Profundae diversitas: the uncharted genetic diversity in a newly studied group of fungal root endophytes (original) (raw)
Related papers
Phytobiomes Journal, 2021
Over the last decade, the microbiome has received increasing attention as a key factor in macroorganism fitness. Sustainable pest management requires an understanding of the complex microbial endophyte communities existing symbiotically within plants and the way synthetic pesticides interact with them. Fungal endophytes are known to benefit plant growth and fitness and may deter pests and diseases. Recent advances in high-throughput sequencing (HTS) have enabled integrative microbiome studies, especially in agricultural contexts. Here, we profile the fungal endophyte community in the phyllosphere of two barley (Hordeum vulgare) cultivars exposed to two systemic foliar fungicides using metabarcoding, an HTS tool that constructs community profiles from environmental DNA. We studied the fungal nuclear ribosomal large subunit D2 and internal transcribed spacer 2 (ITS2) DNA markers through a bioinformatics pipeline introduced here. We found 88 and 128 unique amplicon sequence variants (A...
Environmental stresses are limiting factors in optimal agricultural crop yield, and these stresses, especially drought, are likely to become more acute due to future climate change. Crop wild relatives contain environmentally selected endophytes that can help to increase stress resistance. Our previous work with barley cultivars has shown a positive correlation between endophyte-induced yield increase and increasingly dry conditions. For this study, we hypothesised that a consortium of fungal endophytes recovered from a crop wild relative of barley growing in drought-stressed sites would enhance barley yield in similarly low moisture agricultural sites. We grew three barley cultivars on two environmentally distinct sites under three nitrogen (N) input regimes. We found that the endophyte inoculant induced an increase in grain dry weight at both sites, which experienced abnormally low local rainfall in the early growing season. The yield increase was 1.2 t/ha for standard N input, 1.1 t/ha for half N input and 0.6 t/ha with no N input. Additionally, on both sites, endophyte treatment with half N input recovered yield to that associated with untreated crops with standard N input for all three cultivars. Furthermore, the endophytes still retained their efficacy with regular foliar fungicidal crop treatments. These results show that endophytes recovered from sites with low and similar water status to the targeted barley growing sites can produce large and significant increases in yield regardless of nitrogen input, and hold promise for application in drought-stressed sites with limited access to expensive nitrogen fertilisers.
FEMS microbiology ecology, 2016
Endophytes have profound impacts on plants, including beneficial effects on agriculturally important traits. We hypothesized that endophytes in wild plants include beneficial endophytes that are absent or underrepresented in domesticated crops. In this work, we studied the structure of endophyte communities in wheat-related grasses, Triticum dicoccoides (TD) and Aegilops sharonensis (AS), and compared it to an endophyte community from wheat (Triticum aeastivum). Endophytes were isolated by cultivation and by cultivation-independent methods. In total, 514 intergenic spacer region sequences from single cultures were analyzed. Categorization at 97% sequence similarity resulted in 67 operational taxonomic units (OTUs) that were evenly distributed between the different plant species. A narrow core community of Alternaria spp. was found in all samples, but each plant species also contained a significant portion of unique endophytes. The cultivation independent analysis identified a larger...
Abstract- Sustainable farming systems are required to allow crops to better cope with the simultaneous multiple stresses that they grow under or are likely to be exposed to under future climate change. Fungal endophytes could form part of the solution. They have been shown to improve important agronomic traits under a single stress, but few studies have investigated the impact of endophytes on growth or disease resistance when exposed to multiple stresses. We compared the performance of the barley cultivar Propino when inoculated with five fungal root endophytes, either individually or combined, derived from wall barley (Hordeum murinum) and grown in optimal conditions (OC) and under a combined drought, heat, nutrient and pathogen stress (MS). We found a greater endophyte-induced improvement in important agronomic traits in the MS plants compared with the OC plants. For the MS plants only 13% of the controls survived to the end of the experiment compared with 80% of the endophyte treatments. In MS plants, the endophytes induced increases in the number of tillers and root and shoot biomass. The improvements were most significant for barley inoculated with a combination of all five endophytes. These results demonstrate potential for these endophytes as barley inoculants in similarly multiply-stressed farming environments. To our knowledge, this is the first experiment which has examined the effect of inoculating endophytes from a congeneric wild relative of barley onto abiotically and biotically stressed barley.
SUMMARY The use of chemicals to fertilize crops incurs economic and environmental costs and it is widely recognized that the current level of chemical fertilizer use is unsustainable in many intensive farming systems. Any methods that can reduce fertilizer input and still maintain acceptable yields would be of great benefit to both the farmer and the environment. The use of beneficial endophytes as crop inoculants may go some way towards improving crop yields beyond that achievable using fertilizer increases alone. Field trials were conducted over two seasons on three contrasting field sites to test the effects of fungal endophytes from a wild barley relative on three barley cul-tivars (Mickle, Planet and Propino). Seeds were either untreated or dressed with a consortium of four endophyte strains, and three levels of nitrogen (N) were applied to both treatments: full N, 50% N and 0 N. On the field site with the lowest overall N input, the endophyte treatment with 50% N restored yield for 'Planet' to that associated with untreated plants receiving the full N input. On the same site and with the same cultivar, endophyte treatment increased yield by 15% under full N, and by a mean 12% for all three cultivars with 50% N input. Over both seasons and all three sites, the endophyte treatment increased yield for the cultivar Planet by a mean of 9%. For the endophyte-associated increase in the variety Planet grain yield over the untreated trials strong correlations were found between increased yield and each of low rainfall, greater evaporation and greater number of degree days above the base. Furthermore, the efficacy of the endophytes was not removed by regular foliar fungicidal treatment. These results suggest that fungal endophytes can contribute to improving barley yield grown in low rainfall areas and under a range of fertilizer input regimes, provided that endophyte treatments are applied to compatible crop cultivars and sites.
2021
The root endophyte community of the grass species Elymus repens was investigated using both a culture-dependent approach and a direct amplicon sequencing method across five sites and from individual plants. There was much heterogeneity across the five sites and among individual plants. Focusing on one site, 349 OTUs were identified by direct amplicon sequencing but only 66 OTUs were cultured. The two approaches shared ten OTUs and the majority of cultured endophytes do not overlap with the amplicon dataset. Media influenced the cultured species richness and without the inclusion of 2% MEA and full-strength MEA, approximately half of the unique OTUs would not have been isolated using only PDA. Combining both culture-dependent and -independent methods for the most accurate determination of root fungal species richness is therefore recommended. High inter-plant variation in fungal species richness was demonstrated, which highlights the need to rethink the scale at which we describe end...
Molecular ecology, 2017
Studying community structure and dynamics of plant-associated fungi is the basis for unravelling their interactions with hosts and ecosystem functions. A recent sampling revealed that only a few fungal groups, as defined by ITS sequence similarity, dominate culturable root endophytic communities of non-mycorrhizal Microthlaspi spp. plants across Europe. Strains of these fungi display a broad phenotypic and functional diversity, which suggests a genetic variability masked by ITS clustering into operational taxonomic units (OTUs). The aims of this study were to identify how genetic similarity patterns of these fungi change across environments and to evaluate their ability to disperse and adapt to ecological conditions. A first ITS-based haplotype analysis of ten widespread OTUs mostly showed a low to moderate genotypic differentiation, with the exception of a group identified as Cadophora sp. that was highly diverse. A multilocus phylogeny based on additional genetic loci (TEF-1α, TUB...