Landscape scale ecology of Tetracladium spp. fungal root endophytes

Diurnal Rhythmicity in the Rhizosphere Microbiome-Mechanistic Insights and Significance for Rhizosphere Function

The rhizosphere is a key interface between plants, microbes and the soil which influences plant health and nutrition and modulates terrestrial biogeochemical cycling. Recent research has shown that the rhizosphere environment is far more dynamic than previously recognised, with evidence emerging for diurnal rhythmicity in rhizosphere chemistry and microbial community composition. This rhythmicity is in part linked to the host plant's circadian rhythm, although some heterotrophic rhizosphere bacteria and fungi may also possess intrinsic rhythmicity. We review the evidence for diurnal rhythmicity in rhizosphere microbial communities and its link to the plant circadian clock. Factors which may drive microbial rhythmicity are discussed, including diurnal change in root exudate flux and composition, rhizosphere physico-chemical properties and plant immunity. Microbial processes which could contribute to community rhythmicity are considered, including self-sustained microbial rhythms, bacterial movement into and out of the rhizosphere, and microbe-microbe interactions. We also consider evidence that changes in microbial composition mediated by the plant circadian clock may affect microbial function and its significance for plant health and broader soil biogeochemical cycling processes. We identify key knowledge gaps and approaches which could help to resolve the spatial and temporal variation and functional significance of rhizosphere microbial rhythmicity. This includes unravelling the factors which determine the oscillation of microbial activity, growth and death, and cross-talk with the host over diurnal time frames. We conclude that diurnal rhythmicity is an inherent characteristic of the rhizosphere and that temporal factors should be considered and reported in rhizosphere studies.

From treetops to river bottoms: Exploring the role of phyllosphere fungi in aquatic fungal communities

Fungi play a crucial role in aquatic leaf litter decomposition. Aquatic fungi have long been thought to spend the majority of their lives in the water. Here, we explore the possibility of an amphibious life cycle, where phyllosphere fungi spend part of their life cycle in aquatic systems. We used internal transcribed spacer (ITS) fungal sequencing to follow phyllosphere fungi onto submerged litter, and quantitative stable isotope probing (qSIP) to differentiate active and inactive fungi. We found that around 30% of fungi active on aquatic litter entered the stream with the leaf and that these phyllosphere fungi were as active, if not more active than, as the fungi colonizing from the water column. These results demonstrate that phyllosphere fungi are an important part of aquatic fungal communities.

Regional scale diversity and distribution of soil inhabiting Tetracladium

The genus Tetracladium has historically been regarded as an aquatic hyphomycete. However, sequencing of terrestrial ecosystems has shown that Tetracladium species might also be terrestrial soil and plant-inhabiting fungi. The diversity of Tetracladium species, their distribution across ecosystems, and the factors that shape community composition remain largely unknown. Using internal transcribed spacer (ITS) amplicon sequencing, we investigated the spatial distribution of Tetracladium in 970 soil samples representing the major ecosystems found across the British landscape. Species of the genus were found in 57% of the samples and across all vegetation types. The Tetracladium sequences we recovered included species common in aquatic ecosystems. However, we found five additional clades that clustered with environmental sequences previously found in terrestrial environments. The community composition of the Tetracladium OTUs was mainly related to vegetation type and soil pH. Strikingly, both taxon richness and overall abundance were highest in arable soils and showed positive relationships with soil pH. T. maxilliforme and a taxon of environmental sequences, Tetracladium group 1, was the biggest group, had the most relative abundance across ecosystems and was found in all vegetation types. Overall, this study provides insights into the community composition patterns of Tetracladium in terrestrial ecosystems and highlights the importance of vegetation characteristics in shaping Tetracladium communities.

Understanding the ecological versatility of Tetracladium species in temperate forest soils

Although Tetracladium species have traditionally been studied as aquatic saprotrophs, the growing number of metagenomic and metabarcoding reports detecting them in soil environments raises important questions about their ecological adaptability and versatility. We investigated the factors associated with the relative abundance, diversity and ecological dynamics of Tetracladium in temperate forest soils. Through amplicon sequencing of soil samples collected from 54 stands in six forest sites across the eastern United States, we identified 29 distinct Amplicon Sequence Variants (ASVs) representing Tetracladium, with large differences in relative abundance and small changes in ASV community composition among sites. Tetracladium richness was positively related to soil pH, soil temperature, total sulphur and silt content, and negatively related to plant litter quality, such as the lignin-to-nitrogen ratio and the lignocellulose index. Co-occurrence network analysis indicated negative relationships between Tetracladium and other abundant fungal groups, including ectomycorrhizal and arbuscular mycorrhizal fungi. Collectively, our findings highlight the ecological significance of Tetracladium in temperate forest soils and emphasize the importance of site-specific factors and microbial interactions in shaping their distribution patterns and ecological dynamics.

Combating wheat yellow mosaic virus through microbial interactions and hormone pathway modulations

BACKGROUND

The rhizosphere microbiome is critical for promoting plant growth and mitigating soil-borne pathogens. However, its role in fighting soil-borne virus-induced diseases, such as wheat yellow mosaic virus (WYMV) transmitted by Polymyxa graminis zoospores, remains largely underexplored. In this study, we hypothesized that during viral infections, plant microbiomes engage in critical interactions with plants, with key microbes playing vital roles in maintaining plant health. Our research aimed to identify microbial taxa that not only suppress the disease but also boost wheat yield by using a blend of techniques, including field surveys, yield assessments, high-throughput sequencing of plant and soil microbiomes, microbial isolation, hydroponic experiments, and transcriptome sequencing.

RESULTS

We found that, compared with roots and leaves, the rhizosphere microbiome showed a better performance in predicting wheat yield and the prevalence of P. graminis and WYMV across the three WYMV-impacted regions in China. Using machine learning, we found that healthy rhizospheres were marked with potentially beneficial microorganisms, such as Sphingomonas and Allorhizobium-Neorhizobium-Parararhizobium-Rhizobium, whereas diseased rhizospheres were associated with a higher prevalence of potential pathogens, such as Bipolaris and Fusicolla. Structural equation modeling showed that these biomarkers both directly and indirectly impacted wheat yield by modulating the rhizosphere microbiome and P. graminis abundance. Upon re-introduction of two key healthy rhizosphere biomarkers, Sphingomonas azotifigens and Rhizobium deserti, into the rhizosphere, wheat growth and health were enhanced. This was attributed to the up-regulation of auxin and cytokinin signaling pathways and the regulation of jasmonic acid and salicylic acid pathways during infections.

CONCLUSIONS

Overall, our study revealed the critical role of the rhizosphere microbiome in combating soil-borne viral diseases, with specific rhizosphere microbes playing key roles in this process. Video Abstract.

Bacillus-derived consortium enhances Ginkgo biloba's health and resistance to Alternaria tenuissima

BACKGROUND

Bacillus, as a plant-growth-promoting rhizobacteria, can enhance the resistance of plants to phytopathogens. In our study, Bacillus strains showing excellent biocontrol were screened and used to control ginkgo leaf blight (Alternaria tenuissima).

RESULTS

Four biocontrol Bacillus strains-Bsa537, Bam337, Bso544, and Bsu503-were selected from 286 isolates based on their capacity to inhibit pathogens and promote plant growth. The four Bacillus strains significantly improved the resistance of ginkgo to leaf blight. This was especially the case when the four strains were used as a mixture, which contributed to a decrease in lesion area of >40%. Hence, a mixture of Bacillus strains was used to control ginkgo leaf blight in the field. Treatment efficiency varied from 30% to 100% (average 81.5%) and was higher than that of the control (-2% to -18%, average - 8.5%); the antioxidant capacity of the treated ginkgo was also stronger. In addition, ginkgo biomass increased as a result of treatment with the Bacillus mixture, including leaf weight, area, thickness, number of lateral roots and root weight. Furthermore, the Bacillus mixture improved the ginkgo rhizosphere soil by boosting the number of beneficial microorganisms, lowering the number of pathogens and hastening soil catabolism.

CONCLUSION

The Bacillus mixture improved the health status of ginkgo by protecting it from pathogen attack, promoting its growth and improving the microorganism community in the rhizosphere. This work closes a technological gap in the biological control of ginkgo leaf blight, investigates application methods for compound Bacillus biofertilizers and establishes a framework for the popularity and commercialization of these products. © 2024 Society of Chemical Industry.

Metabolomics analysis of flavor differences in Shuixian (Camellia sinensis) tea from different production regions and their microbial associations

Shuixian is renowned for its "rock flavor". However, the variations in Shuixian flavor are unclear, as the discussion mainly considers regional factors and overlooks the role of microorganisms. Sensory evaluation of Shuixian from three different regions (Zhengyan, Banyan, and Waishan) revealed that each had unique flavor characteristics: a woody aroma with slight acidity, a strong floral and fruity aroma with good freshness, and a distinct sweet aroma and sourness. Metabolomic analyses have revealed that 2-methylpyrazine was a crucial component of the woody aroma, whereas other metabolites contributed to sweet aroma, freshness, and acidity. Moreover, examinations of the relationship between flavor metabolites and microorganisms revealed that fungi had a more pronounced influence on the metabolite content of Shuixian. The study evaluated the role of fermentation microorganisms in shaping the flavor based on Shuixian flavor analyses, contributing to further research into the "rock flavor", as well as potential microbial interventions.

Temporal patterns of endophytic microbial heterogeneity across distinct ecological compartments within the Panax ginseng root system following deforestation for cultivation

Alterations in the microbial community significantly impact the yield and quality of ginseng. Yet, the dynamics of microbial community shifts within the root endophytes of ginseng across varying cultivation periods remain inadequately understood. This study zeroes in on the microbial community variations within the xylem (M), phloem (R), and fibrous roots (X) of ginseng during the fourth (F4) and fifth (F5) years of cultivation, aiming to bridge this research gap. We assessed soil physicochemical properties, enzyme activities, and nine individual saponins, complemented by high-throughput sequencing techniques (16S rDNA and ITS) to determine their profiles. The results showed that cultivation years mainly affected the microbial diversity of endophytic bacteria in ginseng fibrous roots compartment: the ASVs number and α-diversity Chao1 index of bacteria and fungi in F5X compartment with higher cultivation years were significantly higher than those in F4X compartment with lower cultivation years. It is speculated that the changes of fibrous roots bacterial groups may be related to the regulation of amino acid metabolic pathway. Such as D-glutamine and D-glutamate metabolism D-glutamine, cysteine and methionine metabolism regulation. The dominant bacteria in ginseng root are Proteobacteria (relative abundance 52.07-80.35%), Cyanobacteria (1.97-42.52%) and Bacteroidota (1.11-5.08%). Firmicutes (1.28-3.76%). There were two dominant phyla: Ascomycota (60.10-93.71%) and Basidiomycota (2.25-30.57%). Endophytic fungi were more closely related to soil physicochemical properties and enzyme activities. AN, TK, OP, SWC and EC were the main driving factors of endophytic flora of ginseng root. Tetracladium decreased with the increase of cultivation years, and the decrease was more significant in phloem (F4R: 33.36%, F5R: 16.48%). The relative abundance of Bradyrhizobium, Agrobacterium and Bacillus in each ecological niche increased with the increase of cultivation years. The relative abundance of Bradyrhizobium and Agrobacterium in F5X increased by 8.35 and 9.29 times, respectively, and Bacillus in F5M increased by 5.57 times. We found a variety of potential beneficial bacteria and pathogen antagonists related to ginseng biomass and saponins, such as Bradyrhizobium, Agrobacterium, Bacillus and Exophiala, which have good potential for practical application and development.

Fungal and bacterial communities and their associations in snow-free and snow covered (sub-)alpine Pinus cembra forest soils

BACKGROUND

In Europe, Pinus cembra forests cover subalpine and alpine areas and they are of high conservational and ecological relevance. These forests experience strong seasonality with alternating snow-free and snow covered periods. Although P. cembra is known for mycorrhization and mycorrhizae usually involve fungi, plants and bacteria, the community compositions of fungi and bacteria and their associations in (sub-)alpine P. cembra forests remain vastly understudied. Here, we studied the fungal and bacterial community compositions in three independent (sub-)alpine P. cembra forests and inferred their microbial associations using marker gene sequencing and network analysis. We asked about the effect of snow cover on microbial compositions and associations. In addition, we propose inferring microbial associations across a range of filtering criteria, based on which we infer well justified, concrete microbial associations with high potential for ecological relevance that are typical for P. cembra forests and depending on snow cover.

RESULTS

The overall fungal and bacterial community structure was comparable with regards to both forest locations and snow cover. However, occurrence, abundance, and diversity patterns of several microbial taxa typical for P. cembra forests differed among snow-free and snow covered soils, e.g. Russula, Tetracladium and Phenoliphera. Moreover, network properties and microbial associations were influenced by snow cover. Here, we present concrete microbial associations on genus and species level that were repeatedly found across microbial networks, thereby confirming their ecological relevance. Most importantly, ectomycorrhizal fungi, such as Basidioascus, Pseudotomentella and Rhizopogon, as well as saprobic Mortierella changed their bacterial association partners depending on snow cover.

CONCLUSION

This is the first study researching fungal-bacterial associations across several (sub-)alpine P. cembra forests. The poorly investigated influence of snow cover on soil fungi and bacteria, especially those mycorrhizing P. cembra roots, but also saprobic soil organisms, underlines the relevance of forest seasonality. Our findings highlight that the seasonal impact of snow cover has significant consequences for the ecology of the ecosystem, particularly in relation to mycorrhization and nutrient cycling. It is imperative to consider such effects for a comprehensive understanding of the functioning resilience and responsiveness of an ecosystem.

Study of the Bacterial, Fungal, and Archaeal Communities Structures near the Bulgarian Antarctic Research Base "St. Kliment Ohridski" on Livingston Island, Antarctica

As belonging to one of the most isolated continents on our planet, the microbial composition of different environments in Antarctica could hold a plethora of undiscovered species with the potential for biotechnological applications. This manuscript delineates our discoveries after an expedition to the Bulgarian Antarctic Base "St. Kliment Ohridski" situated on Livingston Island, Antarctica. Amplicon-based metagenomics targeting the 16S rRNA genes and ITS2 region were employed to assess the metagenomes of the bacterial, fungal, and archaeal communities across diverse sites within and proximal to the research station. The predominant bacterial assemblages identified included Oxyphotobacteria, Bacteroidia, Gammaprotobacteria, and Alphaprotobacteria. A substantial proportion of cyanobacteria reads were attributed to a singular uncultured taxon within the family Leptolyngbyaceae. The bacterial profile of a lagoon near the base exhibited indications of penguin activity, characterized by a higher abundance of Clostridia, similar to lithotelm samples from Hannah Pt. Although most fungal reads in the samples could not be identified at the species level, noteworthy genera, namely Betamyces and Tetracladium, were identified. Archaeal abundance was negligible, with prevalent groups including Woesearchaeales, Nitrosarchaeum, Candidatus Nitrosopumilus, and Marine Group II.

Influence of cultivation duration on microbial taxa aggregation in Panax ginseng soils across ecological niches

Introduction

Microbial communities are crucial for plant health and productivity. However, the influence of cultivation age on the ecological processes in assembling plant microbiomes at various ecological niches remains unclear.

Methods

We selected 12 samples from ginseng farmlands with different cultivation years (N4: 4 years old, N6: 6 years old). We used soil physicochemical properties, enzyme activities, and high-throughput sequencing (16S rDNA and ITS) to examine the rhizoplane (RP), rhizosphere (RS), and bulk soil (BS).

Results

Our results indicated that cultivation years significantly affect the soil microbiome's diversity and community composition across different ecological niches. The BS microbiome experienced the largest effect, while the RS experienced the smallest. N6 showed a greater impact than N4. This effect was more pronounced on the fungal communities than the bacterial communities of various ecological niches and can be closely related to the soil's physicochemical properties. In N4 soils, we observed an upward trend in both the number of ASVs (amplicon sequence variations) and the diversity of soil microbial taxa across various ecological niches. In N4RP, the bacteria Sphingomonas, known for degrading toxic soil compounds, was present. All ecological niches in N4 showed significant enrichment of Tetracladium fungi, positively associated with crop yield (N4RP at 6.41%, N4RS at 11.31%, and N4BS at 3.45%). In N6 soils, we noted a stark decline in fungal diversity within the BS, with a 57.5% reduction in ASVs. Moreover, Sphingomonas was abundantly present in N6RS and N6BS soils. The relative abundance of the pathogen-inhibiting fungus Exophiala in N6RP and N6RS reached 34.18% and 13.71%, respectively, marking increases of 4.9-fold and 7.7-fold. Additionally, another pathogeninhibiting fungus, Humicola, showed significant enrichment in N6BS, with a 7.5-fold increase. The phenolic acid-producing fungus Pseudogymnoascus in N6RP, N6RS, and N6BS showed increases of 2.41-fold, 2.55-fold, and 4.32-fold, respectively. We hypothesize that functional genes related to the metabolism of terpenoids and polyketides, as well as signaling molecules and interactions, regulate soil microbial taxa in ginseng from different cultivation years.

Discussion

In conclusion, our study enhances understanding of plant-microbe interactions and aids the sustainable development of medicinal plants, particularly by addressing ginseng succession disorder.

The effect of plant compartment and geographical location on shaping microbiome of Pulsatilla chinensis

The plant-associated microbiome has an effect on plant growth. Pulsatilla chinensis (Bge.) Regel is an important Chinese medicinal plant. Currently, there is little understanding of the P. chinensis-associated microbiome and its diversity and composition. Here, the core microbiome associated with the root, leaf, and rhizospheric soil compartments of P. chinensis from five geographical locations was analyzed by the metagenomics approach. The alpha and beta diversity analysis showed that the microbiome associated with P. chinensis was shaped by the compartment, especially in the bacterial community. The geographical location had little influence on microbial community diversity associated with root and leaf. Hierarchical clustering distinguished the microbial communities of rhizospheric soil based on their geographical location and among the soil properties, pH was showed the more stronger effect on the diversity of rhizospheric soil microbial communities. Proteobacteria was the most dominant bacterial phylum in the root, leaf, and rhizospheric soil. Ascomycota and Basidiomycota were the most dominant fungal phyla in different compartments. Rhizobacter, Anoxybacillus, and IMCC26256 were the most important marker bacterial species for root, leaf, and rhizospheric soil screened by random forest, respectively. The fungal marker species for root, leaf, and rhizospheric soil were not only different across the compartments but also the geographical locations. Functional analysis showed that P. chinensis-associated microbiome had the similar function which had no obvious relationship with geographical location and compartment. The associated microbiome indicated in this study can be used for identifying microorganisms related to the quality and growth of P. chinensis. KEY POINTS: • Microbiome associated with P. chinensis was shaped by the compartment • Microbiome composition and abundance associated with rhizospheric soil were affected by the geographical location • Compared with fungi, bacterial associated with P. chinensis composition and diversity were more stable in different geographical locations and compartments.