent metagenomic data have demonstrated that there is still biosynthetic potential encoded in but transcriptionally silent in cultivatable bacterial genomes. However, the culture conditions required to identify and express silent biosynthetic gene clusters that yield natural products with antimicrobial activity are largely unknown. Here, we describe a new antibiotic discovery scheme, dubbed the modified crowded plate technique (mCPT), that utilizes complex microbial interactions to elicit antimicrobial production from otherwise silent biosynthetic gene clusters. Using the mCPT as part of the antibiotic crowdsourcing educational program Tiny EarthTM, we isolated over 1400 antibiotic-producing microbes, including 62 showing activity against multidrug-resistant pathogens. The natural product extracts generated from six microbial isolates showed potent activity against vancomycin-intermediate resistant Staphylococcus aureus. We utilized a targeted approach that coupled mass spectrometry data with bioactivity, yielding a new macrolactone class of metabolite, desertomycin H. In this study, we successfully demonstrate a concept that significantly increased our ability to quickly and efficiently identify microbes capable of the silent antibiotic production.

Frenemies: Interactions between Rhizospheric Bacteria and Fungi from Metalliferous Soils

Is it possible to improve the efficiency of bioremediation technologies? The use of mixed cultures of bacteria and fungi inoculated at the rhizosphere level could promote the growth of the associated hyperaccumulating plant species and increase the absorption of metals in polluted soils, broadening new horizons on bioremediation purposes. This work investigates interactions between Ni-tolerant plant growth-promoting bacteria and fungi (BF) isolated from the rhizosphere of a hyperaccumulating plant. The aim is to select microbial consortia with synergistic activity to be used in integrated bioremediation protocols. Pseudomonas fluorescens (Pf), Streptomyces vinaceus (Sv) Penicillium ochrochloron (Po), and Trichoderma harzianum group (Th) were tested in mixes (Po-Sv, Po-Pf, Th-Pf, and Th-Sv). These strains were submitted to tests (agar overlay, agar plug, and distance growth co-growth tests), tailored for this aim, on Czapek yeast agar (CYA) and tryptic soy agar (TSA) media and incubated at 26 ± 1 °C for 10 days. BF growth, shape of colonies, area covered on plate, and inhibition capacity were evaluated. Most BF strains still exhibit their typical characters and the colonies separately persisted without inhibition (as Po-Sv) or with reciprocal confinement (as Th-Sv and Th-Pf). Even if apparently inhibited, the Po-Pf mix really merged, thus obtaining morphological traits representing a synergic co-growth, where both strains reached together the maturation phase and developed a sort of mixed biofilm. Indeed, bacterial colonies surround the mature fungal structures adhering to them without any growth inhibition. First data from in vivo experimentation with Po and Pf inocula in pot with metalliferous soils and hyperaccumulator plants showed their beneficial effect on plant growth. However, there is a lack of information regarding the effective co-growth between bacteria and fungi. Indeed, several studies, which directly apply the co-inoculum, do not consider suitable microorganisms consortia. Synergic rhizosphere BFs open new scenarios for plant growth promotion and soil bioremediation.

Bacterial-fungal interactions revealed by genome-wide analysis of bacterial mutant fitness

Microbial interactions are expected to be major determinants of microbiome structure and function. Although fungi are found in diverse microbiomes, their interactions with bacteria remain largely uncharacterized. In this work, we characterize interactions in 16 different bacterial-fungal pairs, examining the impacts of 8 different fungi isolated from cheese rind microbiomes on 2 bacteria (Escherichia coli and a cheese-isolated Pseudomonas psychrophila). Using random barcode transposon-site sequencing with an analysis pipeline that allows statistical comparisons between different conditions, we observed that fungal partners caused widespread changes in the fitness of bacterial mutants compared to growth alone. We found that all fungal species modulated the availability of iron and biotin to bacterial species, which suggests that these may be conserved drivers of bacterial-fungal interactions. Species-specific interactions were also uncovered, a subset of which suggested fungal antibiotic production. Changes in both conserved and species-specific interactions resulted from the deletion of a global regulator of fungal specialized metabolite production. This work highlights the potential for broad impacts of fungi on bacterial species within microbiomes.

Chemical Mediators at the Bacterial-Fungal Interface

Interactions among microbes are key drivers of evolutionary progress and constantly shape ecological niches. Microorganisms rely on chemical communication to interact with each other and surrounding organisms. They synthesize natural products as signaling molecules, antibiotics, or modulators of cellular processes that may be applied in agriculture and medicine. Whereas major insight has been gained into the principles of intraspecies interaction, much less is known about the molecular basis of interspecies interplay. In this review, we summarize recent progress in the understanding of chemically mediated bacterial-fungal interrelations. We discuss pairwise interactions among defined species and systems involving additional organisms as well as complex interactions among microbial communities encountered in the soil or defined as microbiota of higher organisms. Finally, we give examples of how the growing understanding of microbial interactions has contributed to drug discovery and hypothesize what may be future directions in studying and engineering microbiota for agricultural or medicinal purposes.

Exploring Rice Root Microbiome; The Variation, Specialization and Interaction of Bacteria and Fungi In Six Tropic Savanna Regions in Ghana

We investigated the root microbiomes of rice sampled from six major rice-producing regions in Ghana using Illumina MiSeq high-throughput amplicon sequencing analysis. The result showed that both bacterial and fungal community compositions were significantly varied across the regions. Bacterial communities were shaped predominantly by biotic factors, including root fungal diversity and abundance. In contrast, fungal communities were influenced by abiotic factors such as soil nitrate, total carbon and soil pH. A negative correlation between the diversity and abundance of root fungi with soil nitrate (NO3-) level was observed. It suggested that there were direct and indirect effects of NO3- on the root-associated bacterial and fungal community composition. The gradient of soil nitrate from North to South parts of Ghana may influence the composition of rice root microbiome. Bacterial community composition was shaped by fungal diversity and abundance; whereas fungal community composition was shaped by bacterial abundance. It suggested the mutualistic interaction of bacteria and fungi at the community level in the rice root microbiome. Specific bacterial and fungal taxa were detected abundantly in the ‘Northern’ regions of Ghana, which were very low or absent from the samples of other regions. The analysis of indicator species suggested that an ‘ecological specialization’ may have occurred which enabled specific microbial taxa to adapt to the local environment, such as the low-nitrate condition in the Northern regions.

Temporal discrepancy of airborne total bacteria and pathogenic bacteria between day and night

As the most abundant microbes in the atmosphere, airborne bacteria are closely involved in affecting human health, regional climate and ecological balance. The mobility of airborne microorganisms makes it necessary to study the community dynamic in short cycle. Nevertheless, it remains obscure how the airborne bacteria especially the pathogenic bacteria vary on the small time scale of day and night. To investigate the nycterohemeral discrepancy of airborne total bacteria and pathogenic bacteria, PM_2.5 samples were collected in Hangzhou between day and night. Microbial taxonomic information was obtained through 16S rRNA gene sequencing and "human pathogens database" screening. Further analyses based on Multiple Regression Matrices (MRM) approach and Concentration Weighted Trajectory (CWT) model were conducted to elucidate the effect of local environmental factors and long-range transport. The community composition of total bacteria tended to be similar in the daytime while pathogenic bacteria turned out to be homogeneous in the nighttime. To be vigilant, the diversity of airborne pathogenic bacteria echoed the frequency of anthropogenic activities with the pathogen inhalation rate roughly at 428 copies/h and 235 copies/h respectively in daytime and nighttime. The nycterohemeral discrepancy of total bacteria was principally driven by the filtering of environmental factors, i.e., CO and NO₂, indicating that anthropogenic activities brought about the homogeneity. Airborne pathogenic bacteria coupled with the strong resistances of environmental filtering stood out from their non-pathogenic counterpart, which enabled the long-range transport. Indeed, the nycterohemeral discrepancy of pathogenic bacteria was shaped by the transport of air masses. This research filled the gaps in temporal variance of airborne microorganisms on the small time scale of day and night, providing crucial foundation for precisely predicting ecological and health effects of bioaerosols.

Mechanism of interaction of an endofungal bacterium Serratia marcescens D1 with its host and non-host fungi

Association of bacteria with fungi is a major area of research in infection biology, however, very few strains of bacteria have been reported that can invade and reside within fungal hyphae. Here, we report the characterization of an endofungal bacterium Serratia marcescens D1 from Mucor irregularis SS7 hyphae. Upon re-inoculation, colonization of the endobacterium S. marcescens D1 in the hyphae of Mucor irregularis SS7 was demonstrated using stereo microscopy. However, S. marcescens D1 failed to invade into the hyphae of the tested Ascomycetes (except Fusarium oxysporum) and Basidiomycetes. Remarkably, Serratia marcescens D1 could invade and spread over the culture of F. oxysporum that resulted in mycelial death. Prodigiosin, the red pigment produced by the Serratia marcescens D1, helps the bacterium to invade fungal hyphae as revealed by the increasing permeability in fungal cell membrane. On the other hand, genes encoding the type VI secretion system (T6SS) assembly protein TssJ and an outer membrane associated murein lipoprotein also showed significant up-regulation during the interaction process, suggesting the involvement of T6SS in the invasion process.

Beneficial Endophytic Bacteria-Serendipita indica Interaction for Crop Enhancement and Resistance to Phytopathogens

Serendipita (=Piriformospora) indica is a fungal endophytic symbiont with the capabilities to enhance plant growth and confer resistance to different stresses. However, the application of this fungus in the field has led to inconsistent results, perhaps due to antagonism with other microbes. Here, we studied the impact of individual bacterial isolates from the endophytic bacterial community on the in vitro growth of S. indica. We further analyzed how combinations of bacteria and S. indica influence plant growth and protection against the phytopathogens Fusarium oxysporum and Rhizoctonia solani. Bacterial strains of the genera Bacillus, Enterobacter and Burkholderia negatively affected S. indica growth on plates, whereas Mycolicibacterium, Rhizobium, Paenibacillus strains and several other bacteria from different taxa stimulated fungal growth. To further explore the potential of bacteria positively interacting with S. indica, four of the most promising strains belonging to the genus Mycolicibacterium were selected for further experiments. Some dual inoculations of S. indica and Mycolicibacterium strains boosted the beneficial effects triggered by S. indica, further enhancing the growth of tomato plants, and alleviating the symptoms caused by the phytopathogens F. oxysporum and R. solani. However, some combinations of S. indica and bacteria were less effective than individual inoculations. By analyzing the genomes of the Mycolicibacterium strains, we revealed that these bacteria encode several genes predicted to be involved in the stimulation of S. indica growth, plant development and tolerance to abiotic and biotic stresses. Particularly, a high number of genes related to vitamin and nitrogen metabolism were detected. Taking into consideration multiple interactions on and inside plants, we showed in this study that some bacterial strains may induce beneficial effects on S. indica and could have an outstanding influence on the plant-fungus symbiosis.

Excision of endosymbiotic bacteria from yeast under aging and starvation stresses

Although infrequent in our laboratory, growth of bacterial colonies has been observed on top of the purified cultures of yeasts. In this study, the likelihood of bacterial excision from yeast under aging and starvation stresses was assessed using 10 gastric and 10 food-borne yeasts. Yeasts were identified as members of Candida or Saccharomyces genus by amplification and sequencing of D1/D2 region of 26S rDNA. For aging stress, yeasts were cultured on brain heart infusion agar supplemented with sheep blood and incubated at 30 °C for 3-4 weeks. For starvation stress, yeasts were inoculated into distilled water and incubated similarly. After seven days, starved yeasts were cultured on yeast extract glucose agar, incubated similarly and examined daily for appearance of bacterial colonies on top of the yeast's growth. Outgrowth of excised bacteria was observed on top of the cultures of 4 yeasts (Y1, Y3, Y13 and Y18) after 3-7 days. The excised bacteria (B1, B3, B13 and B18) were isolated and identified at the genus level according to their biochemical characteristics as well as amplification and sequencing of 16S rDNA. B1 (Arthrobacter) were excised from Y1 (Candida albicans) upon aging and B3 (Staphylococcus), B13 (Cellulomonas) and B18 (Staphylococcus) were excised from their respective yeasts; Y3 (Candida tropicalis), Y13 (Saccharomyces cerevisiae) and Y18 (Candida glabrata) upon starvation. DNA from yeasts was used for detection of 16S rDNA of their intracellular bacteria and sequencing. Amplified products from yeasts showed sequence similarity to those of excised bacteria. Under normal conditions, yeast exerts tight control on multiplication of its intracellular bacteria. However, upon aging and starvation the control is no longer effective and bacterial outgrowth occurs. Unlimited multiplication of excised bacteria might provide yeast with plenty of food in close vicinity. This could be an evolutionary dialogue between yeast and bacteria that ensures the survival of both partners.

Causes and consequences of biotic interactions within microbiomes

An integrative pattern-process-mechanism approach is revealing the roles of biotic interactions in microbiome assembly. Patterns of microbiome diversity observed in metagenomic studies can be partly explained by interaction processes (e.g. competition, facilitation) and underlying molecular or genetic mechanisms (e.g. antibiotic production, nutrient cross-feeding). Exciting opportunities remain to fully understand the significance and generalizability of biotic interactions within microbiomes. Many microbial interactions have been studied by chasing easily quantifiable phenotypes including changes in growth or pigmentation, but it is likely that diverse cryptic interactions occur without obvious growth changes or macroscopic phenotypes. A narrow phylogenetic breadth of well-studied microbes limits our understanding of whether there are conserved genetic or molecular mechanisms of microbial interactions. Biotic interactions can impose strong selective pressures that could shape rates and modes of microbial evolution, but few studies have examined the evolutionary consequences of interactions within microbiomes. Continued exploration of the chemical and genetic mechanisms underlying biotic interactions may provide novel tools to manipulate and manage microbiomes.

Genome Mining Reveals Endopyrroles from a Nonribosomal Peptide Assembly Line Triggered in Fungal-Bacterial Symbiosis

The bacterial endosymbiont (Burkholderia rhizoxinica) of the rice seedling blight fungus (Rhizopus microsporus) harbors a large number of cryptic biosynthesis gene clusters. Genome mining and sequence similarity networks based on an encoded nonribosomal peptide assembly line and the associated pyrrole-forming enzymes in the symbiont indicated that the encoded metabolites are unique among a large number of tentative pyrrole natural products in diverse and unrelated bacterial phyla. By performing comparative metabolic profiling using a mutant generated with an improved pheS Burkholderia counterselection marker, we found that the symbionts' biosynthetic pathway is mainly activated under salt stress and exclusively in symbiosis with the fungal host. The cryptic metabolites were fully characterized as novel pyrrole-substituted depsipeptides (endopyrroles). A broader survey showed that endopyrrole production is a hallmark of geographically distant endofungal bacteria, which produce the peptides solely under symbiotic conditions.

Engineering Synthetic Microbial Communities through a Selective Biofilm Cultivation Device for the Production of Fermented Beverages

Production of Cambodian rice wine involves complex microbial consortia. Indeed, previous studies focused on traditional microbial starters used for this product revealed that three microbial strains with complementary metabolic activities are required for an effective fermentation, i.e., filamentous fungi (Rhizopus oryzae), yeast (Saccharomycescerevisiae), and lactic acid bacteria (Lactobacillusplantarum). Modulating the ratio between these three key players led to significant differences, not only in terms of ethanol and organic acid production, but also on the profile of volatile compounds, in comparison with natural communities. However, we observed that using an equal ratio of spores/cells of the three microbial strains during inoculation led to flavor profile and ethanol yield close to that obtained through the use of natural communities. Compartmentalization of metabolic tasks through the use of a biofilm cultivation device allows further improvement of the whole fermentation process, notably by increasing the amount of key components of the aroma profile of the fermented beverage (i.e., mainly phenylethyl alcohol, isobutyl alcohol, isoamyl alcohol, and 2-methyl-butanol) and reducing the amount of off-flavor compounds. This study is a step forward in our understanding of interkingdom microbial interactions with strong application potential in food biotechnology.

Dynamic of inorganic nitrogen and amino sugar to glucosamine addition in forest soils

Amino sugars (AS) are routinely used as microbial biomarkers to investigate the dynamics of soil carbon (C) and nitrogen (N) under different environments. However, the effect of any AS on soil C and N, or other AS, is not well-defined. In this study, acid soils from Dongbei (D) and Fujian (F) and alkaline soil from Henan (H) were selected to perform an incubation experiment under glucosamine addition for 36 days. In the present study, the dynamics of soil soluble organic C (SOC), NH₄⁺-N, NO₃^--N, soluble organic N (SON), and four AS: glucosamine (GluN), mannosamine (ManN), galactosamine (GalN), and muramic acid (MurN), were investigated. The results showed that AS was different among the three soils, but had similar dynamics in the same soil. The higher total C and inorganic N in the D and F relative to the H soil were related to the greater AS in two soils. With incubation, AS decreased in D soil and increased in F soil before 1 week, while after 1 week, the inverse dynamics were observed, which suggest that SOC or SOC combined with inorganic N may be a mechanism to adjust the dynamics of C from AS. Overall, glucosamine addition did not significantly affect AS in D, while the reverse was true for F and H soils. Glucosamine addition decreased AS at day 0 for D soil and at day 3 for F and H soils, and increased SOC. The lowered NH₄⁺-N and AS in D soil, but the higher values of these, were observed in F soil after 1 week of incubation. The increase of SON in D soil with glucosamine addition might be due to the depolymerization of soil organic matter (SOM) into SON. However, the decrease of SON in F soil could be attributed to the mineralization of SON.

Bacterial-fungal interactions: ecology, mechanisms and challenges

Fungi and bacteria are found living together in a wide variety of environments. Their interactions are significant drivers of many ecosystem functions and are important for the health of plants and animals. A large number of fungal and bacterial families engage in complex interactions that lead to critical behavioural shifts of the microorganisms ranging from mutualism to antagonism. The importance of bacterial-fungal interactions (BFI) in environmental science, medicine and biotechnology has led to the emergence of a dynamic and multidisciplinary research field that combines highly diverse approaches including molecular biology, genomics, geochemistry, chemical and microbial ecology, biophysics and ecological modelling. In this review, we discuss recent advances that underscore the roles of BFI across relevant habitats and ecosystems. A particular focus is placed on the understanding of BFI within complex microbial communities and in regard of the metaorganism concept. We also discuss recent discoveries that clarify the (molecular) mechanisms involved in bacterial-fungal relationships, and the contribution of new technologies to decipher generic principles of BFI in terms of physical associations and molecular dialogues. Finally, we discuss future directions for research in order to stimulate synergy within the BFI research area and to resolve outstanding questions.

Interkingdom microbial consortia mechanisms to guide biotechnological applications

Microbial consortia are capable of surviving diverse conditions through the formation of synergistic population-level structures, such as stromatolites, microbial mats and biofilms. Biotechnological applications are poised to capitalize on these unique interactions. However, current artificial co-cultures constructed for societal benefits, including biosynthesis, agriculture and bioremediation, face many challenges to perform as well as natural consortia. Interkingdom microbial consortia tend to be more robust and have higher productivity compared with monocultures and intrakingdom consortia, but the control and design of these diverse artificial consortia have received limited attention. Further, feasible research techniques and instrumentation for comprehensive mechanistic insights have only recently been established for interkingdom microbial communities. Here, we review these recent advances in technology and our current understanding of microbial interaction mechanisms involved in sustaining or developing interkingdom consortia for biotechnological applications. Some of the interactions among members from different kingdoms follow similar mechanisms observed for intrakingdom microbial consortia. However, unique interactions in interkingdom consortia, including endosymbiosis or interkingdom-specific cell-cell interactions, provide improved mitigation to external stresses and inhibitory compounds. Furthermore, antagonistic interactions among interkingdom species can promote fitness, diversification and adaptation, along with the production of beneficial metabolites and enzymes for society. Lastly, we shed light on future research directions to develop study methods at the level of metabolites, genes and meta-omics. These potential research methods could lead to the control and utilization of highly diverse microbial communities.

Antagonistic Interaction of Staphylococcus aureus Toward Candida glabrata During in vitro Biofilm Formation Is Caused by an Apoptotic Mechanism

Background: Infections caused by Candida species and Staphylococcus aureus are associated with biofilm formation. C. albicans–S. aureus interactions are synergistic due to the significant increase in mixed biofilms and improved resistance to vancomycin of S. aureus. C. glabrata and S. aureus both are nosocomial pathogens that cause opportunistic infections in similar host niches. However, there is scarce information concerning the interaction between these last microorganisms.

Results: The relationship between C. glabrata and S. aureus was evaluated by estimating the viability of both microorganisms in co-culture of planktonic cells and in single and mixed biofilms. An antagonistic behavior of S. aureus and their cell-free bacterial supernatant (CFBS) toward C. glabrata, both in planktonic form and in biofilms, was demonstrated. Scanning electron microscopy (SEM), transmission electron microscopy (TEM), and confocal laser scanning microscopy (CLSM) images showed yeast cells surrounded by bacteria, alterations in intracytoplasmic membranes, and non-viable blastoconidia with intact cell walls. Concomitantly, S. aureus cells remained viable and unaltered. The antagonistic activity of S. aureus toward C. glabrata was not due to cell-to-cell contact but the presence of CFBS, which causes a significant decrement in yeast viability and the formation of numerous lipid droplets (LDs), reactive oxygen species (ROS) accumulation, as well as nuclear alterations, and DNA fragmentation indicating the induction of an apoptotic mechanism.

Conclusion: Our results demonstrate that the S. aureus CFBS causes cell death in C. glabrata by an apoptotic mechanism.

Ecology of Contaminant Biotransformation in the Mycosphere: Role of Transport Processes

Fungi and bacteria often share common microhabitats. Their co-occurrence and coevolution give rise to manifold ecological interactions in the mycosphere, here defined as the microhabitats surrounding and affected by hyphae and mycelia. The extensive structure of mycelia provides ideal "logistic networks" for transport of bacteria and matter in structurally and chemically heterogeneous soil ecosystems. We describe the characteristics of the mycosphere as a unique and highly dynamic bacterial habitat and a hot spot for contaminant biotransformation. In particular, we emphasize the role of the mycosphere for (i) bacterial dispersal and colonization of subsurface interfaces and new habitats, (ii) matter transport processes and contaminant bioaccessibility, and (iii) the functional stability of microbial ecosystems when exposed to environmental fluctuations such as stress or disturbances. Adopting concepts from ecological theory, the chapter disentangles bacterial-fungal impacts on contaminant biotransformation in a systemic approach that interlinks empirical data from microbial ecosystems with simulation data from computational models. This approach provides generic information on key factors, processes, and ecological principles that drive microbial contaminant biotransformation in soil. We highlight that the transport processes create favorable habitat conditions for efficient bacterial contaminant degradation in the mycosphere. In-depth observation, understanding, and prediction of the role of mycosphere transport processes will support the use of bacterial-fungal interactions in nature-based solutions for contaminant biotransformation in natural and man-made ecosystems, respectively.

Current Trends and Potential Applications of Microbial Interactions for Human Welfare

For a long time, it was considered that interactions between microbes are only inhibitory in nature. However, latest developments in research have demonstrated that within our environment, several classes of microbes exist which produce different products upon interaction and thus embrace a wider scope of useful and potentially valuable aspects beyond simple antibiosis. Therefore, the current review explores different types of microbial interactions and describes the role of various physical, chemical, biological, and genetic factors regulating such interactions. It further explains the mechanism of action of biofilm formation and role of secondary metabolites regulating bacteria-fungi interaction. Special emphasis and focus is placed on microbial interactions which are important in medicine, food industry, agriculture, and environment. In short, this review reveals the recent contributions of microbial interaction for the benefit of mankind.

Two Types of Threonine-Tagged Lipopeptides Synergize in Host Colonization by Pathogenic Burkholderia Species

Bacterial infections of agriculturally important mushrooms and plants pose a major threat to human food sources worldwide. However, structures of chemical mediators required by the pathogen for host colonization and infection remain elusive in most cases. Here, we report two types of threonine-tagged lipopeptides conserved among mushroom and rice pathogenic Burkholderia species that facilitate bacterial infection of hosts. Genome mining, metabolic profiling of infected mushrooms, and heterologous expression of orphan gene clusters allowed the discovery of these unprecedented metabolites in the mushroom pathogen Burkholderia gladioli (haereogladin, burriogladin) and the plant pathogen Burkholderia glumae (haereoglumin and burrioglumin). Through targeted gene deletions, the molecular basis of lipopeptide biosynthesis by nonribosomal peptide synthetases was revealed. Surprisingly, both types of lipopeptides feature unusual threonine tags, which yield longer peptide backbones than one would expect based on the canonical colinearity of the NRPS assembly lines. Both peptides play an indirect role in host infection as biosurfactants that enable host colonization by mediating swarming and biofilm formation abilities. Moreover, MALDI imaging mass spectrometry was applied to investigate the biological role of the lipopeptides. Our results shed light on conserved mechanisms that mushroom and plant pathogenic bacteria utilize for host infection and expand current knowledge on bacterial virulence factors that may represent a new starting point for the targeted development of crop protection measures in the future.

Fungal Secretome Analysis via PepSAVI-MS: Identification of the Bioactive Peptide KP4 from Ustilago maydis

Fungal secondary metabolites represent a rich and largely untapped source for bioactive molecules, including peptides with substantial structural diversity and pharmacological potential. As methods proceed to take a deep dive into fungal genomes, complimentary methods to identify bioactive components are required to keep pace with the expanding fungal repertoire. We developed PepSAVI-MS to expedite the search for natural product bioactive peptides and herein demonstrate proof-of-principle applicability of the pipeline for the discovery of bioactive peptides from fungal secretomes via identification of the antifungal killer toxin KP4 from Ustilago maydis P4. This work opens the door to investigating microbial secretomes with a new lens, and could have broad applications across human health, agriculture, and food safety. Graphical Abstract.

The Hydrophobin-Like OmSSP1 May Be an Effector in the Ericoid Mycorrhizal Symbiosis

Mutualistic and pathogenic plant-colonizing fungi use effector molecules to manipulate the host cell metabolism to allow plant tissue invasion. Some small secreted proteins (SSPs) have been identified as fungal effectors in both ectomycorrhizal and arbuscular mycorrhizal fungi, but it is currently unknown whether SSPs also play a role as effectors in other mycorrhizal associations. Ericoid mycorrhiza is a specific endomycorrhizal type that involves symbiotic fungi mostly belonging to the Leotiomycetes (Ascomycetes) and plants in the family Ericaceae. Genomic and RNASeq data from the ericoid mycorrhizal fungus Oidiodendron maius led to the identification of several symbiosis-upregulated genes encoding putative SSPs. OmSSP1, the most highly symbiosis up-regulated SSP, was found to share some features with fungal hydrophobins, even though it lacks the Pfam hydrophobin domain. Sequence alignment with other hydrophobins and hydrophobin-like fungal proteins placed OmSSP1 within Class I hydrophobins. However, the predicted features of OmSSP1 may suggest a distinct type of hydrophobin-like proteins. The presence of a predicted signal peptide and a yeast-based signal sequence trap assay demonstrate that OmSSP1 is secreted. OmSSP1 null-mutants showed a reduced capacity to form ericoid mycorrhiza with Vaccinium myrtillus roots, suggesting a role as effectors in the ericoid mycorrhizal interaction.

Compost bacteria and fungi that influence growth and development of Agaricus bisporus and other commercial mushrooms

Mushrooms are an important food crop for many millions of people worldwide. The most important edible mushroom is the button mushroom (Agaricus bisporus), an excellent example of sustainable food production which is cultivated on a selective compost produced from recycled agricultural waste products. A diverse population of bacteria and fungi are involved throughout the production of Agaricus. A range of successional taxa convert the wheat straw into compost in the thermophilic composting process. These initially break down readily accessible compounds and release ammonia, and then assimilate cellulose and hemicellulose into compost microbial biomass that forms the primary source of nutrition for the Agaricus mycelium. This key process in composting is performed by a microbial consortium consisting of the thermophilic fungus Mycothermus thermophilus (Scytalidium thermophilum) and a range of thermophilic proteobacteria and actinobacteria, many of which have only recently been identified. Certain bacterial taxa have been shown to promote elongation of the Agaricus hyphae, and bacterial activity is required to induce production of the mushroom fruiting bodies during cropping. Attempts to isolate mushroom growth-promoting bacteria for commercial mushroom production have not yet been successful. Compost bacteria and fungi also cause economically important losses in the cropping process, causing a range of destructive diseases of mushroom hyphae and fruiting bodies. Recent advances in our understanding of the key bacteria and fungi in mushroom compost provide the potential to improve productivity of mushroom compost and to reduce the impact of crop disease.

Quantifying Re-association of a Facultative Endohyphal Bacterium with a Filamentous Fungus

We present here a method to quantify reassociation between facultative endohyphal bacteria and filamentous fungal hosts. Our method takes advantage of the capabilities of fungal cell walls to selectively protect internal bacteria from gentamicin treatment, an assay adapted from studies of internalized bacterial pathogens in cell culture. We report the efficacy of gentamicin to kill planktonic bacteria treated during fungal coculture, and also describe and characterize a sampling scheme to recover and quantify culturable bacteria from the growing edge of fungal mycelium in vitro. This assay enables qualitative and quantitative tests of reassociation capabilities for facultative endohyphal bacteria with host fungi and provides a means to investigate the genetic basis for these associations in a repeatable way.