Regulation of Tomato Specialised Metabolism after Establishment of Symbiosis with the Endophytic Fungus Serendipita indica

Specialised metabolites produced during plant-fungal associations often define how symbiosis between the plant and the fungus proceeds. They also play a role in the establishment of additional interactions between the symbionts and other organisms present in the niche. However, specialised metabolism and its products are sometimes overlooked when studying plant-microbe interactions. This limits our understanding of the specific symbiotic associations and potentially future perspectives of their application in agriculture. In this study, we used the interaction between the root endophyte Serendipita indica and tomato (Solanum lycopersicum) plants to explore how specialised metabolism of the host plant is regulated upon a mutualistic symbiotic association. To do so, tomato seedlings were inoculated with S. indica chlamydospores and subjected to RNAseq analysis. Gene expression of the main tomato specialised metabolism pathways was compared between roots and leaves of endophyte-colonised plants and tissues of endophyte-free plants. S. indica colonisation resulted in a strong transcriptional response in the leaves of colonised plants. Furthermore, the presence of the fungus in plant roots appears to induce expression of genes involved in the biosynthesis of lignin-derived compounds, polyacetylenes, and specific terpenes in both roots and leaves, whereas pathways producing glycoalkaloids and flavonoids were expressed in lower or basal levels.

To the study of a complex of micromycetes of wild grapes growing in the floodplain forest of the Krasnodar Territory

Для понимания формирования закономерностей грибных сообществ и реакции ампелоценозов на усиление абиотических и антропогенных нагрузок изучение ассоциаций растений и грибов имеет важное значение. Целью исследований было установить количественный и качественный состав сообществ микромицетов, ассоциированных с однолетними побегами дикорастущих растений винограда в естественных условиях пойменных лесов Краснодарского края. В результате исследований было установлено, что на поверхности однолетних лоз численность грибных популяций достигала 837,6 КОЕ/г сухого вещества в образце, произрастающем на склоне и 1191,7 КОЕ/г сухого вещества в образце лозы произрастающей в пойме реки Псебепс. В комплексе микромицетов доля гифальных грибов составляла 93,7-95,9%, дрожжи занимали 3,7-5,9 и 0,4% - дрожжеподобные грибы. Гифальные микромицеты были представлены 7 видами и стерильной формой светлого мицелия. По частоте встречаемости первое место заняли грибы родов Phoma, Botryodiplodia, Cladosporium, Alternaria (100%), второе место - Coryneum (70%). Следующую группу микромицетов с частотой встречаемости 14% составили грибы из рода Fusarium и Aspergillus niger Tiegh. В качестве доминант на однолетней лозе дикорастущего винограда отмечены микромицеты родов Phoma (46,75%) и Botryodiplodia (43,15%). Доля видов рода Cladosporium spp. и Coryneum spp. в общем объеме микромицетов составляла 4,6 и 3,85 % соответственно. Различия в количестве и соотношении таксонов грибов, исследованных биообразцов связаны, вероятно, с различным режимом влажности. To understand the pattern formation of fungal communities and the reaction of ampelocenoses to increased abiotic and anthropogenic loads, the study of plant and fungal associations is important. The aim of the research was to establish the quantitative and qualitative composition of micromycete communities associated with annual shoots of wild-growing grape plants in natural conditions of floodplain forests of the Krasnodar Territory. As a result of the research, it was found that on the surface of annual vines, the number of fungal populations reached 837,6 CFU/g of dry matter in a sample growing on a slope and 1191,7 CFU/g of dry matter in a sample of a vine growing in the floodplain of the Psebeps River. In the micromycete complex, the proportion of hyphal fungi was 93,7%-95,9%, yeast - 3,7%-5,9% and yeast-like fungi - 0,4%. Hyphal micromycetes were represented by 7 species and a sterile form of light mycelium. According to the frequency index, the first place was taken by fungi of the genera Phoma , Botryodiplodia , Cladosporium , Alternaria (100%), the second place was taken by Coryneum (70%). The next group of micromycetes with a frequency index of 14% consisted of fungi from the genus Fusarium and Aspergillus niger Tiegh. Micromycetes of the genera Phoma (46,75%) and Botryodiplodia (43,15%) were registered as dominants on the annual vines of wild-growing grapes. The proportion of species of the genera Cladosporium spp. and Coryneum spp. in the total volume of micromycetes was 4,6% and 3,85%, respectively. The differences in the number and ratio of fungal taxa and the studied biological samples are probably related to the different humidity regime.

Root-associated fungal community reflects host spatial co-occurrence patterns in a subtropical forest

Plant roots harbor and interact with diverse fungal species. By changing these belowground fungal communities, focal plants can affect the performance of surrounding individuals and the outcome of coexistence. Although highly host related, the roles of these root-associated fungal communities per se in host plant spatial co-occurrence is largely unknown. Here, we evaluated the host dependency of root-associated communities for 39-plant species spatially mapped throughout a 50-ha subtropical forest plot with relevant environmental properties. In addition, we explored whether the differentiation in root fungal associations among plant species can reflect their observed co-occurrence patterns. We demonstrated a strong host-dependency by discriminating the differentiation of root-associated fungal communities regardless of background soil heterogeneity. Furthermore, Random Forest modeling indicated that these nonrandom root fungal associations significantly increased our ability to explain spatial co-occurrence patterns, and to a greater degree than the relative abundance, phylogenetic relatedness, and functional traits of the host plants. Our results further suggested that plants harbor more abundant shared, “generalist” pathogens are likely segregated, while hosting more abundant unique, “specialist” ectomycorrhizal fungi might be an important strategy for promoting spatial aggregation, particularly between early established trees and the heterospecific adults. Together, we provide a conceptual and testable approach to integrate this host-dependent root fungal “fingerprinting” into the plant diversity patterns. We highlight that this approach is complementary to the classic cultivation-based scheme and can deepen our understanding of the community-level effect from overall fungi and its contribution to the pairwise plant dynamics in local species-rich communities.

Floral Trait and Mycorrhizal Similarity between an Endangered Orchid and Its Natural Hybrid

Hybridization can often lead to the formation of novel taxa which can have traits that resemble either or both parental species. Determining the similarity of hybrid traits to parental taxa is particularly important in plant conservation, as hybrids that form between rare and common taxa may more closely resemble a rare parental species, thereby putting the rare parental taxon at further risk of extinction via increased backcrossing and introgression. We investigated the floral (morphological and chemical) traits and orchid mycorrhizal (OrM) fungal associations of the endangered orchid Orchis patens, its more common sister species O. provincialis, and their natural hybrid O. × fallax in natural sympatric populations. We found that both morphological and chemical floral traits of O. × fallax are shared by the parents but are more similar to O. patens than O. provincialis. OrM fungi were shared among all three taxa, indicating that the availability of OrM fungi should not represent a barrier to establishment of individuals of any of these taxa. These results suggest that O. × fallax may be able to expand its distribution within a similar niche to O. patens. This highlights the importance of quantifying differences between hybrids and parental taxon in species conservation planning.

Genetic Elucidation of Quorum Sensing and Cobamide Biosynthesis in Divergent Bacterial-Fungal Associations Across the Soil-Mangrove Root Interface

Plant roots in soil host a repertoire of bacteria and fungi, whose ecological interactions could improve their functions and plant performance. However, the potential microbial interactions and underlying mechanisms remain largely unknown across the soil-mangrove root interface. We herein analyzed microbial intra- and inter-domain network topologies, keystone taxa, and interaction-related genes across four compartments (non-rhizosphere, rhizosphere, episphere, and endosphere) from a soil-mangrove root continuum, using amplicon and metagenome sequencing technologies. We found that both intra- and inter-domain networks displayed notable differences in the structure and topology across four compartments. Compared to three peripheral compartments, the endosphere was a distinctive compartment harboring more dense co-occurrences with a higher average connectivity in bacterial-fungal network (2.986) than in bacterial (2.628) or fungal network (2.419), which could be related to three bacterial keystone taxa (Vibrio, Anaerolineae, and Desulfarculaceae) detected in the endosphere as they are known to intensify inter-domain associations with fungi and stimulate biofilm formation. In support of this finding, we also found that the genes involved in cell-cell communications by quorum sensing (rhlI, lasI, pqsH, and lasR) and aerobic cobamide biosynthesis (cobG, cobF, and cobA) were highly enriched in the endosphere, whereas anaerobic cobamide biosynthesis (encoded by cbiT and cbiE) was dominant in three peripheral compartments. Our results provide genetic evidence for the intensified bacterial-fungal associations of root endophytes, highlighting the critical role of the soil-root interface in structuring the microbial inter-domain associations.

Advances in understanding of mycorrhizal-like associations in bryophytes

Mutually beneficial associations between plants and soil fungi, mycorrhizas, are one of the most important terrestrial symbioses. These partnerships are thought to have propelled plant terrestrialisation some 500 million years ago and today they play major roles in ecosystem functioning. It has long been known that bryophytes harbour, in their living tissues, fungal symbionts, recently identified as belonging to the three mycorrhizal fungal lineages Glomeromycotina, Ascomycota and Basidiomycota. Latest advances in understanding of fungal associations in bryophytes have been largely driven by the discovery, nearly a decade ago, that early divergent liverwort clades, including the most basal Haplomitriopsida, and some hornworts, engage with a wider repertoire of fungal symbionts than previously thought, including endogonaceous members of the ancient sub-phylum Mucoromycotina. Subsequent global molecular and cytological studies have revealed that Mucoromycotina symbionts, alongside Glomeromycotina, are widespread in both complex and simple thalloid liverworts and throughout hornworts, with physiological studies confirming that, in liverworts at least, these associations are mycorrhizal-like, and highlighting important functional differences between Mucoromycotina and Glomeromycotina symbioses. Whether a more prominent role of Mucoromycotina symbionts in plant nitrogen nutrition, as identified in liverworts, extends to other plant lineages, including the flowering plants, is a major topic for future research. The latest finding that ascomycete symbionts of leafy liverworts are not restricted to one fungus, Rhizoscyphus ericae, but include species in the genus Meliniomyces, as shown here in Mylia anomala, together with the recent demonstration that R. ericae forms nutritional mutualisms with the rhizoids of Cephalozia bicuspidata, fill other major gaps in our growing knowledge of fungal associations across land plants.

Diversity of Endo and Exo-Bacteria Associated With Fungi Isolated From Plant Rhizospheres: A Pilot Study

Background: Over the past several years, the scientific community has described the diversity of microbial communities in a variety of soils associated with plants, but at present, little is known about the specific diversity of the soil fungal microbiome involving bacteria colonizing the surface of fungi (i.e., exo-bacteria) or existing within fungal hypha (i.e., endobacteria). This study aimed to collect, identify, and characterize several fungi and their associated (endo- and exo-) microbiome obtained from the rhizosphere of six different plants. Microcosm devices called fungal highway columns, containing one of four plant-based media as attractants, were placed in the rhizosphere of six different plants. The isolated fungi and their associated endo- and exo- bacteria were identified by sequencing of the ITS (fungi) or 16S (bacteria) rRNA regions, followed by Scanning Electron Microscope (SEM), and fluorescence in situ hybridization (FISH) imaging.Results: Most of the fungi recovered are known plant pathogens, such as Fusarium, Pleosporales, and Cladosporium together with species associated with the soil, e.g. Kalmusia. The exo-bacteria recovered were previously described as plant promoters, such as Bacillus, Rhizobium, Acinetobacter or Ensifer. The interactions between fungi and exo-bacteria recovered from fungal highway columns were further investigated via confrontation assays. From the reconstruction of the potential co-occurring bacterial-fungal associations in the rhizosphere, we discovered that the most promiscuous exo-bacterium group (associated with diverse fungi) was Bacillus. From the study of the endobacterial community, emerged a core of shared endosymbionts with a potential implication in the nitrogen cycle.Conclusions: The present study demonstrated the importance of selecting and studying cultivable fungi and bacteria from the rhizosphere. Our findings demonstrated that at the rhizosphere level, the range of interactions between fungi and bacteria, both internal and external to the fungal hypha, could vary even among closely related species.

Problematic issues of diagnosis and treatment of vulvovaginitis of mixed bacterial-candidiasis etiology

The aim of the study is to evaluate the effectiveness of modern antiseptic agent Gynodek in the treatment of mixed bacterial-candidiasis vulvovaginitis.Materials and methods. There were 67 patients with bacterial-candidiasis vulvovaginitis under observation. The diagnosis of candidiasis infection was verified according to the data of clinical and laboratory research methods. Patients received vaginal gel Gynodek 5 ml once a day for 7 days. The effectiveness of treatment was assessed according to the data of the clinical examination before treatment and on the 7th day of observation, and according to the laboratory (bacterioscopic, bacteriological) data before and after treatment. Complete clinical and bacterial debridement was criteria of the treatment effectiveness.Results and discussion. The clinical picture of bacterial-fungal vulvovaginitis was characterized by a decrease in the number and severity of symptoms such as hyperemia and edema of the mucous membrane, discharge from the genital tract was not typical.There were no complaints in 95.5% of the examined women after end of therapy, there were no objective symptoms in all women on the 7th day of treatment. Bacteriological examination after 2 weeks confirmed the therapy effectiveness in 86.6% of women. Peptostreptococcus spp. after treatment sowed at significant concentrations 106–107 CFU/ml only in 1.5% of patients, Streptococcus spp. in 8.9% of women, Candida albicans in 13.4%. Lactobacilli in the amount of 107 CFU/ml were in 86.6% of patients, which indicates a rapid restoration of normal vaginal microflora.Conclusions. Bacterial-fungal associations of microorganisms in the vaginal biotope lead to a complex clinical symptoms, which makes it difficult to make a timely diagnosis. Gynodek vaginal gel is highly effective against gram-positive, gram-negative and fungal microflora, which makes it the drug of choice in the treatment of bacterial-candidiasis vulvovaginitis. Gynodek creates a comfortable pH, promotes the rapid restoration of own lactoflora, and increases the functional activity of the vaginal mucosa epithelium, which ensures the prevention of vaginal infection recurrence.