Priming of rhizobial nodulation signaling in the mycosphere accelerates nodulation of legume hosts.

The simultaneous symbiosis of leguminous plants with two root mutualists, endophytic fungi and rhizobia is common in nature, yet how two mutualists interact and co-exist before infecting plants and the concomitant effects on nodulation are less understood. Using a combination of metabolic analysis, fungal deletion mutants and comparative transcriptomics, we demonstrated that Bradyrhizobium and a facultatively biotrophic fungus, Phomopsis liquidambaris, interacted to stimulate fungal flavonoid production, and thereby primed Bradyrhizobial nodulation signaling, enhancing Bradyrhizobial responses to root exudates and leading to early nodulation of peanut (Arachis hypogaea), and such effects were compromised when disturbing fungal flavonoid biosynthesis. Stress sensitivity assays and reactive oxygen species (ROS) determination revealed that flavonoid production acted as a strategy to alleviate hyphal oxidative stress during P. liquidambaris-Bradyrhizobial interactions. By investigating the interactions between P. liquidambaris and a collection of 38 rhizobacteria, from distinct bacterial genera, we additionally showed that the flavonoid-ROS module contributed to the maintenance of fungal and bacterial co-existence, and fungal niche colonization under soil conditions. Our results demonstrate for the first time that rhizobial nodulation signaling can be primed by fungi before symbiosis with host plants and highlight the importance of flavonoid in tripartite interactions between legumes, beneficial fungi and rhizobia.

SubPhaser: a robust allopolyploid subgenome phasing method based on subgenome-specific k-mers.

With advanced sequencing technology, dozens of complex polyploid plant genomes have been characterized. However, for many polyploid species, their diploid ancestors are unknown or extinct, making it impossible to unravel the subgenomes and genome evolution directly. We developed a novel subgenome-phasing algorithm, SubPhaser, specifically designed for a neoallopolyploid or a homoploid hybrid. SubPhaser first searches for the subgenome-specific sequence (k-mer), then assigns homoeologous chromosomes into subgenomes, and further provides tools to annotate and investigate specific sequences. SubPhaser works well on neoallopolyploids and homoploid hybrids containing subgenome-specific sequences like wheat, but fails on autopolyploids lacking subgenome-specific sequences like alfalfa, indicating that SubPhaser can phase neoallopolyploid/homoploid hybrids with high accuracy, sensitivity and performance. This highly accurate, highly sensitive, ancestral data free chromosome phasing algorithm, SubPhaser, offers significant application value for subgenome phasing in neoallopolyploids and homoploid hybrids, and for the subsequent exploration of genome evolution and related genetic/epigenetic mechanisms.

Root endophyte differentially regulates plant response to NO3- and NH4+ nutrition by modulating N fluxes at the plant-fungal interface.

In the soil, plant roots associated with fungi often encounter uneven distribution of nitrate (NO3- )/ammonium (NH4+ ) patches, but the mechanism underlying N form-influenced plant-fungal interactions remains limited. We inoculated Arabidopsis with a root endophyte Phomopsis liquidambaris, and evaluated the effects of P. liquidambaris on plant performance under NO3- or NH4+ nutrition. Under NO3- nutrition, P. liquidambaris inoculation promoted seedling growth, whereas under NH4+ nutrition, P. liquidambaris suppressed seedling growth. Under high NH4+ conditions, fungus-colonized roots displayed increased NH4+ accumulation and NH4+ efflux, similar to the effect of ammonium stress caused by elevated NH4+ levels. Notably, this fungus excluded NH4+ during interactions with host roots, thereby leading to increased NH4+ levels at the plant-fungal interface under high NH4+ conditions. A nitrite reductase-deficient strain that excludes NO3- but absorbs NH4+ , decreased NH4+ levels in Arabidopsis shoots and rescued plant growth and nitrogen metabolism under high NH4+ levels. Transcriptomic analysis highlighted that P. liquidambaris had altered transcriptional responses associated with plant response to inorganic N forms. Our results demonstrate that fungus-regulated NO3- /NH4+ dynamics at the plant-fungal interface alters plant response to NO3- /NH4+ nutrition. This study highlights the essential functions of root endophytes in plant adaptation to soil nitrogen nutrients.

Combined System of Organic Substrate and Straw-Degrading Microbial Agents Improved Soil Organic Matter Levels and Microbial Abundance in a Rice-Wheat Rotation.

Rice-wheat rotation is one of the most intensive agricultural planting modes in China and is pivotal to develop optimized straw-returning management in situ to improve soil fertility and productivity in agricultural ecosystems. Previous studies have mainly focused on the effects of straw return with a single application of organic fertilizers. The integrated management of different fertilizers in improving the management of straw return in situ is not well known. In this study, a field experiment was conducted from 2017 to 2019 to explore the effects of a combined system of modified organic substrate (MOS) and straw-degrading compound microbial agent (CMA) on soil physiochemical properties, labile organic carbon, microbial activities, and soil microbial community composition under the background of direct crop straw return and chemical fertilizer utilization. Four treatments were designed: (1) control check; (2) CMA; (3) MOS; and (4) MOS + CMA. The results showed that the MOS + CMA treatment had the combined advantages of soil organic matter (SOM) accumulation, soil nutrient increase and soil microbial community alteration, which may be more suitable for improving the quality and fertility of sandy loam soil. This study provides novel insights for further understanding the effects of organic substrates and composite microbial agents on SOM changes and microbial community composition and function in the field, which has important implications for sustainable crop production and agricultural development.

Flowering-mediated root-fungus symbiosis loss is related to jasmonate-dependent root soluble sugar deprivation.

The role of flowering in root-fungal symbiosis is not well understood. Because flowering and fungal symbionts are supported by carbohydrates, we hypothesized that flowering modulates root-beneficial fungal associations through alterations in carbohydrate metabolism and transport. We monitored fungal colonization and soluble sugars in the roots of Arabidopsis thaliana following inoculation with a mutualistic fungus Phomopsis liquidambari across different plant developmental stages. Jasmonate signalling of wild-type plants, sugar transport, and root invertase of wild-type and jasmonate-insensitive plants were exploited to assess whether and how jasmonate-dependent sugar dynamics are involved in flowering-mediated fungal colonization alterations. We found that flowering restricts root-fungal colonization and activates root jasmonate signalling upon fungal inoculation. Jasmonates reduce the constitutive and fungus-induced accumulation of root glucose and fructose at the flowering stage. Further experiments with sugar transport and metabolism mutant lines revealed that root glucose and fructose positively influence fungal colonization. Diurnal, jasmonate-dependent inhibitions of sugar transport and soluble invertase activity were identified as likely mechanisms for flowering-mediated root sugar depletion upon fungal inoculation. Collectively, our results reveal that flowering drives root-fungus cooperation loss, which is related to jasmonate-dependent root soluble sugar depletion. Limiting the spread of root-fungal colonization may direct more resources to flower development.

The Distal Gut Bacterial Community of Some Primates and Carnivora.

Huge numbers of bacteria reside in the digestive tract of host and these microorganisms play a vital role in the host health, especially in the digestion of food and the development of immune system. Host phylogeny and diet, especially long-term diet, both have great influence on the gut bacterial community. Other aspects of host, such as gender, age, and the geography and weather they lived, are also correlated to their gut bacterial community. Feces are usually used for gut bacteria study and fecal bacteria can represent the distal gut bacteria. In order to determine the influence of the host phylogeny and diet on the composition of distal gut bacterial community and to interpret bacterial population and diversity in the intestinal of animals, the distal gut bacterial community of four kinds of primates and five kinds of carnivora (including herbivorous, omnivorous, and carnivorous) were investigated using high-throughput sequencing and the isolation of the Actinobacteria from fresh feces of several primates was processed. The results showed the host phylogeny had a greater influence on the distal gut bacterial community of the primates and carnivora than the host diet. A total of 44 bacteria phyla and two archaea phyla were detected, which indicated that the distal gut bacteria of these animals were abundant. The distal gut bacteria were relatively stable and wildly shared in primates and carnivora. The difference in distal gut bacteria of the two animal orders is mainly determined by relative abundance of most distal gut bacteria rather than by the taxa of these bacteria.

Kineococcus terrestris sp. nov. and Kineococcus aureolus sp. nov., isolated from saline sediment.

Two novel actinobacteria, designated YIM 121936T and YIM 121940T, were isolated from alkaline sediment in Yuanjiang, China. The cells of the novel strains were Gram-stain-positive, aerobic, motile, non-spore-forming and coccus-shaped. The two strains both contained meso-diaminopimelic acid as the diagnostic diamino acid. The whole-cell sugars were arabinose, galactose, glucose, mannose and ribose. The predominant menaquinone was MK-9(H2). The polar lipid profile of both strains comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, one unknown phosphoglycolipid and five unknown phospholipids. The predominant fatty acids of both strains were anteiso-C15 : 0. The genomic DNA G+C contents of strains YIM 121936T and YIM 121940T were 74.7 and 75.2 %, respectively. Strain YIM 121936T was closely related to Kineococcus aurantiacus IFO 15268T (97.19 %), Kineococcus gypseus YIM 121300T (97.00 %) and Kineococcus mangrovi NBRC 110933T (97.00 %). Strain YIM 121940T was closely related to K. aurantiacus IFO 15268T (97.41 %), Kineococcus endophytica KLBMP 1274T (97.18 %), Kineococcus rhizosphaerae RP-B16T (97.09 %), Kineococcus radiotolerans SRS 30216T (97.09 %), K. gypseus YIM 121300T (97.00 %) and K. mangrovi NBRC 110933T (97.00 %). Strain YIM 121936T shared high 16S rRNA gene sequence similarity (99 %) with YIM 121940T. Similarities of two strains with other species of the genus Kineococcus were <97 %. The DNA-DNA hybridization values were below 70 % among all the strains studied. YIM 121936T and YIM 121940T are representatives of two new species in the genus Kineococcus, for which names Kineococcus terreus sp. nov. (type strain YIM 121936T=KCTC 39738T=DSM 102155T) and Kineococcus aureolus sp. nov. (type strain YIM 121940T=KCTC 39739T=DSM 102158T) are proposed, respectively.

Mobilicoccus caccae sp. nov., isolated from the faeces of the primate Rhinopithecus roxellanae.

A novel actinobacterium, designated YIM 101593T, was isolated from the faeces of a primate (Rhinopithecus roxellanae) living in Yunnan Wild Animal Park in Yunnan province, south-west China. The isolate was Gram-stain-positive, facultatively anaerobic, coccus-shaped, oxidase-negative and motile. The cell wall contained meso-diaminopimelic acid as its diagnostic diamino acid, and mannose, ribose, glucose, galactose and arabinose were detected as the main whole-cell sugars. The predominant menaquinone was MK-8(H2). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two glycolipids, three unidentified phospholipids and two unidentified lipids. The major fatty acids were C17 : 1ω8c, C15 : 0 and summed feature 4 (anteiso-C17 : 1 B and/or iso-C17 : 1 I). The DNA G+C content was 69.8 mol%. The 16S rRNA gene sequence similarity between strain YIM 101593T and Mobilicoccus pelagius was 97.9 %, and the two strains formed a distinct lineage stably on the basis of phylogenetic analysis. In addition, DNA-DNA relatedness between the two strains was 49.0±5.1 %. On the basis of chemotaxonomical and physiological characteristics and the phylogenetic analysis, strain YIM 101593T should be considered to represent a novel species of the genus Mobilicoccus, for which we propose the name Mobilicoccus caccae sp. nov., with the type strain YIM 101593T (=DSM 27611T=CCTCC AB 2013229T).

Tessaracoccus rhinocerotis sp. nov., isolated from the faeces of Rhinoceros unicornis.

A novel Gram-stain-positive, non-spore-forming, irregular rod-shaped, non-motile and facultatively anaerobic actinobacterium, designated strain YIM 101269T, was isolated from the faeces of Rhinoceros unicornis living in Yunnan Wild Animal Park, Yunnan province, south-west China. The isolate grew at 10-35 °C, at pH 6-12 and with 0-9 % (w/v) NaCl. The cell-wall peptidoglycan of the organism contained ll-diaminopimelic acid as the diagnostic diamino acid. The polar lipids detected were diphosphatidylglycerol, phosphatidylglycerol, three unidentified polar lipids, one unidentified aminophospholipid and three unknown glycolipids. The major cellar fatty acid was anteiso-C15 : 0.MK-10(H4) was the predominant menaquinone. The DNA G+C content was 69.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain YIM 101269T belonged to the genus Tessaracoccus, closely related to Tessaracoccus flavescens DSM 18582T (97.4 % similarity). Based on the evidence from the present study, strain YIM 101269T is considered to represent a novel species of the genus Tessaracoccus, for which the name Tessaracoccus rhinocerotis sp. nov. is proposed. The type strain is YIM 101269T ( = DSM 27579T = CCTCC AB 2013217T).

Microbacterium faecale sp. nov., isolated from the faeces of Columba livia.

A novel, yellow, aerobic strain, YIM 101168T, isolated from the faeces of a dove (Columba livia), was studied to determine its taxonomic position. Cells were Gram-stain-positive, short rod-shaped, oxidase-negative, catalase-positive and non-motile. The strain could grow at 7-37 °C, at pH 6-10 and in the presence of 0-13 % (w/v) NaCl. The strain had a 16S rRNA gene sequence similarity and DNA-DNA hybridization relatedness value with Microbacteriumgubbeenense NCIMB 30129T of 97.8 % and 41.5±8.7 %, respectively. Ornithine was detected as the diagnostic amino acid in the hydrolysate of the cell wall. Whole-cell sugars were found to be galactose, glucose, rhamnose, mannose and ribose. Major fatty acids (>10 %) were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. Major menaquinones were identified as MK-10, MK-11 and MK-12. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, glycolipids and four unidentified lipids. The phylogenetic analyses as well as the chemotaxonomic and phenotypic characteristics indicate that strain YIM 101168T represents a novel species of the genus Microbacterium; the name Microbacterium faecale sp. nov. is proposed for the novel species and the type strain is YIM 101168T (=DSM 27232T=KCTC 39554T=CGMCC 1.15152T).

Microbacterium gilvum sp. nov., isolated from civet faeces.

A novel aerobic, non-motile, Gram-positive, rod-shaped actinobacterium, designated YIM 100951(T), was isolated from the faeces of civets (Viverra zibetha) living in the National Nature Protect Region in Selangor, Malaysia. Strain YIM 100951(T) shows high similarities with Microbacterium barkeri DSM 20145(T) (97.6 %), Microbacterium oryzae MB10(T) (97.3 %), Microbacterium lemovicicum ViU22(T) (97.1 %) and Microbacterium indicum BBH6(T) (97.0 %) based on their 16S rRNA genes. However, phylogenetic analysis showed that strain YIM 100951(T) formed a clade with Microbacterium halotolerans YIM 70130(T) (96.7 %), Microbacterium populi 10-107-8(T) (96.7 %) and Microbacterium sediminis YLB-01(T) (96.9 %). DNA-DNA hybridization was carried out between strains YIM 100951(T) and M. barkeri DSM 20145(T), the result showed a value of 23.2 ± 4.5 %. In addition, some of the physiological, biochemical and chemotaxonomic characteristics of strain YIM 100951(T) are different from the closely related strains. Thus, we suggest that strain YIM 100951(T) represents a novel species of the genus Microbacterium, for which the name Microbacterium gilvum sp. nov. is proposed. The type strain is YIM 100951(T) (=DSM 26235(T) = CCTCC AB 2012971(T)).

Sphingobacterium rhinocerotis sp. nov., isolated from the faeces of Rhinoceros unicornis.

A novel Gram-negative, strictly aerobic, short rod-shaped, non-motile bacterium, designated YIM 101302(T), was isolated from the faeces of Rhinoceros unicornis dwelling in the Yunnan Wild Animal Park, Yunnan province, South-West China. The 16S rRNA gene sequence analysis revealed a clear affiliation of strain YIM 101302(T) to the genus Sphingobacterium. The newly isolated bacterium was found to be closely related to Sphingobacterium composti T5-12(T) (97.1% 16S rRNA sequence identity) and Sphingobacterium alimentarium WCC 4521(T) (95.6% 16S rRNA sequence identity) forming a distinct clade with these two species. Polar lipids of strain YIM 101302(T) were identified as phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unidentified aminophospholipid, and three unidentified polar lipids; the predominant menaquinone as MK-7 and the major fatty as iso-C15:0. The genomic DNA G+C content was determined to be 38.9 mol%. The DNA-DNA hybridization values between strain YIM 101302(T) and S. composti T5-12(T), was 53.6 ± 5.8%. These results indicates that strain YIM 101302(T) represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium rhinocerotis sp. nov. is proposed. The type strain is YIM 101302(T) (=CCTCC AB 2013218(T) = KCTC 42533(T)).

Endofungal Bacterial Microbiota Promotes the Absorption of Chelated Inorganic Phosphorus by Host Pine through the Ectomycorrhizal System.

Ectomycorrhizal fungi play an irreplaceable role in phosphorus cycling. However, ectomycorrhizal fungi have a limited ability to dissolve chelated inorganic phosphorus, which is the main component of soil phosphorus. Endofungal bacteria in ectomycorrhizal fruiting bodies are always closely related to the ecological function of ectomycorrhizal fungi. In this study, we explore endofungal bacteria in the fruiting body of Tylopilus neofelleus and their function during the absorption of chelated inorganic phosphorus by host pine through the ectomycorrhizal system. The results showed that the endofungal bacterial microbiota in the fruiting body of T. neofelleus might be related to the dissolution of chelated inorganic phosphorus in soil. The soluble phosphorus content in the combined system of T. neofelleus and endofungal bacteria Bacillus sp. strain B5 was five times higher than the sum of T. neofelleus-only treatment and Bacillus sp. strain B5-only treatment in the dissolution experiment of chelated inorganic phosphorus. The results showed that T. neofelleus not only promoted the proliferation of Bacillus sp. strain B5 in the combined system but also improved the expression of genes related to organic acid metabolism, as assesed by transcriptomic analysis. Lactic acid content was five times higher in the combined system than the sum of T. neofelleus-only treatment and Bacillus sp. strain B5-only treatment. Two essential genes related to lactate metabolism of Bacillus sp. strain B5, gapA and pckA, were significantly upregulated. Finally, in a pot experiment, we verified that T. neofelleus and Bacillus sp. strain B5 could synergistically promote the absorption of chelated inorganic phosphorus by Pinus sylvestris in a ternary symbiotic system. IMPORTANCE Ectomycorrhizal fungi (ECMF) have a limited ability to dissolve chelated inorganic phosphorus, which is the main component of soil phosphorus. In the natural environment, the extraradical hyphae of ECMF alone may not satisfy the phosphorus demand of the plant ectomycorrhizal system. In this study, our results innovatively show that the ectomycorrhizal system might be a ternary symbiont in which ectomycorrhizal fungi might recruit endofungal bacteria that could synergistically promote the mineralization of chelated inorganic phosphorus, which ultimately promotes plant phosphorus absorption by the ectomycorrhizal system.

Alteration of plant immunity in the interaction of roots with the endophytic fungus Phomopsis liquidambaris in response to external nitrogen conditions.

The complex environments of plants force them to prioritize their immune responses to stimuli occurring simultaneously, including colonization by microbes or nutrient availability. Little is known about how the interplay between endophytes and nutrient status affects the immune responses of both plants and fungi. We primarily monitored immune responses in rice following inoculation with the endophytic fungus Phomopsis liquidambaris under different nitrogen (N) conditions. Ph. liquidambaris promoted plant growth under low N (LN) conditions, concomitant with higher root colonization. Plant production of oxidative signals, including hydrogen peroxide and nitric oxide, was activated by Ph. liquidambaris colonization under LN conditions, while salicylic acid (SA) was maintained at high levels and was involved in controlling rice-fungal interactions. High N (HN) conditions enhanced the ability of Ph. liquidambaris in suppressing plant cell death and the ability of roots to degrade Ph. liquidambaris cell walls. Furthermore, under both LN and HN conditions, the activity of plant defence-associated enzymes and fungal antioxidases was not affected in the interactive association. Our data reveal the alteration of plant immunity, including oxidative signalling and plant cell death, by fungal colonization in response to external N conditions and identify SA signalling as a potential controller for rice-Ph. liquidambaris interaction.

Root endophyte-enhanced peanut-rhizobia interaction is associated with regulation of root exudates.

Root exudates play a crucial role in the symbiosis between leguminous plants and rhizobia. Our previous studies have shown that a fungal endophyte Phomopsis liquidambaris promotes peanut-rhizobia nodulation and nitrogen fixation, but the underlying mechanism are largely unknown. Here, we explore the role of peanut root exudates in Ph. liquidambaris-mediated nodulation enhancement. We first collected root exudates from Ph. liquidambaris-inoculated and un-inoculated peanuts and determined their effects on rhizobial growth, biofilm formation, chemotaxis, nodC gene expression, and peanut nodulation. Our results found a positive effect of Ph. liquidambaris-inoculated root exudates on these characteristics of rhizobia. Next, we compared the root exudates profile of Ph. liquidambaris-inoculated and un-inoculated plants and found that Ph. liquidambaris altered the concentrations of phenolic acids, flavonoids, organic acids and amino acids in root exudates. Furthermore, the rhizobial chemotaxis, growth and biofilm formation in response to the changed compounds at different concentrations showed that all of the test compounds induced rhizobial chemotactic behavior, and organic acids (citric acid and oxalic acid) and amino acid (glutamate, glycine and glutamine) at higher concentrations increased rhizobial growth and biofilm formation. Collectively, our results suggest that root exudates alterations contribute to Ph. liquidambaris-mediated peanut-rhizobia nodulation enhancement.

Soil legacy of arbuscular mycorrhizal fungus Gigaspora margarita: The potassium-sequestering glomalin improves peanut (Arachis hypogaea) drought resistance and pod yield.

In agroecosystems, drought stress severely threatens crops development. Although potassium (K) is required in amounts by crops under drought stress, the mobilization and availablity of K are limited by the soil water status. Arbuscular mycorrhizal (AM) fungi can form mutualistic associations with most crops and play direct or indirect roles in the host drought resistance. Considering that the glomalin generated by living AM fungal hyphae can sequester multiple minerals, however, the function of mineral-sequestering glomalin in the crop drought resistance remains unclear. In this study, peanuts cultivated in the sterilized soil with a history of AM fungi inoculation showed significantly enhanced leaf K accumulation, drought resistance and pod yield under drought stress. Through the collection of different types of mineral-sequestering glomalin from living AM fungal hyphae, the peanut drought resistance was improved only when K-sequestering glomalin was added. Moreover, we found that peanut root exudates could prime the dissociation of glomalin-bound K and further satisfy the K requirement of crops. Our study is the first report that K-sequestering glomalin could improve drought performance and peanut pod yield, and it helps us to understand the ecological importance of improving AM symbiosis to face agricultural challenges.

Effects of multi-phase inoculation on the fungal community related with the improvement of medicinal herbal residues composting.

Composting has become the most important way to recycle medicinal herbal residues (MHRs). The traditional composting method, adding a microbial agent at one time, has been greatly limited due to its low composting efficiency, mutual influence of microbial agents, and unstable compost products. This study was conducted to assess the effect of multi-phase inoculation on the lignocellulose degradation, enzyme activities, and fungal community during MHRs composting. The results showed that multi-phase inoculation treatment had the highest thermophilic temperature (68.2 °C) and germination index (102.68%), significantly improved available phosphorus content, humic acid, and humic substances concentration, accelerated the degradation of cellulose and lignin, and increased the activities of cellulase in the mature phase, xylanase, manganese peroxidase, and utilization of phenolic compounds. Furthermore, the non-metric multi-dimensional scaling showed that the composting process and inoculation significantly influenced fungal community composition. In multi-phase inoculation treatment, Thermomyces in mesophilic, thermophilic, and mature phase, unclassified_Sordariales, and Coprinopsis in mature phase were the dominant genus that might be the main functional groups to degrade lignocellulose and improve the MHRs composting process.

Mycelial network-mediated rhizobial dispersal enhances legume nodulation.

The access of rhizobia to legume host is a prerequisite for nodulation. Rhizobia are poorly motile in soil, while filamentous fungi are known to grow extensively across soil pores. Since root exudates-driven bacterial chemotaxis cannot explain rhizobial long-distance dispersal, mycelia could constitute ideal dispersal networks to help rhizobial enrichment in the legume rhizosphere from bulk soil. Thus, we hypothesized that mycelia networks act as vectors that enable contact between rhizobia and legume and influence subsequent nodulation. By developing a soil microcosm system, we found that a facultatively biotrophic fungus, Phomopsis liquidambaris, helps rhizobial migration from bulk soil to the peanut (Arachis hypogaea) rhizosphere and, hence, triggers peanut-rhizobium nodulation but not seen in the absence of mycelia. Assays of dispersal modes suggested that cell proliferation and motility mediated rhizobial dispersal along mycelia, and fungal exudates might contribute to this process. Furthermore, transcriptomic analysis indicated that genes associated with the cell division, chemosensory system, flagellum biosynthesis, and motility were regulated by Ph. liquidambaris, thus accounting for the detected rhizobial dispersal along hyphae. Our results indicate that rhizobia use mycelia as dispersal networks that migrate to legume rhizosphere and trigger nodulation. This work highlights the importance of mycelial network-based bacterial dispersal in legume-rhizobium symbiosis.

Nitrogen fertilizer-regulated plant-fungi interaction is related to root invertase-induced hexose generation.

The mechanisms underlying nitrogen (N)-regulated plant-fungi interactions are not well understood. N application modulates plant carbohydrate (C) sinks and is involved in the overall plant-fungal association. We hypothesized that N regulates plant-fungi interactions by influencing the carbohydrate metabolism. The mutualistic fungus Phomopsis liquidambaris was found to prioritize host hexose resources through in vitro culture assays and in planta inoculation. Rice-Ph. liquidambaris systems were exposed to N gradients ranging from N-deficient to N-abundant conditions to study whether and how the sugar composition was involved in the dynamics of N-mediated fungal colonization. We found that root soluble acid invertases were activated, resulting in increased hexose fluxes in inoculated roots. These fluxes positively influenced fungal colonization, especially under N-deficient conditions. Further experiments manipulating the carbohydrate composition and root invertase activity through sugar feeding, chemical treatments and the use of different soil types revealed that the external disturbance of root invertase could reduce endophytic colonization and eliminate endophyte-induced host benefits under N-deficient conditions. Collectively, these results suggest that the activation of root invertase is related to N deficiency-enhanced endophytic colonization via increased hexose generation. Certain combinations of farmland ecosystems with suitable N inputs could be implemented to maximize the benefits of plant-fungi associations.

Enhanced nitrogen and phosphorus activation with an optimized bacterial community by endophytic fungus Phomopsis liquidambari in paddy soil.

The endophytic fungus Phomopsis liquidambari play a key role in habitat adaptation of rice (Oryza sativa L.) with potential multiple beneficial. However, our previous published work on this subject remains incomplete. Here, we performed a soil nutrient (nitrogen and phosphorus) transformation with related functional genes and elucidated how rhizosphere microbiota vary their response to P. liquidambari interaction throughout the plant's life cycle under field conditions by Illumina Miseq sequencing platforms in a nutrient-limited paddy soil. Our results showed that P. liquidambari symbiosis decreased the nitrogen and phosphorus loss by 24.59% and 17.46% per pot, respectively. Additionally, we suggest that the application of P. liquidambari altered the activation of soil nitrogen and phosphorus functional genes to accelerate nutrient turnover in the rice rhizosphere. High-throughput sequencing with co-occurrence network and species-related network analysis further revealed that P. liquidambari colonization influenced the patterns of microbiota shift in the rhizosphere, especially during the heading stages. This led to an optimized microbial community through the promotion and inhibition of indigenous soil microbes with a higher level of available nutrient supplies. Our study strongly proposes rice-P. liquidambari symbiosis as a useful candidate for improving N and P acquisition and utilization.