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.

Genetic Diversity of the Symbiotic Fungus Epichloë festucae in Naturally Occurring Host Grass Populations

Epichloë festucae is a common symbiont of the perennial and widely distributed cool season grass, Festuca rubra. The symbiosis is highly integrated involving systemic growth of the fungus throughout above-ground host parts and vertical transmission from plant to its offspring via host seeds. However, the nature of symbiosis is labile ranging from antagonistic to mutualistic depending on prevailing selection pressures. Both the loss of fungus in the maternal host lineage and horizontal transmission through sexual spores within the host population may partly explain the detected variation in symbiosis in wild grass populations. Epichloë species are commonly considered as pathogens when they produce sexual spores and partly castrate their host plant. This is the pathogenic end of the continuum from antagonistic to mutualistic interactions. Here we examined the population genetic structure of E. festucae to reveal the gene flow, importance of reproduction modes, and alkaloid potential of the symbiotic fungus in Europe. Epichloë-species are highly dependent on the host in survival and reproduction whilst benefits to the host are largely linked to defensive mutualism attributable to fungal-origin bioactive alkaloids that negatively affect vertebrate and/or invertebrate herbivores. We detected decreased genetic diversity in previously glaciated areas compared to non-glaciated regions during the last glacial maximum period and found three major genetic clusters in E. festucae populations: southern, northeastern and northwestern Europe. Sexual reproduction may have a higher role than expected in Spanish E. festucae populations due to the predominance of unique genotypes and presence of both mating types in the region. In contrast, asexual reproduction via host seeds predominates in the Faroe Island and Finland in northern Europe due to the presence of biased mating-type ratios and large dominant genotypes in the E. festucae populations within the region. A substantially larger variation of alkaloid genotypes was observed in the fungal populations than expected, although the variability of the alkaloid genotypes within populations is considerably lower in northern than Spanish populations in southern Europe. E. festucae populations consist of different combinations of alkaloid classes from the gene clusters of ergot alkaloid and indole-terpenes, and from pyrrolopyrazine alkaloid gene. We suggest that the postglacial distribution history of the host grass, prevailing reproduction strategies of E. festucae, and local selection pressures likely explain a large part of the genetic variation observed in fungal populations among geographic regions. The identified alkaloid genotypes can be used by turfgrass breeders to improve resistance against herbivores in red fescue varieties and to develop new sustainable cultivars in Europe.

Seed-Transmitted Bacteria and Fungi Dominate Juvenile Plant Microbiomes

Plant microbiomes play an important role in agricultural productivity, but there is still much to learn about their provenance, diversity, and organization. In order to study the role of vertical transmission in establishing the bacterial and fungal populations of juvenile plants, we used high-throughput sequencing to survey the microbiomes of seeds, spermospheres, rhizospheres, roots, and shoots of the monocot crops maize (B73), rice (Nipponbare), switchgrass (Alamo), Brachiaria decumbens, wheat, sugarcane, barley, and sorghum; the dicot crops tomato (Heinz 1706), coffee (Geisha), common bean (G19833), cassava, soybean, pea, and sunflower; and the model plants Arabidopsis thaliana (Columbia-0) and Brachypodium distachyon (Bd21). Unsterilized seeds were planted in either sterile sand or farm soil inside hermetically sealed jars, and after as much as 60 days of growth, DNA was extracted to allow for amplicon sequence-based profiling of the bacterial and fungal populations that developed. Seeds of most plants were dominated by Proteobacteria and Ascomycetes, with all containing operational taxonomic units (OTUs) belonging to Pantoea and Enterobacter. All spermospheres also contained DNA belonging to Pseudomonas, Bacillus, and Fusarium. Despite having only seeds as a source of inoculum, all plants grown on sterile sand in sealed jars nevertheless developed rhizospheres, endospheres, and phyllospheres dominated by shared Proteobacteria and diverse fungi. Compared to sterile sand-grown seedlings, growth on soil added new microbial diversity to the plant, especially to rhizospheres; however, all 63 seed-transmitted bacterial OTUs were still present, and the most abundant bacteria (Pantoea, Enterobacter, Pseudomonas, Klebsiella, and Massilia) were the same dominant seed-transmitted microbes observed in sterile sand-grown plants. While most plant mycobiome diversity was observed to come from soil, judging by read abundance, the dominant fungi (Fusarium and Alternaria) were also vertically transmitted. Seed-transmitted fungi and bacteria appear to make up the majority of juvenile crop plant microbial populations by abundance, and based on occupancy, there seems to be a pan-angiosperm seed-transmitted core bacterial microbiome. Further study of these seed-transmitted microbes will be important to understand their role in plant growth and health, as well as their fate during the plant life cycle and may lead to innovations for agricultural inoculant development.

Early response of soil fungal communities to the conversion of monoculture cropland to a temperate agroforestry system

Background Alley-cropping systems in the temperate zone are a type of agroforestry in which rows of fast-growing trees are alternated with rows of annual crops. With numerous environmental benefits, temperate agroforestry is considered a promising alternative to conventional agriculture and soil fungi may play a key in maintaining productivity of these systems. Agroforestry systems that are established for more than 10 years have shown to increase the fungal biomass and impact the composition of soil fungal communities. Investigations of soil fungi in younger temperate agroforestry systems are scarce and the temporal dynamic of these changes is not understood. Methods Our study was conducted in a young poplar-based alley cropping and adjacent monoculture cropland system in an Arenosol soil in north-west Germany. We investigated the temporal dynamics of fungal populations after the establishment of agroforestry by collecting soil samples half, one, and one and a half years after conversion of cropland to agroforestry. Samples were collected within the agroforestry tree row, at 1, 7, and 24 m distance from the tree row within the crop row, and in an adjacent conventional monoculture cropland. The biomass of soil fungi, Asco-, and Basidiomycota was determined by real-time PCR. Soil fungal community composition and diversity were obtained from amplicon sequencing. Results Differences in the community composition of soil fungi in the tree row and arable land were detected as early as half a year following the conversion of monoculture cropland to agroforestry. In the tree row, soil fungal communities in the plots strongly diverged with the age of the system. The presence of young trees did not affect the biomass of soil fungi. Conclusions The composition of soil fungal communities responded rapidly to the integration of trees into arable land through agroforestry, whereas the fungal biomass was not affected during the first one and a half years after planting the trees. Fungal communities under the trees gradually diversified. Adaptation to spatially heterogeneous belowground biomass of the trees and understory vegetation or stochastic phenomena due to limited exchange among fungal populations may account for this effect; long-term monitoring might help unravelling the cause.

Redefining the Subsurface Biosphere: Characterization of Fungi Isolated From Energy-Limited Marine Deep Subsurface Sediment

The characterization of metabolically active fungal isolates within the deep marine subsurface will alter current ecosystem models and living biomass estimates that are limited to bacterial and archaeal populations. Although marine fungi have been studied for over fifty years, a detailed description of fungal populations within the deep subsurface is lacking. Fungi possess metabolic pathways capable of utilizing previously considered non-bioavailable energy reserves. Therefore, metabolically active fungi would occupy a unique niche within subsurface ecosystems, with the potential to provide an organic carbon source for heterotrophic prokaryotic populations from the transformation of non-bioavailable energy into substrates, as well as from the fungal necromass itself. These organic carbon sources are not currently being considered in subsurface energy budgets. Sediments from South Pacific Gyre subsurface, one of the most energy-limited environments on Earth, were collected during the Integrated Ocean Drilling Program Expedition 329. Anoxic and oxic sediment slurry enrichments using fresh sediment were used to isolate multiple fungal strains in media types that varied in organic carbon substrates and concentration. Metabolically active and dormant fungal populations were also determined from nucleic acids extracted from in situ cryopreserved South Pacific Gyre sediments. For further characterization of physical growth parameters, two isolates were chosen based on their representation of the whole South Pacific Gyre fungal community. Results from this study show that fungi have adapted to be metabolically active and key community members in South Pacific Gyre sediments and potentially within global biogeochemical cycles.

Conservation Status of Milkcaps (Basidiomycota, Russulales, Russulaceae), with Notes on Poorly Known Species

Mycological conservation has finally come of age. The increasingly recognized crucial role played by fungi in ecosystem functioning has spurred a wave of attention toward the status of fungal populations across the world. Milkcaps (Lactarius and Lactifluus) are a large and widespread group of ectomycorrhizal basidiomycetes; besides their ecological relevance, many species of milkcaps are of socio-economic significance because of their edibility. We analysed the presence of milkcaps in fungal Red Lists worldwide, ending up with an impressive list of 265 species assessed in various threat categories. Lactarius species are disproportionally red-listed with respect to Lactifluus (241 versus 24 species). Two species of Lactarius (L. maruiaensis and L. ogasawarashimensis) are currently considered extinct, and four more are regionally extinct; furthermore, 37 species are critically endangered at least in part of their distribution range. Several problems with the red-listing of milkcaps have been identified in this study, which overall originate from a poor understanding of the assessed species. Wrong or outdated nomenclature has been applied in many instances, and European names have been largely used to indicate taxa occurring in North America and Asia, sometimes without any supporting evidence. Moreover, several rarely recorded and poorly known species, for which virtually no data exist, have been included in Red Lists in some instances. We stress the importance of a detailed study of the species of milkcaps earmarked for insertion in Red Lists, either at national or international level, in order to avoid diminishing the value of this important conservation tool.

Biological control of soil-borne phytopathogenic fungi through onion waste composting: implications for circular economy perspective

The production of onion waste derived mainly from bulbs affected by fungal diseases, during onion classification and storage presents an important agro-environmental issue in onion production regions. Composting is an environmentally friendly strategy to recycle agricultural waste and produce organic fertilizers. Modifications of the microbial community in soil can affect the ability of pathogen propagules to survive, germinate and infect plant roots. Hence, the main objective of this work was to exploring the mechanisms involved on the presence of three soil-borne phytopathogenic fungi during the composting process of onion waste under the hypothesis if that the resulting compost effectively prevents or minimizes the dispersion of phytopathogenic fungi. To this end, three composting piles of 60 tonnes each were built by layering onion waste affected by phytopathogenic fungi and cow dung at 1:1 ratio. Temperature, moisture, pH, electrical conductivity (EC) and Aspergillus niger, Penicillium sp. and Fusarium sp. growth were monitored for 100 days. During the first 28 days of composting, the presence of phytopathogenic fungi increased significantly showing thereafter a downward trend. Final estimations of fungal populations densities indicated a predominance of A. niger and an effective reduction in the abundance of Fusarium sp. This pilot-scale work demonstrates the feasibility of composting onion waste contaminated with phytopathogenic fungi and highlights the positive environmental impact associated with this practice. Therefore, the composting of onion waste and cow dung is a feasible and sustainable procedure to recycle onion waste and to promote circular economy in onion production regions.

Generalist Taxa Shape Fungal Community Structure in Cropping Ecosystems

Fungi regulate nutrient cycling, decomposition, symbiosis, and pathogenicity in cropland soils. However, the relative importance of generalist and specialist taxa in structuring soil fungal community remains largely unresolved. We hypothesized that generalist fungi, which are adaptable to various environmental conditions, could potentially dominate the community and become the basis for fungal coexisting networks in cropping systems. In this study, we identified the generalist and habitat specialist fungi in cropland soils across a 2,200 kms environmental gradient, including three bioclimatic regions (subtropical, warm temperate, and temperate). A few fungal taxa in our database were classified as generalist taxa (~1%). These generalists accounted for >35% of the relative abundance of all fungal populations, and most of them are Ascomycota and potentially pathotrophic. Compared to the specialist taxa (5–17% of all phylotypes in three regions), generalists had a higher degree of connectivity and were often identified as hub within the network. Structural equation modeling provided further evidence that after accounting for spatial and climatic/edaphic factors, generalists had larger contributions to the fungal coexistence pattern than habitat specialists. Taken together, our study provided evidence that generalist taxa are crucial components for fungal community structure. The knowledge of generalists can provide important implication for understanding the ecological preference of fungal groups in cropland systems.