Fusarium species, recognised as global priority pathogens, frequently induce severe diseases in crops; however, certain species exhibit alternative symbiotic lifestyles and are either non-pathogenic or endophytic. In this study, we characterised the mutualistic relationship between the eFp isolate of F. pseudograminearum and five poplar species, resulting in formation root structures reminiscent of ectomycorrhizal (ECM) symbiosis. This functional symbiosis is evidenced by enhanced plant growth, reciprocal nutrient exchange, improved nitrogen and phosphorus uptake and upregulation of root sugar transporter gene expression (PtSweet1). Comparative and population genomics confirmed that eFp maintains a structurally similar genome, but exhibits significant divergence from ten conspecific pathogenic isolates. Notably, eFp enhanced the growth of diverse plant lineages (Oryza, Arabidopsis, Pinus and non-vascular liverworts), indicating a near-complete loss of virulence. Although this specialised symbiosis has only been established in vitro, it holds significant value in elucidating the evolutionary track from endophytic to mycorrhizal associations.

Modern evolutionary theory and population genetics posit that adaptation and habitat expansion of plants result from processes exclusive to their genomes. Here, we present studies showing that plants can grow across complex habitat gradients by modulating symbiotic associations with Class 2 fungal endophytes. Endophyte analysis of three native (Leymus mollis, Distichlis spicata, and Salicornia pacifica) and one invasive (Spartina anglica) plant growing across adjacent microhabitats in the San Juan Archipelago altered associations with Class 2 fungal endophytes in response to soil salinity levels. At the microhabitat interfaces where the gradation of salinity varied, the plants were colonized by endophytes from both microhabitats. A reciprocal transplant study along a salt gradient demonstrated that Leymus mollis (dunegrass) required endophytes indigenous to each microhabitat for optimal fitness and/or survival. In contrast, when dunegrass and Grindelia integrifolia (gumweed) were found growing in low salinity, but high drought habitats, these plant species had their own unique dominant endophyte association regardless of geographic proximity and conferred drought but not high salt stress tolerance. Modulation of endophyte abundance occurred in planta based on the ability of the symbiont to confer tolerance to the stress imposed on plants. The ability of an endophyte to confer appropriate stress tolerance resulted in a significant increase of in planta fungal abundance. Conversely, the inability of an endophyte to confer stress tolerance resulted in a decrease of in planta fungal abundance. Our studies indicate that Class 2 fungal endophytes can provide a symbiotic mechanism for niche expansion and phenotypic plasticity across environmental gradients.

Studies were undertaken to determine if fungal endophytes from plants in stressful habitats could be commercialized to generate climate resilient crop plants. Fungal endophytes were isolated from weedy rice plants and grasses from South Korea and the USA, respectively. Endophytes (Curvularia brachyspora and Fusarium asiaticum) from weedy rice plants from high salt or drought stressed habitats in South Korea conferred salt and drought stress tolerance to weedy rice and commercial varieties reflective of the habitats from which they were isolated. Fungal endophytes isolated from grasses in arid habitats of the USA were identified as Trichoderma harzianum and conferred drought and heat stress tolerance to monocots and eudicots. Two T. harzianum isolates were exposed to UV mutagenesis to derive strains resistant to fungicides in seed treatment plant protection packages. Three strains that collectively had resistance to commonly used fungicides were used for field testing. The three-strain mixture (ThSM3a) increased crop yields proportionally to the level of stress plants experienced with average yields up to 52% under high and 3–5% in low stress conditions. This study demonstrates fungal endophytes can be developed as viable commercial tools for rapidly generating climate resilient crops to enhance agricultural sustainability.

Genus Fusarium (Ascomycota, Hypocreales, Nectriaceae) includes many economically important plant pathogens that cause devastating diseases of a wide range of crops and trees. Interestingly, there is increasing evidence that some Fusarium species also live as endophytes and benefit plant growth and stress tolerance. In this work, we sequence the whole genomes of endophytic F. culmorum and F. pseudograminearum, isolated from a coastal dunegrass (Leymus mollis), using long-read single-molecule real-time sequencing technology. Their genomes are assembled into four chromosomes and a mitochondrial genome with a total assembly size of 40.05 and 42.90 M, respectively. This resource should not only facilitate functional studies designed to better understand what makes the two Fusarium species such successful plant-beneficial fungi but should also reveal their genome evolution and adaptation. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

All plants in natural ecosystems are thought to be symbiotic with mutualistic fungal endophytes that can significantly improve plant fitness by enhancing root growth, fertility, nutrient acquisition and biotic or abiotic stress tolerance. Recently, Adaptive Symbiotic Technologies developed the product line BioEnsure® comprised of fungal endophytes that confer abiotic stress tolerance (drought, temperature, salinity) to food crops (www.adsymtech.com). These endophytes communicate similarly with monocots and eudicots to enhance crop production on marginal lands and mitigate the impacts of high daytime or nighttime temperatures on crop fertilization. Yield benefits in endophyte-colonized plants are remarkable and directly proportional to stress levels with average yield increases of 3-5% above control plants under low stress and >26% under high stress. The relationship between stress and yield enhancement was best exemplified in Rajasthan, India, where BioEnsure®-treated pearl millet and mung bean seeds were provided to 400 small landholding farmers. Under the hot, dry growing conditions that are typical in Rajasthan, the average yield increases were 29% for pearl millet and 64% for mung bean compared to untreated plants. This demonstrated the power of this technology to increase food security, animal fodder, carry-over seed and revenues. Interest in the USA is growing with BioEnsure®-treated seeds planted in 300,000 acres in 2017 and 900,000 acres in 2018, and >2,000,000 acres are projected for 2019.

Cold environments represent the largest fraction of Earth's biosphere, and are known habitats for cold-adapted microorganisms. The aim of this study was to assess the occurrence and biodiversity of cold-adapted fungi associated with the Castaño Overo glacier, Mount Tronador, Patagonia, Argentina. Samples of naked soil, glacial ice and snow were collected and analyzed using tag-encoded 454 pyrosequencing of the nuclear ribosomal internal transcribed spacer (ITS). A total of 1082 OTUs (operational taxonomic units) and 151,669 sequences were obtained. OTUs obtained from soil samples corresponded mainly to the phylum Ascomycota, whereas for snow and ice samples the phylum Basidiomycota was the most represented group. Metabarcoding analysis showed high biodiversity in glacial environments and allowed the detection of hitherto unknown taxa for Patagonia. To the best of our knowledge, this is the first report of fungal diversity in an extreme glacial environment of Patagonian Argentina using amplicon sequencing.

In this work, we explore the biodiversity of culturable microfungi from the water column of a permanently ice-covered lake in Taylor Valley, Antarctica from austral field seasons in 2003, 2008 and 2010, as well as from glacial stream input (2010). The results revealed that there was a sharp decline in total culturable fungal abundance between 9 and 11 m lake depth with a concurrent shift in diversity. A total of 29 species were identified from all three water sources with near even distribution between Ascomycota and Basidomycota (15 and 14 respectively). The most abundant taxa isolated from Lake Fryxell in 2008 were Glaciozyma watsonii (59%) followed by Penicillium spp. (10%), both of which were restricted to 9 m and above. Although seven species were found below the chemocline of 11 m in 2008, their abundance comprised only 10% of the total culturable fungi. The taxa of isolates collected from glacial source input streams had little overlap with those found in Lake Fryxell. The results highlight the spatial discontinuities of fungal populations that can occur within connected oligotrophic aquatic habitats.

Root microbiota is a crucial determinant of plant productivity and stress tolerance. Here, we hypothesize that the superior halo-tolerance of seepweed Suaeda salsa is tightly linked to a specialized belowground microbiome. To test this hypothesis, we performed a phylogenetic trait-based framework analysis based on bacterial 16S rRNA gene and fungal nuclear rRNA internal transcribed spacer profiling. Data showed that the dominant α-proteobacteria and γ-proteobacteria communities in bulk soil and root endosphere tend to be phylogenetically clustered and at the same time exhibit phylogenetic over-dispersion in rhizosphere. Likewise, the dominant fungal genera occurred at high phylogenetic redundancy. Interestingly, we found the genomes of rhizospheric and endophytic bacteria associated with S. salsa to be enriched in genes contributing to salt stress acclimatization, nutrient solubilization and competitive root colonization. A wide diversity of rhizobacteria with similarity to known halotolerant taxa further supported this interpretation. These findings suggest that an ecological patterned root-microbial interaction strategy has been adopted in S. salsa system to confront soil salinity. We also demonstrated that the potential core microbiome members improve non-host plants growth and salt tolerance. This work provides a platform to improve plant fitness with halophytes-microbial associates and novel insights into the functions of plant microbiome under salinity.

DATA REPORT article Front. Microbiol., 17 September 2015Sec. Plant Pathogen Interactions Volume 6 - 2015 | https://doi.org/10.3389/fmicb.2015.00978

Major threats to agricultural sustainability in the 21st century are drought, increasing temperatures, soil salinity and soilborne pathogens, all of which are being exacerbated by climate change and pesticide abolition and are burning issues related to agriculture in the Middle East. We have found that Class 2 fungal endophytes adapt native plants to environmental stresses (drought, heat and salt) in a habitat-specific manner, and that these endophytes can confer stress tolerance to genetically distant monocot and eudicot hosts. In the past, we generated a uv non-pathogenic endophytic mutant of Colletotrichum magna (path-1) that colonized cucurbits, induced drought tolerance and enhanced growth, and protected 85% - 100% against disease caused by certain pathogenic fungi. We propose: 1) utilizing path-1 and additional endophtyic microorganisms to be isolated from stress-tolerant local, wild cucurbit watermelon, Citrulluscolocynthis, growing in the Dead Sea and Arava desert areas, 2) generate abiotic and biotic tolerant melon crop plants, colonized by the isolated endophytes, to increase crop yields under extreme environmental conditions such as salinity, heat and drought stress, 3) manage soilborne fungal pathogens affecting curubit crop species growing in the desert areas. This is a unique and novel "systems" approach that has the potential to utilize natural plant adaptation for agricultural development. We envisage that endophyte-colonized melons will eventually be used to overcome damages caused by soilborne diseases and also for cultivation of this crop, under stress conditions, utilizing treated waste water, thus dealing with the limited resource of fresh water.

Endophytic associations with plants have a beneficial effect for many different plant species with some of them being host specific. Several endophytes isolated from poplar and willow were screened for their effects on commercially important crops including corn, tomato, pepper, squash, sunflower, and grasses. Most of these endophytes produce growth hormones such as indoleacetic acid (IAA) and have the nitrogenase gene required for nitrogen fixation. The effects of these isolates on plant growth and yield were evaluated under greenhouse conditions. We found that inoculated plants not only had better viability and earlier flowering and fruiting, they also had increased plant growth and fruit yields when grown in nitrogen-limited soil. In a particular variety of perennial rye grass, the endophytes increased the total nitrogen content of the plants, indicative of nitrogen fixation, in addition to promoting plant growth. The use of specific endophytes may be preferable to the use of chemical fertilizers because of the monetary and environmental costs, contributing to more sustainable agricultural systems.

Climate change and catastrophic events have contributed to rice shortages in several regions due to decreased water availability and soil salinization. Although not adapted to salt or drought stress, two commercial rice varieties achieved tolerance to these stresses by colonizing them with Class 2 fungal endophytes isolated from plants growing across moisture and salinity gradients. Plant growth and development, water usage, ROS sensitivity and osmolytes were measured with and without stress under controlled conditions. The endophytes conferred salt, drought and cold tolerance to growth chamber and greenhouse grown plants. Endophytes reduced water consumption by 20-30% and increased growth rate, reproductive yield, and biomass of greenhouse grown plants. In the absence of stress, there was no apparent cost of the endophytes to plants, however, endophyte colonization decreased from 100% at planting to 65% compared to greenhouse plants grown under continual stress (maintained 100% colonization). These findings indicate that rice plants can exhibit enhanced stress tolerance via symbiosis with Class 2 endophytes, and suggest that symbiotic technology may be useful in mitigating impacts of climate change on other crops and expanding agricultural production onto marginal lands.