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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. [ABSTRACT FROM AUTHOR]

The deficiency of N-P availability in soil is a primary cause for crop yield and nutrient loss. Since plant-beneficial microbial symbiosis is an eco-friendly method for compensating this negative effect, understanding the interconnection between endophytic fungus colonization and mineral nutrient accumulation in edible parts of crop is important in agricultural production. In this study, we focused on the effects of endophytic fungus Phomopsis liquidambaris on the absorption and distribution of 14 essential mineral elements in vegetative organs (root and shoot) and reproductive organs (grain) of rice during its growing period with reduced N-P fertilizer application, as well as the changes in yield, quality, and mineral nutrition of rice grains. The possible mechanisms including the transcriptional level of the transport-related genes and the structure of endophytic community were also investigated. The results indicated that the P. liquidambaris significantly increased the accumulation of N, P, Fe, Mn, Zn, Mo, and Se in rice grains by 20.5%, 18.9%, 18.2%, 9.5%, 17.9%, 13.3%, and 17.1%, respectively, accompanied by the significant increase in yield (23.8%) and protein content (17.3%). These beneficial effects were attributed to the enhancement formation of iron plaque, the upregulation of nutrient transporters genes, and the altered endophyte community by P. liquidambaris symbiosis. In conclusion, P. liquidambaris could promote the partition of nutrients to the grains by increasing the efficiency of nutrient uptake and remobilization. Our results suggest P. liquidambaris symbiosis as a useful candidate for improving the mineral nutrition, quality, and yield of rice grains under N-P-deficient field condition. [ABSTRACT FROM AUTHOR]

Summary: 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. [ABSTRACT FROM AUTHOR]

Summary: 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. Brief Summary: We determined how to root endophyte affects plant response to different forms of N. Our results suggest that root endophyte differentially regulates plant response to NO3− and NH4+ nutrition through modulating N fluxes at the plant–fungal interface rather than through regulating defense responses. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. In the present study, we determined whether and how plant flowering affects root‐fungal mutualism. Our results revealed a novel metabolic network in which plant flowering‐mediated root fungal colonization is related to jasmonate‐dependent root glucose and fructose deprivation. The reductions of root glucose and fructose were probably due to the inhibitions of phloem sugar transport and root soluble invertase activity. Our results highlight importance of plant flowering in root microbiota composition. [ABSTRACT FROM AUTHOR]

Previously, the application of the fungal endophyte Phomopsis liquidambari B3 exhibited notable effect in alleviating soil obstacles caused by continuous cropping of peanut. It was supposed that P. liquidambari B3 could enhance the efficiency of nodulation and nitrogen fixation by enriching the diversity of nodular endophytic bacteria under continous monocropping system. To verify this hypothesis, a pot experiment was conducted under natural conditions. Four treatments were set as follow: discontinuous cropping soil (NS), continuous cropping soil (CK), continuous cropping soil inoculate with actived P. liquidambari B3 (CSB3), and continuous cropping soil inoculate with sterilized P. liquidambari B3 (CSIB3). As a result, a total of 120 isolates were obtained. Our study clearly declared that the addition of fungal endophyte effectively enriched the genetic diversity and the community composition in CSB3. In contrast, a low genetic diversity level and simplex community structure were exhibited in CK and CSIB3. Meanwhile, the positive percentage rate and corresponding community composition of the plant growth-promoting isolates in NS and CSB3 were larger and more abundant than the other. This is the first time to describe the effects of fungal endophytes on the diversity of the nodular culturable endophytic bacteria associated with continuous cropping of peanut. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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

A novel Gram-negative, strictly aerobic, short rod-shaped, non-motile bacterium, designated YIM 101302, 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 to the genus Sphingobacterium. The newly isolated bacterium was found to be closely related to Sphingobacterium composti T5-12 (97.1 % 16S rRNA sequence identity) and Sphingobacterium alimentarium WCC 4521 (95.6 % 16S rRNA sequence identity) forming a distinct clade with these two species. Polar lipids of strain YIM 101302 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-C. The genomic DNA G+C content was determined to be 38.9 mol%. The DNA-DNA hybridization values between strain YIM 101302 and S. composti T5-12, was 53.6 ± 5.8 %. These results indicates that strain YIM 101302 represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium rhinocerotis sp. nov. is proposed. The type strain is YIM 101302 (=CCTCC AB 2013218 = KCTC 42533). [ABSTRACT FROM AUTHOR]