Rhizospheric fungi and their link with the nitrogen-fixing Frankia harbored in host plant Hippophae rhamnoides L

Chromosome-level genome assembly of Hippophae tibetana provides insights into high-altitude adaptation and flavonoid biosynthesis

BACKGROUND

As an endemic shrub of the Qinghai-Tibetan Plateau (QTP), the distribution of Hippophae tibetana Schlecht. ranges between 2800 and 5200 m above sea level. As the most basal branch of the Hippophae genus, H. tibetana has an extensive evolutionary history. The H. tibetana is a valuable tree for studying the ecological evolution of species under extreme conditions.

RESULTS

Here, we generated a high-quality chromosome-level genome of H. tibetana. The total size of the assembly genome is 917 Mb. The phylogenomic analysis of 1064 single-copy genes showed a divergence between 3.4 and 12.8 Mya for H. tibetana. Multiple gene families associated with DNA repair and disease resistance were significantly expanded in H. tibetana. We also identified many genes related to DNA repair with signs of positive selection. These results showed expansion and positive selection likely play important roles in H. tibetana's adaptation to comprehensive extreme environments in the QTP. A comprehensive genomic and transcriptomic analysis identified 49 genes involved in the flavonoid biosynthesis pathway in H. tibetana. We generated transgenic sea buckthorn hairy root producing high levels of flavonoid.

CONCLUSIONS

Taken together, this H. tibetana high-quality genome provides insights into the plant adaptation mechanisms of plant under extreme environments and lay foundation for the functional genomic research and molecular breeding of H. tibetana.

Chromosome-level genome assembly of Hippophae gyantsensis

Hippophae gyantsensis, which is a native tree species in China, is ideal for windbreak and sand-fixing forests. It is an economically and ecologically valuable tree species distributed exclusively in the Qinghai-Tibet Plateau in China. In our study, we assembled a chromosome-level genome of H. gyantsensis using Illumina sequencing, Nanopore sequencing and chromosome structure capture technique. The genome was 716.32 Mb in size with scaffold N50 length of 64.84 Mb. A total of 716.25 Mb genome data was anchored and orientated onto 12 chromosomes with a mounting rate of up to 99.99%. Additionally, the genome was found to comprise approximately 56.84% repeat sequences, of which long terminal repeats(LTRs) that accounted for 33.19% of the entire genome. Meanwhile, a total of 32,316 protein-coding genes were predicted, and 91.07% of these genes were functionally annotated. We also completed a series of comparative genomic analyses to provide researchers with useful reference material for future studies on seabuckthorn.

Current Insight into Traditional and Modern Methods in Fungal Diversity Estimates

Fungi are an important and diverse component in various ecosystems. The methods to identify different fungi are an important step in any mycological study. Classical methods of fungal identification, which rely mainly on morphological characteristics and modern use of DNA based molecular techniques, have proven to be very helpful to explore their taxonomic identity. In the present compilation, we provide detailed information on estimates of fungi provided by different mycologistsover time. Along with this, a comprehensive analysis of the importance of classical and molecular methods is also presented. In orderto understand the utility of genus and species specific markers in fungal identification, a polyphasic approach to investigate various fungi is also presented in this paper. An account of the study of various fungi based on culture-based and cultureindependent methods is also provided here to understand the development and significance of both approaches. The available information on classical and modern methods compiled in this study revealed that the DNA based molecular studies are still scant, and more studies are required to achieve the accurate estimation of fungi present on earth.

Alone Yet Not Alone: Frankia Lives Under the Same Roof With Other Bacteria in Actinorhizal Nodules

Actinorhizal plants host mutualistic symbionts of the nitrogen-fixing actinobacterial genus Frankia within nodule structures formed on their roots. Several plant-growth-promoting bacteria have also been isolated from actinorhizal root nodules, but little is known about them. We were interested investigating the in planta microbial community composition of actinorhizal root nodules using culture-independent techniques. To address this knowledge gap, 16S rRNA gene amplicon and shotgun metagenomic sequencing was performed on DNA from the nodules of Casuarina glauca. DNA was extracted from C. glauca nodules collected in three different sampling sites in Tunisia, along a gradient of aridity ranging from humid to arid. Sequencing libraries were prepared using Illumina NextEra technology and the Illumina HiSeq 2500 platform. Genome bins extracted from the metagenome were taxonomically and functionally profiled. Community structure based off preliminary 16S rRNA gene amplicon data was analyzed via the QIIME pipeline. Reconstructed genomes were comprised of members of Frankia, Micromonospora, Bacillus, Paenibacillus, Phyllobacterium, and Afipia. Frankia dominated the nodule community at the humid sampling site, while the absolute and relative prevalence of Frankia decreased at the semi-arid and arid sampling locations. Actinorhizal plants harbor similar non-Frankia plant-growth-promoting-bacteria as legumes and other plants. The data suggests that the prevalence of Frankia in the nodule community is influenced by environmental factors, with being less abundant under more arid environments.

HrCYP90B1 modulating brassinosteroid biosynthesis in sea buckthorn (Hippophae rhamnoides L.) against fruit fly (Rhagoletis batava obseuriosa Kol.) infection

Sea buckthorn is an important ecological and economic tree species, and its berries have been severely damaged by sea buckthorn fruit fly, Rhagoletis batava obseuriosa Kol. (Diptera: Tephritidae) (RBO). Brassinosteroid (BR) is widely involved in stress tolerance of plant. However, limited knowledge exists regarding the molecular mechanisms underlying insect resistance. Here, we found that BR content was much higher in sea buckthorn fruits with RBO infection than non-infection, and the damage rates of fruit with BR treatment were significantly lower than that of non-treatment. It indicated that BR could enhance RBO resistance in sea buckthorn. Several BR biosynthesis-related HrCYPs genes (CYP85A1/85A2/90A1/90B1/90C1/90D1/92A6/724B/734A1) were obtained and identified based on transcriptome analysis, of which the most up-regulated gene in fruits was HrCYP90B1 under RBO and mechanical damage. Overexpression of HrCYP90B1 in Arabidopsis thaliana showed BR and salicylic acid (SA) content was significantly increased, and the substrate campesterol (CR) of HrCYP90B1 content decreased. Further studies revealed that silencing HrCYP90B1 by virus-induced gene silencing resulted in decrease of BR, SA and defense-related enzymes contents, and increase of CR content. Silencing HrCYP90B1 also caused suppression of SA and activation of jasmonic acid pathways, enabling enhanced RBO susceptibility and more damage of fruits. Taken together, we obtained evidence that HrCYP90B1 was a positive regulator in RBO resistance improvement in sea buckthorn, which will provide comprehensive insights into the tree defense system of sea buckthorn to pest infection.

GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies

Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com . The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.

Diversity of rhizosphere and endophytic fungi in Atractylodes macrocephala during continuous cropping

Rhizospheric and endophytic fungi are key factors which influence plant fitness and soil fertility. Atractylodes macrocephala is one of the best-known perennial herbs used in traditional Chinese medicine. Continuous cropping has been shown to have a negative effect on its growth and renders it more susceptible to microbial pathogen attacks. In this study, we investigated the effects of continuous cropping on the endophytic and rhizospheric fungi associated with A.  macrocephala using culture-independent Illumina MiSeq. Continuous cropping was found to decrease fungal diversity inside plant roots, stems, leaves and tubers. Additionally, we found that the structure and diversity of rhizospheric and endophytic fungal communities were altered by root-rot disease. Fusarium was overrepresented among root-rot rhizospheric and endophytic fungi, indicating that it has a major negative impact on plant health during A.  macrocephala monocropping. Canonical correspondence analysis of the control and diseased samples revealed that pH, hydrolysis N, electrical conductivity and Hg content were well-correlated with fungal community composition during continuous cropping. Taken together, these results highlight the ecological significance of fungal communities in maintaining plant fitness and will guide the development strategies to attenuate the negative impacts of A.  macrocephala continuous cropping.

Connection the Rhizomicrobiome and Plant MAPK Gene Expression Response to Pathogenic Fusarium oxysporum in Wild and Cultivated Soybean

Little known the connections between soybeans mitogen-activated protein kinase (MAPK) gene expression and the rhizomicrobiome upon invasion of the root pathogen Fusarium oxysporum. To address this lack of knowledge, we assessed the rhizomicrobiome and root transcriptome sequencing of wild and cultivated soybean during the invasion of F. oxysporum. Results indicated F. oxysporum infection enriched Bradyrhizobium spp. and Glomus spp. and induced the expression of more MAPKs in the wild soybean than cultivated soybean. MAPK gene expression was positively correlated with Pseudomonadaceae but negatively correlated with Sphingomonadaceae and Glomeraceae in both cultivated and wild soybean. Specifically, correlation profiles revealed that Pseudomonadaceae was especially correlated with the induced expression of GmMAKKK13-2 (Glyma.14G195300) and GmMAPK3-2 (Glyma.12G073000) in wild and cultivated soybean during F. oxysporum invasion. Main fungal group Glomeraceae was positively correlated with GmMAPKKK14-1 (Glyma.18G060900) and negatively correlated with GmRaf6-4 (Glyma.02G215300) in the wild soybean response to pathogen infection; while there were positive correlations between Hypocreaceae and GmMAPK3-2 (Glyma.12G073000) and between Glomeraceae and GmRaf49-3 (Glyma.06G055300) in the wild soybean response, these correlations were strongly negative in the response of cultivated soybean to F. oxysporum. Taken together, MAPKs correlated with different rhizomicrobiomes indicating the host plant modulated by the host self-immune systems in response to F. oxysporum.

Arbuscular Mycorrhizal Fungal Communities Are Influenced by Host Tree Species on the Loess Plateau, Northwest China

Arbuscular mycorrhizal (AM) fungi can establish mutualistic symbioses with most terrestrial plants and therefore play a crucial role in the re-vegetation and rehabilitation of degraded ecosystems. Yet, little information is available on AM fungal communities associated with dominant tree species in the semi-arid region of the Loess Plateau, Northwest China. In this study, topsoil (0–20 cm) and subsoil (20–40 cm) samples were collected from the rhizosphere of five dominant tree species in northern Shaanxi Province, to investigate the distribution and diversity of their associated AM fungi. The tree species were Hippophae rhamnoides Linn., Juniperus communis L., Populus cathayana Rehd., Robinia pseudoacacia L., and Salix matsudana Koidz. In total, 24 AM fungal species of eight genera were isolated from the rhizosphere soil samples and identified based on their spore morphology. Funneliformis and Funneliformis monosporum were respectively the most abundant genus and species of AM fungi. The distribution and diversity of AM fungi differed among the five tree species and also between the two soil depths. Across different tree species, the spore density of AM fungi varied from 2.85 to 15.32 spores g−1 fresh soil, with a species richness of 3–7, Shannon–Wiener index of 0.81–1.08, and evenness index of 0.30–0.53. The mycorrhizal colonization rate had a significant negative correlation with both the Shannon-Wiener index and species richness, whereas it was positively correlated with the evenness index. Permutational multivariate analysis of variance, non-metric multidimensional scaling, and structural equation modeling revealed that tree species, rather than soil depth or its interactions with tree species, had significant effects on the composition of AM fungal communities. In conclusion, the distribution and diversity of AM fungi associated with the dominant tree species were mainly affected by host tree species identity in the semi-arid ecosystem. Claroideoglomus etunicatum (W.N. Becker & Gerdemann) C. Walker & A. Schüßler and Glomus reticulatum Bhattacharjee & Mukerji appeared to be promising candidates for ecological restoration in the Loess Plateau region because of their adaptation to its semi-arid conditions with a broad spectrum of host tree species.

Comparative analysis of the rhizomicrobiome of the wild versus cultivated crop: insights from rice and soybean

Plant domestication was a pivotal accomplishment in human history, which led to a reduction in genetic diversity of crop species; however, there was less research focus on how this reduced genetic diversity of crops in affecting rhizosphere microbial communities during crop domestication process. Here, we used high-throughput sequencing to explore the different effects of crops domestication on rhizosphere microbial community structure of rice (Oryza sativa L. and Oryza rufipogon Griff.) and soybean (Glycine max L. and Glycine soja Sieb. et Zucc.). Results indicated that rhizosphere fungal communities are more strongly influenced by crop domestication than bacterial communities. There was a stronger relationship for fungi and bacteria in the cultivated crops than in the wild relatives. Results also showed that the wild varieties had a higher abundance of beneficial symbionts and a lower abundance of pathogens comparing with the cultivated varieties. There was a similar tendency for both rice and soybean in rhizosphere microbial communities by comparing wild crops and their cultivated varieties. In conclusion, crop domestication had a stronger effect on the fungal communities than on the bacterial communities and had improved the microbial relationship in rhizosphere of cultivated crops.

Hippophae rhamnoides berry related Pichia kudriavzevii yeast volatiles modify behaviour of Rhagoletis batava flies

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Pichia kudriavzevii yeasts were isolated from ripe Hippophae rhamnoides berries.

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Thirty-five yeast volatiles were identified from the headspace of P. kudriavzevii.

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Esters and alcohols contributed by 32% and 66% to the total blend amount.

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Ten of those volatiles elicited antenna responses of Rhagoletis batava flies.

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Mixture of synthetic olfactory active compounds attracted R. batava males and females.

Olfactory cues have a large impact on insect behaviour and fitness consequently showing potential in pest management. Yeast released volatiles are used by insects as olfactory cues for finding feeding and oviposition sites. The yeast strain SB-16-15 was isolated from spontaneous fermentation of Hippophae rhamnoides berries and identified as Pichia kudriavzevii. Thirty-nine volatiles were sampled from the headspace of P. kudriavzevii yeasts by solid phase micro extraction and identified by gas chromatography and mass spectrometry techniques. Ten of those volatiles elicited antennal responses of Rhagoletis batava flies, one of the most serious pest of H. rhamnoides berries. In the two-choice experiments, R. batava flies preferred the mixture composed of nine synthetic compounds analogous to electroanntenographic active volatiles released by the yeasts compare to the solvent control. Female flies were significantly attracted to the mixture at the concentration 0.1 µL mL⁻¹ and showed no preference to the mixture at the concentration 1 µL mL⁻¹ versus control while males reacted positively to the synthetic blend at the concentration 1 µL mL⁻¹. Herein, for the first time, behaviour modifying effect of H. rhamnoides berry related yeast volatiles was shown suggesting these semiochemicals have potential in use for monitoring R. batava flies.

The rhizomicrobiomes of wild and cultivated crops react differently to fungicides

The fungicides used to control diseases in cereal production can have adverse effects on non-target microbial communities, with possible consequences for plant health and productivity. Although we know that fungicides affect microbial community structure and soil activities, it is unclear how crop cultivars have altered the impact of fungicides on rhizomicrobiomes. In this study, the rhizosphere bacterial and fungal communities and structures of cultivated crops and their wild relatives were studied by Illumina MiSeq sequencing analysis. The results indicated that the rhizomicrobiome communities of wild crops reacted more strongly to fungicides than that of their cultivated relatives. Furthermore, fungal community composition was more affected by fungicides than bacterial community composition. Remarkably, the same trend was observed in both soybean and rice with regard to the influence of crop cultivar on the response of the rhizomicrobiome to fungicide application, although the level of the response was not similar. We report for the first time that the rhizomicrobiomes of wild crops reacted more strongly to fungicides than the rhizomicrobiomes of cultivated crops.