Diverse Plant-Associated Pleosporalean Fungi from Saline Areas: Ecological Tolerance and Nitrogen-Status Dependent Effects on Plant Growth

Endophytic fungus Stagonosporopsis ajaci NEAU-BLH1 from Adonis amurensis enhances seed germination under low-temperature stress and increases grain yield in direct-seeded rice

Rice direct-seeding technology is regarded as a promising alternative to traditional transplanting due to its labor- and water-saving benefits. However, poor seedling emergence and growth under low-temperature stress remain major obstacles to its widespread adoption in Heilongjiang Province, China. Here, we isolated an endophytic fungus Stagonosporopsis ajaci NEAU-BLH1 from the cold-resistant plant Adonis amurensis, which effectively enhanced rice seed germination and seedling growth under low-temperature stress. Two years of pot and field experiments demonstrated that soaking rice seeds in a spore suspension of NEAU-BLH1 significantly increased tillering, resulting in a 16.0-47.8 % improvement in yield for direct-seeded rice. Mechanistic investigations revealed that NEAU-BLH1 treatment elevated gibberellin levels and reduced abscisic acid, accelerating starch hydrolysis into soluble sugars, thus improving germination under low temperature. Comprehensive physiological, transcriptomic, and metabolomic analyses indicated that NEAU-BLH1 enhances seedling growth by boosting respiratory metabolism, mitigating oxidative damage, and modulating hormone pathways. These findings indicate that seed-soaking with NEAU-BLH1 has good potential to enhance seed germination under low-temperature stress and increases grain yield in direct-seeded rice.

Symbiotic fungal inoculation promotes the growth of Pinus tabuliformis seedlings in relation to the applied nitrogen form

BACKGROUND

Nitrogen (N) deposition has become a major driving factor affecting the balance of terrestrial ecosystems, changing the soil environment, element balance and species coexistence relationships, driving changes in biodiversity and ecosystem structure and function. Human-induced nitrogen input leads to a high NH4+/ NO3- ratio in soil. However, relatively few studies have investigated the effects of different nitrogen sources on forest plant-microbial symbionts. In this study, the effects of four nitrogen sources, N free, NH4Cl, L-glutamic acid, and Na(NO3)2 (N-, NH4+-N, Org-N, and NO3--N) on four fungal species, Suillus granulatus (Sg), Pisolithus tinctorius (Pt), Pleotrichocladium opacum (Po), and Pseudopyrenochaeta sp. (Ps), which were isolated from the roots of Pinus tabulaeformis, were studied in vitro. The effects of inoculation with the four fungi on the growth performance, nutrient uptake and nitrogen metabolism-related enzymes of Pinus tabuliformis under different nitrogen source conditions were subsequently studied.

RESULTS

The biomass and N concentration of the Sg and Po strains were the highest under the NO3--N treatment, while the biomass and N concentration of the Pt and Ps strains were significantly greater under the NH4+-N and NO3--N treatments than under the Org-N and N- treatments. All four fungi could effectively colonize the roots of P. tabuliformis and formed a symbiotic relationship with it. Under all nitrogen conditions, the inoculation of the four fungi had positive effects on the growth, root development and nutrient concentration of the P. tabuliformis seedlings. Under the Org-N and NO3--N treatments, the nitrate reductase (NR) activity of the inoculated plants was significantly greater than that of the noninoculated control (CK) plants. Under all nitrogen conditions, the glutamine synthetase (GS) activity of the inoculated plants was significantly greater than that of the CK plants.

CONCLUSIONS

The four fungi can establish good symbiotic relationships with P. tabuliformis seedlings and promote their growth and development under different nitrogen source treatments.

Halophilomyces hongkongensis, a Novel Species and Genus in the Lulworthiaceae with Antibacterial Potential, Colonizing the Roots and Rhizomes of the Seagrass Halophila ovalis

Seagrass serves as a quintessential reservoir for obligate marine Lulworthiaceae fungi. Our current knowledge of the mycological diversity associated with seagrass in Hong Kong remains poor. We analyzed the diversity of fungi associated with the most widely distributed seagrass species in Hong Kong Halophila ovalis (Hydrocharitaceae), using a combination of culture-based methods and high-throughput amplicon sequencing. Halophilomyces hongkongensis, a novel fungal species in a newly proposed genus within the Lulworthiaceae family, was isolated from H. ovalis roots and rhizomes. The novel fungus showed distinct morphological characteristics, while both combined 18S-28S and internal transcribed spacer (ITS) phylogenetic trees based on maximum likelihood and Bayesian methods supported its discrimination from other existing Lulworthiaceae members. The ITS2 region in the Illumina sequencing results of multiple H. ovalis compartments, water, and adjacent non-seagrass sediments revealed continuous recruitment of H. hongkongensis by H. ovalis throughout the year despite dramatically fluctuating environmental conditions, with remarkably high proportions of this taxon found in root and rhizome internal tissues, possibly indicating a strong and specialized relationship established between the Lulworthiaceae fungal partner and its seagrass host. The inhibitory abilities exhibited by H. hongkongensis against Staphylococcus aureus SA29213 and ATCC 43300 (methicillin-resistant) may imply its capacity in producing (novel) antibacterial compounds. The discovery of H. hongkongensis as the first novel Lulworthiaceae taxon in Hong Kong, along with its distributional pattern in the seagrass meadow, provides valuable insights into the systematics and ecology of this strictly marine fungal family.

Comparative Bioactive Compounds and Mineral Properties of South African and Lesotho Artemisia afra (Jacq.) Genotypes

Artemisia afra is a plant that grows in the northern, central, and coastal regions of South Africa, as well as in neighboring countries such as Eswatini and Lesotho. These phytochemicals can be used as active compounds in plant-based medicine. Therefore, it is important to determine how plant minerals and phytochemicals, particularly bioactive compounds, are affected by the geolocation in which they grow. This study aimed to evaluate the mineral and phytochemical properties of A. afra genotypes in the southern regions of Africa. Leaf samples of A. afra genotypes were collected from Lesotho, in Mohale's Hoek and Roma. In South Africa, leaf samples were collected in Wepener and Hobhouse, and 80 plants were randomly selected for phytochemical and mineral analyses. This study reveals that phosphorus, calcium, potassium, iron, and zinc loaded positively to the first principal component, while copper loaded positively to the second principal component with variabilities of 29.95% and 21.12%, respectively. Furthermore, both the Mohale's Hoek and Hobhouse genotypes exhibited relatively high levels of ascorbic acid, phenolic compounds, flavonoids, and tannins. It is worth noting that genotypes from Roma and Wepener showed higher levels of foliar magnesium. Thus, the Mohale's Hoek and Hobhouse genotypes could be recommended for their better phytochemical contents.

Effect of arbuscular mycorrhizal symbiosis on growth and biochemical characteristics of Chinese fir (Cunninghamia lanceolata) seedlings under low phosphorus environment

Background

The continuous establishment of Chinese fir (Cunninghamia lanceolata) plantations across multiple generations has led to the limited impact of soil phosphorus (P) on tree growth. This challenge poses a significant obstacle in maintaining the sustainable management of Chinese fir.

Methods

To investigate the effects of Arbuscular mycorrhizal fungi (AMF) on the growth and physiological characteristics of Chinese fir under different P supply treatments. We conducted an indoor pot simulation experiment in the greenhouse of the Forestry College of Fujian Agriculture and Forestry University with one-and-half-year-old seedlings of Chinese fir from March 2019 to June 2019, with the two P level treatment groups included a normal P supply treatment (1.0 mmol L-1 KH2PO4, P1) and a no P supply treatment (0 mmol L-1 KH2PO4, P0). P0 and P1 were inoculated with Funneliformis mosseae (F.m) or Rhizophagus intraradices (R.i) or not inoculated with AMF treatment. The AMF colonization rate in the root system, seedling height (SH), root collar diameter (RCD) growth, chlorophyll (Chl) photosynthetic characteristics, enzyme activities, and endogenous hormone contents of Chinese fir were estimated.

Results

The results showed that the colonization rate of F.m in the roots of Chinese fir seedlings was the highest at P0, up to 85.14%, which was 1.66 times that of P1. Under P0 and P1 treatment, root inoculation with either F.m or R.i promoted SH growth, the SH of R.i treatment was 1.38 times and 1.05 times that of F.m treatment, respectively. In the P1 treatment, root inoculation with either F.m or R.i inhibited RCD growth. R.i inhibited RCD growth more aggressively than F.m. In the P0 treatment, root inoculation with F.m and R.i reduced the inhibitory effect of phosphorus deficiency on RCD. At this time, there was no significant difference in RCD between F.m, R.i and CK treatments (p < 0.05). AMF inoculation increased Fm, Fv, Fv/Fm, and Fv/Fo during the chlorophyll fluorescence response in the tested Chinese fir seedlings. Under the two phosphorus supply levels, the trend of Fv and Fm of Chinese fir seedlings in different treatment groups was F.m > R.i > CK. Under P0 treatment, The values of Fv were 235.86, 221.86 and 147.71, respectively. The values of Fm were 287.57, 275.71 and 201.57, respectively. It increased the antioxidant enzyme activity and reduced the leaf's malondialdehyde (MDA) content to a certain extent.

Conclusion

It is concluded that AMF can enhance the photosynthetic capacity of the host, regulate the distribution of endogenous hormones in plants, and promote plant growth by increasing the activity of antioxidant enzymes. When the P supply is insufficient, AMF is more helpful to plants, and R.i is more effective than F.m in alleviating P starvation stress in Chinese fir.

Phosphorus/nitrogen sensing and signaling in diverse root-fungus symbioses

Establishing mutualistic relationships between plants and fungi is crucial for overcoming nutrient deficiencies in plants. This review highlights the intricate nutrient sensing and uptake mechanisms used by plants in response to phosphate and nitrogen starvation, as well as their interactions with plant immunity. The coordination of transport systems in both host plants and fungal partners ensures efficient nutrient uptake and assimilation, contributing to the long-term maintenance of these mutualistic associations. It is also essential to understand the distinct responses of fungal partners to external nutrient levels and forms, as they significantly impact the outcomes of symbiotic interactions. Our review also highlights the importance of evolutionarily younger and newly discovered root-fungus associations, such as endophytic associations, which offer potential benefits for improving plant nutrition. Mechanistic insights into the complex dynamics of phosphorus and nitrogen sensing within diverse root-fungus associations can facilitate the identification of molecular targets for engineering symbiotic systems and developing plant phenotypes with enhanced nutrient use efficiency. Ultimately, this knowledge can inform tailored fertilizer management practices to optimize plant nutrition.

Growth of alfalfa in the presence of metabolites from a dark septate endophyte strain Alternaria sp. 17463 cultured with a nonionic surfactant and emulsifier

AIM

Dark septate endophytes (DSE) were widely used in the agriculture and ecological restoration. The objective of this work was to assess the effect of culture media nonionic surfactant and emulsifier on the biomass and metabolites of DSE strain Alternaria sp. 17463.

METHODS AND RESULTS

Changes in the composition of DSE metabolites following the addition of Tween 80 during liquid culture of a DSE fungus were analyzed and used in growth tests of alfalfa.Shaking flask fermentation was carried out and the surfactant was fed to the fungus during the fermentation. The residual sugar content and pH declined significantly in the medium and the biomass of DSE increased by 7.27% over controls with no surfactant. Metabolomic analysis showed that adding the surfactant significantly increased the content of 63 metabolites (P < 0.05). These include lipids and lipid-like molecules, organooxygen compounds, amino acids and organic acids, and flavonoids. Enrichment analysis of metabolic pathways indicates that surfactant addition promoted carbohydrate metabolism and amino acid synthesis. A plant hydroponic experiment indicated that these changes in metabolites altered the root structure of alfalfa seedlings. They also promoted significant increases in root length and root surface area, and increased alfalfa total biomass by 50.2%.

CONCLUSIONS

The addition of the surfactant promoted sugar utilization by the DSE fungus and increased the synthesis of lipids and amino acids, resulting in the ability of the fungal metabolites to change root structure and promote plant growth.

Effect of Glomus intraradices on root morphology, biomass production and phosphorous use efficiency of Chinese fir seedlings under low phosphorus stress

Introduction

Available phosphorus (P) scarcity in the highly weathered soils of the subtropical forests in southern China is a serious concern. To ensure whether inoculation of arbuscular mycorrhizal fungi (AMF) with Chinese fir (Cunninghamia lanceolata) under low P stress conditions could promote its growth and P utilization capacity, an indoor pot simulation experiment was carried out with the different P supply treatments and Chinese fir seedlings as the tested material.

Methods

The experiment had two P supply treatments, no P supply (P0, 0 mmol·L-1 KH2PO4) and normal P supply (P1, 1.0 mmol·L-1 KH2PO4). The seedling in each P supply treatment was inoculated with Glomus intraradices (Gi), a widespread species of AMF in the natural environment, and with no AMF inoculation as a control treatment (CK). The Gi infection rate in the root system, root cortex tissue dissolution rate, root morphological indexes and biomass, whole plant P use efficiency, and root P use efficiency of Chinese fir were determined under different treatment conditions.

Results and Discussion

The results showed that P0 treatment significantly increased the Gi infection rate (p< 0.05). After inoculating AMF with different P supply treatments, the root cortex tissue dissolution rate was considerably enhanced. In contrast, the Chinese fir's root length and surface area were reduced; however, the root volume did not change significantly. The average root diameter in the P0 treatment and inoculated with AMF was significantly more prominent than in the uninoculated treatment (p< 0.05). The root biomass and root-to-shoot ratio at different P supply treatments were significantly higher in the Gi infection treatment than in the CK group. Under different P supply treatments, root inoculation with Gi promoted root P use efficiency and whole plant P use efficiency. In conclusion, low P stress condition promoted the colonization of AMF in the root system, increased the dissolution of root cortex tissue, root volume, and the average diameter, and promoted root biomass accumulation and P use efficiency.

A facultative ectomycorrhizal association is triggered by organic nitrogen

Increasing nitrogen (N) deposition often tends to negatively impact the functions of belowground ectomycorrhizal networks, although the exact molecular mechanisms underlying this trait are still unclear. Here, we assess how the root-associated fungus Clitopilus hobsonii establishes an ectomycorrhiza-like association with its host tree Populus tomentosa and how this interaction is favored by organic N over mineral N. The establishment of a functional symbiosis in the presence of organic N promotes plant growth and the transfer of ¹⁵N from the fungus to above ground plant tissues. Genomic traits and in planta transcriptional signatures suggest that C. hobsonii may have a dual lifestyle with saprotrophic and mutualistic traits. For example, several genes involved in the digestion of cellulose and hemicellulose are highly expressed during the interaction, whereas the expression of multiple copies of pectin-digesting genes is tightly controlled. Conversely, the nutritional mutualism is dampened in the presence of ammonium (NH₄⁺) or nitrate (NO₃^-). Increasing levels of NH₄⁺ led to a higher expression of pectin-digesting genes and a continuous increase in hydrogen peroxide production in roots, whereas the presence of NO₃^- resulted in toxin production. In summary, our results suggest that C. hobsonii is a facultative ectomycorrhizal fungus. Access to various forms of N acts as an on/off switch for mutualism caused by large-scale fungal physiological remodeling. Furthermore, the abundance of pectin-degrading enzymes with distinct expression patterns during functional divergence after exposure to NH₄⁺ or organic N is likely to be central to the transition from parasitism to mutualism.

Fungi Classification in Various Growth Stages Using Shortwave Infrared (SWIR) Spectroscopy and Machine Learning

Dark septate endophytes (DSEs) fungi are beneficial to host plants with regard to abiotic stress. Here, we examined the capability of SWIR spectroscopy to classify fungus types and detected the growth stages of DSEs fungi in a timely, non-destructive and time-saving manner. The SWIR spectral data of five DSEs fungi in six growth stages were collected, and three pre-processing methods and sensitivity analysis (SA) variable selection methods were performed using a machine learning model. The results showed that the De-trending + first Derivative (DET_FST) processing spectra combined with the support vector machine (SVM) model yielded the best classification accuracy for fungi classification at different growth stages and growth stage detection on different fungus types. The mean accuracy of generic model for fungi classification and growth stage detection are 0.92 and 0.99 on the calibration set, respectively. Seven important bands, 1164, 1456, 2081, 2272, 2278, 2448 and 2481 nm, were found to be related to the SVM fungi classification. This study provides a rapid and efficient method for the classification of fungi in different growth stages and the detection of fungi growth stage of various types of fungi and could serve as a tool for fungi study.

Plant association with dark septate endophytes: When the going gets tough (and stressful), the tough fungi get going

Dark septate endophytes (DSEs) comprise a diverse and ubiquitous group of fungal generalists with broad habitat niches that robustly colonize the roots of plants in stressful environments. DSEs possess adaptation strategies that determine their high tolerance to heavy metal (HM) contamination, drought, and salinity. Most DSEs developed efficient melanin-dependent and melanin-independent mechanisms of HM detoxification and osmoprotection, including intracellular immobilization and extracellular efflux of HMs and excess ions, and the scavenging of reactive oxygen species. DSEs form mutualistic relationship with plants according to the hypothesis of "habitat-adapted associations", supporting the survival of their hosts under stressful conditions. As saprophytes, DSEs mineralize a complex soil substrate improving plants' nutrition and physiological parameters. They can protect the host plant from HMs by limiting HM accumulation in plant tissues and causing their sequestration in root cell walls as insoluble compounds, preventing further HM translocation to shoots. The presence of DSE in drought-affected plants can substantially ameliorate the physiology and architecture of root systems, improving their hydraulic properties. Plant growth-promoting features, supported by the versatility and easy culturing of DSEs, determine their high potential to enhance phytoremediation and revegetation projects for HM-contaminated, saline, and desertic lands reclamation.

Fungal endophytes from salt-adapted plants confer salt tolerance and promote growth in wheat (Triticum aestivum L.) at early seedling stage

With increasing human global population, increased yield under saline conditions is a desirable trait for major food crops. Use of endophytes, isolated from halophytic hosts, seems to be an exciting approach for conferring salt tolerance to a salt-sensitive crop. Therefore, in the current study, fungal endophytes were isolated from halophytic plants' roots and their ability to withstand in vitro salt stress was evaluated. The fungal endophytes could withstand up to 1M NaCl concentrations and this tolerance was independent of their host or tissue source. When inoculated on salt-sensitive wheat seeds/seedlings, several of the endophytes showed a positive impact on germination and biomass-related parameters upon salt stress, both in vitro and under glasshouse conditions. One of the isolates from dicot plants (identified as Microsphaeropsis arundinis) could successfully colonize wheat and promote its growth under salt and no-salt conditions. Amongst the fungal isolates that are known to be natural endophytes of wheat, Chaetomium globosum was the best performing isolate and has previously been reported to be an effective biocontrol agent. Based on the results of our preliminary study, we suggest that these fungal endophytes could prove beneficial for enhancing the salt stress tolerance of wheat crop.

Effects of a Dark Septate Fungal Endophyte on the Growth and Physiological Response of Seedlings to Drought in an Epiphytic Orchid

Dark septate endophytes (DSE) are a group of facultative biotrophic root-colonizing fungi that live within a plant for a part of their life cycle without causing any apparent, overt negative effects. These fungi have been found in >600 different plant species, including orchids. Although the precise ecological functions of dark septate fungal endophytes are not yet well understood, there is increasing evidence that they enhance host growth and nutrient acquisition, and improve the plant’s ability to tolerate biotic and abiotic stresses. In this research, we tested the effects of a DSE isolated from the roots of the epiphytic orchid Coelogyne viscosa on the growth and drought tolerance of orchid seedlings. Our results showed that addition of DSE inoculum significantly enhanced biomass of seedlings and increased the activities of drought resistance related enzymes and the accumulation of osmoregulatory substances. These results suggest that DSE can fulfill important ecological functions in stressful environments and potentially play an important role in the life cycle of epiphytic orchids.

Micro-scale Experimental System Coupled with Fluorescence-based Estimation of Fungal Biomass to Study Utilisation of Plant Substrates

The degradation capacity and utilisation of complex plant substrates are crucial for the functioning of saprobic fungi and different plant symbionts with fundamental functions in ecosystems. Measuring the growth capacity and biomass of fungi on such systems is a challenging task. We established a new micro-scale experimental setup using substrates made of different plant species and organs as media for fungal growth. We adopted and tested a reliable and simple titration-based method for the estimation of total fungal biomass within the substrates using fluorescence-labelled lectin. We found that the relationship between fluorescence intensity and fungal dry weight was strong and linear but differed among fungi. The effect of the plant organ (i.e. root vs. shoot) used as substrate on fungal growth differed among plant species and between root endophytic fungal species. The novel microscale experimental system is useful for screening the utilisation of different substrates, which can provide insight into the ecological roles and functions of fungi. Furthermore, our fungal biomass estimation method has applications in various fields. As the estimation is based on the fungal cell wall, it measures the total cumulative biomass produced in a certain environment.

Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus

Understanding how organisms adapt to extreme living conditions is central to evolutionary biology. Dark septate endophytes (DSEs) constitute an important component of the root mycobiome and they are often able to alleviate host abiotic stresses. Here, we investigated the molecular mechanisms underlying the beneficial association between the DSE Laburnicola rhizohalophila and its host, the native halophyte Suaeda salsa, using population genomics. Based on genome-wide Fst (pairwise fixation index) and Vst analyses, which compared the variance in allele frequencies of single-nucleotide polymorphisms (SNPs) and copy number variants (CNVs), respectively, we found a high level of genetic differentiation between two populations. CNV patterns revealed population-specific expansions and contractions. Interestingly, we identified a ~20 kbp genomic island of high divergence with a strong sign of positive selection. This region contains a melanin-biosynthetic polyketide synthase gene cluster linked to six additional genes likely involved in biosynthesis, membrane trafficking, regulation, and localization of melanin. Differences in growth yield and melanin biosynthesis between the two populations grown under 2% NaCl stress suggested that this genomic island contributes to the observed differences in melanin accumulation. Our findings provide a better understanding of the genetic and evolutionary mechanisms underlying the adaptation to saline conditions of the L. rhizohalophila-S. salsa symbiosis.

Combined inoculation with dark septate endophytes and arbuscular mycorrhizal fungi: synergistic or competitive growth effects on maize?

BACKGROUND

Effects on maize were assessed of dual inoculation with arbuscular mycorrhizal fungi (AMF) and dark septate endophytes (DSE) isolated from other plant species.

METHODS

Suspensions of DSE isolated from Stipa krylovii were prepared at different densities (2, 4, and 8 × 10⁵ CFU mL^- 1) and inoculated separately (AMF or DSE) or together (AMF + DSE), to explore their effects on maize growth.

RESULTS

Inoculation with AMF or medium and high densities of DSE and combined inoculation (AMF + DSE) increased plant above-ground growth and altered root morphology. Differences in plant growth were attributable to differences in DSE density, with negative DSE inoculation responsiveness at low density. AMF promoted plant above-ground growth more than DSE and the high density of DSE promoted root development more than AMF. Combined inoculation might lead to synergistic growth effects on maize at low density of DSE and competitive effects at medium and high DSE densities.

CONCLUSIONS

AMF and DSE co-colonized maize roots and they had positive effects on the host plants depending on DSE density. These findings indicate the optimum maize growth-promoting combination of AMF and DSE density and provide a foundation for further exploration of potentially synergistic mechanisms between AMF and DSE in physiological and ecological effects on host plants.

Bioprospecting Desert Plants for Endophytic and Biostimulant Microbes: A Strategy for Enhancing Agricultural Production in a Hotter, Drier Future

Simple Summary

Endophytes are microbes that live inside plants without causing negative effects in their hosts. All land plants are known to have endophytes, and these endophytes have the capacity to be transferred between plants. Taking endophytes from desert plants, which grow in low-nutrient, high-stress environments, and transferring them to crop plants may alleviate some of the challenges being faced by the agricultural industry, such as increasing drought frequency and rising opposition to chemical use in agriculture. Studies have shown that desert endophytes have the capacity to increase nutrient uptake and increase plant resistance to drought and heat stress, salt stress, and pathogen attack. Currently, the agricultural industry focuses on using irrigation, chemical fertilizers, and chemical pesticides to solve such issues, which can be extremely damaging to the environment. While there is still a lot that is unknown about endophytes, particularly desert plant endophytes, current research provides evidence that desert plant endophytes could be an environmentally friendly alternative to the conventional solutions being applied today.

Abstract

Deserts are challenging places for plants to survive in due to low nutrient availability, drought and heat stress, water stress, and herbivory. Endophytes—microbes that colonize and infect plant tissues without causing apparent disease—may contribute to plant success in such harsh environments. Current knowledge of desert plant endophytes is limited, but studies performed so far reveal that they can improve host nutrient acquisition, increase host tolerance to abiotic stresses, and increase host resistance to biotic stresses. When considered in combination with their broad host range and high colonization rate, there is great potential for desert endophytes to be used in a commercial agricultural setting, especially as croplands face more frequent and severe droughts due to climate change and as the agricultural industry faces mounting pressure to break away from agrochemicals towards more environmentally friendly alternatives. Much is still unknown about desert endophytes, but future studies may prove fruitful for the discovery of new endophyte-based biofertilizers, biocontrol agents, and abiotic stress relievers of crops.

Root Morphology and Rhizosphere Characteristics Are Related to Salt Tolerance of Suaeda salsa and Beta vulgaris L

Halophytes are capable of resisting salinity, and their root system is the part in direct contact with the saline soil environment. The aim of this study was to compare the responses of root morphology and rhizosphere characteristics to salinity between a halophyte, Suaeda salsa (suaeda), and a glycophyte, Beta vulgaris L. (sugar beet). The soil salt content was set to four levels (0.7, 1.2, 1.7, and 2.7%) by NaCl-treated plants. We investigated the soil pH, EC, nutrients and soil, plant ion (Na+, Cl-, K+, and Mg2+) concentration to evaluate the rhizospheric processes, and salt tolerance of suaeda by the root mat method. The highest biomass was in the 1.2% salt level for suaeda and in the 0.7% salt level for sugar beet. The root length and root surface area of suaeda showed similar trends to biomass, but the root diameter decreased by 11.5-17.9% with higher salinity. The Na+, Cl-, and K+ accumulations in the shoot of suaeda displayed higher than that in sugar beet, while the Mg2+ accumulation was lower in suaeda than that in sugar beet. High salinity resulted in increased pH and EC values in the rhizosphere for suaeda, but lower values of these parameters for sugar beet. Under high salinity, the Olsen phosphorus content was 0.50 g·kg-1 and 0.99 g·kg-1 higher in the rhizosphere than in the non-rhizosphere for suaeda and sugar beet. We concluded that the two species [halophyte, Suaeda salsa (suaeda), and a glycophyte, B. vulgaris L. (sugar beet)] showed diverse approaches for nutrient absorption under salinity stress. Suaeda altered its root morphology (smaller root diameter and longer roots) under salt stress to increase the root surface area, while sugar beet activated rhizospheric processes to take up more nutrients.

Near-Chromosome-Level Genome Assembly of the Dark Septate Endophyte Laburnicola rhizohalophila: A Model for Investigating Root-Fungus Symbiosis

The novel DSE Laburnicola rhizohalophila (Pleosporales, Ascomycota) is frequently found in the halophytic seepweed (Suaeda salsa). In this article, we report a near-chromosome-level hybrid assembly of this fungus using a combination of short-read Illumina data to polish assemblies generated from long-read Nanopore data. The reference genome for L. rhizohalophila was assembled into 26 scaffolds with a total length of 64.0 Mb and a N50 length of 3.15 Mb. Of them, 17 scaffolds approached the length of intact chromosomes, and 5 had telomeres at one end only. A total of 10,891 gene models were predicted. Intriguingly, 27.5 Mb of repeat sequences that accounted for 42.97% of the genome was identified, and long terminal repeat retrotransposons were the most frequent known transposable elements, indicating that transposable element proliferation contributes to its increased genome size. BUSCO analyses using the Fungi_odb10 data set showed that 95.0% of genes were complete. In addition, 292 carbohydrate active enzymes, 33 secondary metabolite clusters, and 84 putative effectors were identified in silico. The resulting high-quality assembly and genome features are not only an important resource for further research on understanding the mechanism of root-fungi symbiotic interactions but will also contribute to comparative analyses of genome biology and evolution within Pleosporalean species.

Stress tolerance of Xerocomus badius and its promotion effect on seed germination and seedling growth of annual ryegrass under salt and drought stresses

Comparative evaluations were conducted to assess the effects of different pH levels, NaCl-induced salt stress, and PEG-induced drought stress on the mycelial growth of Xerocomus badius. The results showed that X. badius mycelium grew well at a wide pH range of 5.00 ~ 9.00. Although the mycelium remained viable, mycelial growth of X. badius was significantly inhibited with increasing salt and drought stresses. Furthermore, a soilless experiment in Petri dishes was performed to investigate the potential of X. badius to induce beneficial effects on seed germination and seedling growth of annual ryegrass (Lolium multiflorum Lam.) under salt and drought stresses. Seed priming with X. badius enhanced the seedling growth of L. multiflorum Lam. under NaCl-induced salt stress and PEG-induced drought stress. However, X. badius did not significantly improve the seed germination under non-stress and mild stress conditions. It suggested that X. badius inoculation with seeds was not essential for seed germination under non-stress and mild stress conditions, but contributed highly to seedling growth under severe stress conditions. Therefore, seed priming with X. badius on ryegrass could be an effective approach to enhance plant tolerance against drought and salt stresses. X. badius could be a good candidate for the inoculation of ectomycorrhizal plants cultivation programs in mild saline and semiarid areas.

Salt Stress Tolerance of Dark Septate Endophytes Is Independent of Melanin Accumulation

Dark septate endophytes (DSEs) represent a diverse group of root-endophytic fungi that have been isolated from plant roots in many different natural and anthropogenic ecosystems. Melanin is widespread in eukaryotic organisms and possesses various functions such as protecting human skin from UV radiation, affecting the virulence of pathogens, and playing a role in development and physiology of insects. Melanin is a distinctive feature of the cell walls of DSEs and has been thought to protect these fungi from abiotic stress. Melanin in DSEs is assumed to be synthesized via the 1,8-dihydroxynaphthalene (DHN) pathway. Its function in alleviation of salt stress is not yet known. The aims of this study were: (i) investigating the growth responses of three DSEs (Periconia macrospinosa, Cadophora sp., and Leptodontidium sp.) to salt stress, (ii) analyzing melanin production under salt stress and, (iii) testing the role of melanin in salt stress tolerance of DSEs. The study shows that the three DSE species can tolerate high salt concentrations. Melanin content increased in the hyphae of all DSEs at 100 mM salt, but decreased at 500 mM. This was not reflected in the RNA accumulation of the gene encoding scytalone dehydratase which is involved in melanin biosynthesis. The application of tricyclazole, a DHN-melanin biosynthesis inhibitor, did not affect either salt stress tolerance or the accumulation of sodium in the hyphae. In addition, melanin biosynthesis mutants of Leptodontidium sp. did not show decreased growth performance compared to the wild-type, especially not at high salt concentrations. This indicates that DSEs can live under salt stress and withstand these conditions regardless of melanin accumulation.

When Salt Meddles Between Plant, Soil, and Microorganisms

In extreme environments, the relationships between species are often exclusive and based on complex mechanisms. This review aims to give an overview of the microbial ecology of saline soils, but in particular of what is known about the interaction between plants and their soil microbiome, and the mechanisms linked to higher resistance of some plants to harsh saline soil conditions. Agricultural soils affected by salinity is a matter of concern in many countries. Soil salinization is caused by readily soluble salts containing anions like chloride, sulphate and nitrate, as well as sodium and potassium cations. Salinity harms plants because it affects their photosynthesis, respiration, distribution of assimilates and causes wilting, drying, and death of entire organs. Despite these life-unfavorable conditions, saline soils are unique ecological niches inhabited by extremophilic microorganisms that have specific adaptation strategies. Important traits related to the resistance to salinity are also associated with the rhizosphere-microbiota and the endophytic compartments of plants. For some years now, there have been studies dedicated to the isolation and characterization of species of plants' endophytes living in extreme environments. The metabolic and biotechnological potential of some of these microorganisms is promising. However, the selection of microorganisms capable of living in association with host plants and promoting their survival under stressful conditions is only just beginning. Understanding the mechanisms of these processes and the specificity of such interactions will allow us to focus our efforts on species that can potentially be used as beneficial bioinoculants for crops.

Microbial Diversity of Upland Rice Roots and Their Influence on Rice Growth and Drought Tolerance

Among abiotic stresses, drought is one of the most important factors limiting plant growth. To increase their drought tolerance and survival, most plants interact directly with a variety of microbes. Upland rice (Oryza sativa L.) is a rice ecotype that differs from irrigated ecotype rice; it is adapted to both drought-stress and aerobic conditions. However, its root microbial resources have not been explored. We isolated bacteria and fungi from roots of upland rice in Xishuangbanna, China. Four hundred sixty-two endophytic and rhizospheric isolates (337 bacteria and 125 fungi) were distributed. They were distributed among 43 genera on the basis of 16S rRNA and internal transcribed spacer (ITS) gene sequence analysis. Notably, these root microbes differed from irrigated rice root microbes in irrigated environments; for example, members of the Firmicutes phylum were enriched (by 28.54%) in the roots of the upland plants. The plant growth-promoting (PGP) potential of 217 isolates was investigated in vitro. The PGP ability of 17 endophytic and 10 rhizospheric isolates from upland rice roots was evaluated under well-irrigated and drought-stress conditions, and 9 fungal strains increased rice seedling shoot length, shoot and root fresh weight (FW), antioxidant capability, and proline (Pro) and soluble sugar contents. Our work suggests that fungi from upland rice roots can increase plant growth under irrigated and drought-stress conditions and can serve as effective microbial resources for sustainable agricultural production in arid regions.

Plant performance of enhancing licorice with dual inoculating dark septate endophytes and Trichoderma viride mediated via effects on root development

BACKGROUND

This study aimed to assess whether licorice (Glycyrrhiza uralensis) can benefit from dual inoculation by Trichoderma viride and dark septate endophytes (DSE) isolated from other medicinal plants.

METHODS

First, we isolated and identified three DSE (Paraboeremia putaminum, Scytalidium lignicola, and Phoma herbarum) and Trichoderma viride from medicinal plants growing in farmland of China. Second, we investigated the influences of these three DSE on the performance of licorice at different T. viride densities (1 × 106, 1 × 107, and 1 × 108 CFU/mL) under sterilised condition in a growth chamber.

RESULTS

Three DSE strains could colonize the roots of licorice, and they established a positive symbiosis with host plants depending on DSE species and T. viride densities. Inoculation of P. putaminum increased the root biomass, length, surface area, and root:shoot ratio. S. lignicola increased the root length, diameter and surface area and decreased the root:shoot ratio. P. herbarum increased the root biomass and surface area. T. viride increased the root biomass, length, and surface area. Structural equation model (SEM) analysis showed that DSE associated with T. viride augmented plant biomass and height, shoot branching, and root surface area. Variations in root morphology and biomass were attributed to differences in DSE species and T. viride density among treatments. P. putaminum or P. herbarum with low- or medium T. viride density and S. lignicola with low- or high T. viride density improved licorice root morphology and biomass.

CONCLUSIONS

DSE isolated from other medicinal plants enhanced the root growth of licorice plants under different densities T. viride conditions and may also be used to promote the cultivation of medicinal plants.

Response of fungal communities in different soils to biochar and chemical fertilizers under simulated rainfall conditions

Biochar is a good soil additive, which cannot only effectively store carbon, but also improve soil fertility and crop yield. However, the specific response of fungal communities to biochar and chemical fertilizers are still relatively lacking. In addition, most studies do not take into account rainfall factors when conducting culture experiments. In the case of simulated rainfall, we investigated the response of fungal communities in different soils to biochar and fertilizers in China and analyzed the correlation between chemical properties and different fungal species. The tested soils were yellow-brown soil, fluvo-aquic soil, lou soil and black soil, and the simulated daily rainfall was 25 mm. The results indicated that the application of biochar and chemical fertilizers had a greater impact on the alpha diversity of acidic soils (yellow-brown soil, fluvo-aquic soil), but less on alkaline soils (lou soil, black soil). The relative abundance of Ascomycetes was most affected by biochar and fertilizer in any soil. From the point of view of the fungal community, yellow-brown soil was more suitable for single application of biochar, because it not only improved the ability of the soil to degrade persistent organic matter but also inhibited the spread of soil pathogens. In black soil, the relative abundance of Fusarium was significantly reduced by the combined application of biochar and chemical fertilizers (FC), and the decline was much higher than several other bacteria. However, FC caused the greatest changes in the structure of all soil fungal communities. Moreover, there was a significant correlation between the content of available nutrients and composition of fungal community in fluvo-aquic soil. In summary, it can be explained that the effects of biochar and chemical fertilizers on soil fungi may vary depending on the soil type, so it is very urgent to conduct long-term research on different typical soils.

Funneliformis mosseae Enhances Root Development and Pb Phytostabilization in Robinia pseudoacacia in Pb-Contaminated Soil

It is possible that arbuscular mycorrhizal fungi play a pivotal role in root development and Pb phytostabilization in plants grown in Pb-contaminated soil. In this study, a pot experiment was conducted over 4 months to evaluate the effects of Funneliformis mosseae strain BGCXJ01A on root characteristics of black locust (Robinia pseudoacacia L.) seedlings in Pb-contaminated soil. Four Pb treatments (0, 90, 900, and 3,000 mg kg^–1) were applied to soil in the presence and absence of F. mosseae. Inoculation with F. mosseae prominently improved root length, surface area, volume, and tip number in the plants across all Pb treatments. The F. mosseae inoculation also increased root diameter and fork number, especially under high Pb treatments. The presence of F. mosseae significantly increased the root activity and root tolerance index. However, there was little difference in specific root length between inoculated and non-inoculated plants. The biomass of roots, stems, and leaves all increased following inoculation with F. mosseae. Inoculated plants had greater accumulation and translocation capacities for Pb in the roots and stems, but lower capacities were found in the leaves when compared with those in non-inoculated plants. These results highlight that F. mosseae can alleviate the toxic effects of Pb on root development and can immobilize Pb in the roots and stems of R. pseudoacacia grown in Pb-contaminated soil. This study provides a model system for phytoremediation of Pb-contaminated soil via reciprocal symbiosis between arbuscular mycorrhizal fungi and woody legumes.

Insight into a highly polymorphic endophyte isolated from the roots of the halophytic seepweed Suaeda salsa: Laburnicola rhizohalophila sp. nov. (Didymosphaeriaceae, Pleosporales)

We surveyed root endophytic fungi of the coastal halophyte Suaeda salsa and detected a population of a novel species that we described here as Laburnicola rhizohalophila sp. nov. No sexual sporulating structure was observed. Instead, it produced a large amount of thalloconidia, 0-1 transverse septa, hyaline to darkly pigmented, often peanut-shaped and sometimes dumbbell-shaped, both ends enlarged with numerous oil droplets inside the hyphal cells. Surprisingly, a high degree of phenotypic and physiological intraspecific variation (e.g., salinity tolerance, growth under different carbon:nitrogen ratios, and carbon utilization pattern) was recorded. The inoculation test indicated that the isolates could successfully infect host roots and form microsclerotia-like structures in cortical cells, a typical trait of dark septate endophytes (DSEs). Furthermore, most isolates were shown to promote host seedling growth. To evaluate conspecificity and infer its phylogenetic affinity, multiloci data including nuclear rRNA loci (ITS1 and 2, partial 28S), partial RNA Polymerase II second-largest subunit (rpb2), and partial translation elongation factor-1α (tef1) were characterized. Genealogical concordance phylogenetic species recognition (GCPSR) detected a genetically isolated clade of L. rhizohalophila within the Pleosporales in the Didymosphaeriaceae. Maximum likelihood phylogenetic reconstruction revealed that the endophytic fungus was genetically close to Laburnicoladactylidis but separated by a relatively long genetic distance. Our work highlights that the pleosporalean taxa might represent an underexplored reservoir of root DSEs.

Dark septate endophytic fungi increase the activity of proton pumps, efficiency of 15N recovery from ammonium sulphate, N content, and micronutrient levels in rice plants

Plants colonised by dark septate endophytic (DSE) fungi show increased uptake of nutrients available in the environment. The objective of the present study was to evaluate the impact of DSE fungi on the activity of proton pumps, nitrogen (N) recovery from ammonium sulphate, and nutrient accumulation in rice plants. Treatments consisted of non-inoculated plants and plants inoculated with two isolates of DSE fungi, A101 and A103. To determine N recovery from the soil, ammonium sulphate enriched with 15N was added to a non-sterile substrate while parameters associated with the activity of proton pumps and with NO3- uptake were determined in a sterile environment. The A101 and A103 fungal isolates colonised the roots of rice plants, promoting 15N uptake, growth, and accumulation of nutrients as compared with the mock control. A103 induced the expression of the plasma membrane H+-ATPase (PM H+-ATPase) isoforms OsA5 and OsA8, the activity of the PM H+-ATPase and H+-pyrophosphatase. Our results suggest that the inoculation of rice plants with DSE fungi represents a strategy to improve the N recovery from ammonium sulphate and rice plant growth through the induction of OsA5 and OsA8 isoforms and stimulation of the PM H+-ATPase and H+-pyrophosphatase.

Ability of endophytic fungi associated with Withania somnifera L. to control Fusarium Crown and Root Rot and to promote growth in tomato

Fusarium crown and root rot (FCRR), caused by Fusarium oxysporum f. sp. radicis-lycopersici (FORL), is a soilborne tomato disease of increased importance worldwide. In this study, Withania somnifera was used as a potential source of biological control and growth-promoting agents. Seven fungal isolates naturally associated with W. somnifera were able to colonize tomato seedlings. They were applied as conidial suspensions or a cell-free culture filtrate. All isolates enhanced treated tomato growth parameters by 21.5-90.3% over FORL-free control and by 27.6-93.5% over pathogen-inoculated control. All tested isolates significantly decreased by 28.5-86.4% disease severity over FORL-inoculated control. The highest disease suppression, by 86.4-92.8% over control and by 81.3-88.8% over hymexazol-treated control, was achieved by the I6 isolate. FORL radial growth was suppressed by 58.5-82.3% versus control when dual cultured with tested isolates and by 61.8-83.2% using their cell-free culture filtrates. The most active agent was identified as Fusarium sp. I6 (MG835371), which displayed chitinolytic, proteolytic, and amylase activities. This has been the first report on the potential use of fungi naturally associated with W. somnifera for FCRR suppression and for tomato growth promotion. Further investigations are required in regard to mechanisms of action involved in disease suppression and plant growth promotion.

Dark Septate Endophytic Fungi Increase Green Manure-15N Recovery Efficiency, N Contents, and Micronutrients in Rice Grains

An understanding of the interaction between rice and dark septate endophytic (DSE) fungi, under green fertilization, may lead to sustainable agricultural practices. Nevertheless, this interaction is still poorly understood. Therefore, in this study, we aimed to evaluate the accumulation of macro- and micronutrients, dry matter, and protein and N recovery efficiency from Canavalia ensiformis (L.)-¹⁵N in rice inoculated with DSE fungi. An experiment under greenhouse conditions was conducted in a randomized complete block design comprising split-plots, with five replicates of rice plants potted in non-sterilized soil. Rice (Piauí variety) seedlings were inoculated with DSE fungi, A101 and A103, or left uninoculated (control) and transplanted into pots containing 12 kg of soil, which had previously been supplemented with dry, finely ground shoot biomass of C. ensiformis enriched with 2.15 atom % ¹⁵N. Two collections were performed in the experiment: one at 54 days after transplanting (DAT) and one at 130 DAT (at maturation). Growth indicators (at 54 DAT), grain yield, nutrient content, recovery efficiency, and the amount of N derived from C. ensiformis were quantified. At 54 DAT, the N content, chlorophyll content, and plant height of inoculated plants had increased significantly compared with the control, and these plants were more proficient in the use of N derived from C. ensiformis. At maturation, plants inoculated with A103 were distinguished by the recovery efficiency and amount of N derived from C. ensiformis and N content in the grain and shoot being equal to that in A101 inoculation and higher than that in the control, resulting in a higher accumulation of crude protein and dry matter in the full grain and panicle of DSE-rice interaction. In addition, Fe and Ni contents in the grains of rice inoculated with these fungi doubled with respect to the control, and in A103 inoculation, we observed Mn accumulation that was three times higher than in the other treatments. Our results suggest that the inoculation of rice with DSE fungi represents a strategy to improve green manure-N recovery, grain yield per plant, and grain quality in terms of micronutrients contents in cropping systems with a low N input.

Dark Septate Endophytic Fungi Help Tomato to Acquire Nutrients from Ground Plant Material

Dark septate endophytic (DSE) fungi are facultative biotrophs that associate with hundreds of plant species, contributing to their growth. These fungi may therefore aid in the search for sustainable agricultural practices. However, several ecological functions of DSE fungi need further clarification. The present study investigated the effects of DSE fungi inoculation on nutrient recovery efficiency, nutrient accumulation, and growth of tomato plants fertilized with organic and inorganic N sources. Two experiments were carried out under greenhouse conditions in a randomized blocks design, with five replicates of tomato seedlings grown in pots filled with non-sterile sandy soil. Tomato seedlings (cv. Santa Clara I-5300) inoculated with DSE fungi (isolates A101, A104, and A105) and without DSE fungi (control) were transplanted to pots filled with 12 kg of soil which had previously received finely ground plant material [Canavalia ensiformis (L.)] that was shoot enriched with 0.7 atom % 15N (organic N source experiment) or ammonium sulfate-15N enriched with 1 atom % 15N (mineral N source experiment). Growth indicators, nutrient content, amount of nitrogen (N) in the plant derived from ammonium sulfate-15N or C. ensiformis-15N, and recovery efficiency of 15N, P, and K by plants were quantified 50 days after transplanting. The treatment inoculated with DSE fungi and supplied with an organic N source showed significantly higher recovery efficiency of 15N, P, and K. In addition, the 15N, N, P, K, Ca, Mg, Fe, Mn, and Zn content, plant height, leaf number, leaf area (only for the A104 inoculation), and shoot dry matter increased. In contrast, the only positive effects observed in the presence of an inorganic N source were fertilizer-K recovery efficiency, content of K, and leaf area when inoculated with the fungus A104. Inoculation with A101, A104, and A105 promoted the growth of tomato using organic N source (finely ground C. ensiformis-15N plant material).