Network hubs in root-associated fungal metacommunities

Fungal diversity and network analysis in rhizosphere soil of Atractylodes macrocephala across different cultivation regions

This study investigated the impact of rhizosphere fungi on the quality of Atractylodes macrocephala in China by analyzing the physical and chemical properties, enzyme activities, and community structures of soil samples from four distinct regions: Pan'an (PA), Bozhou (BZ), Zhoukou (ZK), and Anguo (AG). The results indicated that both biomass and active components of A. macrocephala were significantly higher in authentic production areas compared to emerging ones. The rhizosphere soil network in PA, identified as an authentic production area, exhibited the most complex structure, with pH levels significantly negatively correlated with 12 major fungal genera. Notably, fungi such as Rozellomycota, Mortierella, and Basidiomycota were linked to the quality of A. macrocephala through their roles in organic matter decomposition. Additionally, Saitozyma was found to be a central component of the rhizosphere fungal community, with a relative abundance of 2.19%, markedly higher than in emerging production areas (< 0.1%). These findings provide critical insights into the factors affecting A. macrocephala quality across different regions, offering valuable guidance for the sustainable cultivation of this essential medicinal plant in China.

Microbial community diversity and assembly processes in the aridification of wetlands on the Qinghai-Tibet Plateau

This study investigates soil microbial community dynamics in high-altitude wetlands on the Qinghai-Tibet Plateau under drought conditions. It compares the composition, structure, and assembly mechanisms of microbial communities in water-rich and water-deficient wetlands. The results show that while α diversity remains stable after aridification, the community undergoes significant phylum reorganization. Aridification leads to increased sensitivity in the β diversity of archaea and bacteria to environmental and geographic factors, while fungal β diversity remains unchanged. Co-occurrence network analysis reveals a more complex and denser microbial network in aridified wetlands. Hub microbial groups are found only in bacteria and fungi, and their richness decreases after aridification. The study suggests a shift from a neutral to a partially deterministic assembly process, marked by reduced dispersal limitations and stronger heterogeneous selections. These findings contribute to understanding microbial community evolution in response to global environmental changes.

Core Mycorrhizal Fungi Promote Seedling Growth in Dendrobium officinale: An Important Medicinal Orchid

The critically endangered orchid Dendrobium officinale, valued for its medicinal properties, depends on specific seedling-associated mycorrhizal fungi (SAMF) for successful early-stage seedling development. However, conservation efforts are often hindered by difficulties in obtaining suitable SAMF, leading to poor seedling establishment in both natural and cultivated environments. In this study, we explored the growth-promoting effects of SAMF and evaluated the performances of synthetic fungal combinations. Our results demonstrated that mycorrhizal fungi, widely distributed across multiple habitats with high isolation frequencies, significantly promoted the growth of D. officinale, with specific fungi favoring different growth parameters. Tulasnella sp. TP-2 and TP-3 significantly improved stem diameter and plant height by 2.622 mm and 4.621 cm, while Tulasnella sp. TP-8 significantly increased tillering by a factor of 4.47. Additionally, Tulasnella sp. TP-11 and TP-13 markedly increased the number of new leaves (4.45) and new roots (2.688), respectively, identifying them as essential core OMFs for D. officinale seedlings. Contrary to expectations, synthetic fungal combinations composed of core orchid mycorrhizal fungi (core OMFs) did not exhibit synergistic growth-promoting effects. Instead, pronounced offset effects were observed, indicating that interactions between fungi may introduce competition or inhibition, limiting their collective ability to enhance plant growth. Our results confirmed that the core OMFs significantly promoted the growth of D. officinale seedlings. These core OMFs can serve as essential components in specialized microbial fertilizers for D. officinale, improving growth efficiency and yield, and supporting the sustainable development of the D. officinale industry.

In-Depth Analysis of Soil Microbial Community Succession Model Construction under Microplastics Stress

Although microplastics (MPs) toxicity to soil microorganisms has been preliminarily explored, the underlying reasons affecting the direction of microbial community succession are unclear. This study aimed to investigate the impacts of MPs infer community assembly mechanisms through phylogenetic bin-based null model analysis, network models, and protein function prediction in five typical Northeast China five typical soils. The results show that microbial communities in soils with high organic matter exhibit a stronger response to MPs, with enhanced protein functionality, network regulation, and assembly processes. The presence of MPs increased the drift process in the soil microbial community assembly by 2%, a deterministic process influenced by MPs, and enhanced the complexity and stability of the community assembly. Overall, MPs altered microbial protein function and regulatory networks by affecting diversity and community assembly processes, leading to shifts in microbial community succession. This study provided a theoretical basis for further study of the ecotoxicological effects of MPs in soil.

Dynamics of wheat rhizosphere microbiome and its impact on grain production across growth stages

Crop plant microbiomes are increasingly seen as important in plant nutrition and health, and a key to maintaining food productivity. Currently, little is known of the temporal changes that occur in the wheat rhizosphere microbiome as the plant develops, and how this varies among different sites. We used a pot-based mesocosm experiment with the same modern wheat cultivar grown in eight soils from across the North China Plain, a major wheat producing area. DNA from rhizosphere soil was taken from wheat plants, from seedling up to grain harvesting stage, and amplicon sequenced for prokaryotes and microeukaryotes, followed by community analysis. Our results showed that rhizosphere diversity of prokaryotes and microeukaryotes increased over time in most sites. While there was turnover between earlier- and later-arriving species, the predominant successional model was accumulation, with early arrivals remaining in place as others colonized the rhizosphere. Rhizosphere community network modularity and stability increased during the development and maturation of the wheat plant. The abundances of certain stage-specific keystone species were correlated with eventual grain yield - suggesting a potentially important role in wheat production. Some keystone species belonged to groups previously implicated in various functions. This study provides a basis for further experimental investigation of the wheat rhizosphere microbiome, its role in determining crop yields, and the potential for microbiome engineering to promote yields. The sequential arrival and accumulation of microbiota suggests that deliberate inoculation might accelerate this process.

Ecological filters shape arbuscular mycorrhizal fungal communities in the rhizosphere of secondary vegetation species in a temperate forest

The community assembly of arbuscular mycorrhizal fungi (AMF) in the rhizosphere results from the recruitment and selection of different AMF species with different functional traits. The aim of this study was to analyze the relationship between biotic and abiotic factors and the AMF community assembly in the rhizosphere of four secondary vegetation (SV) plant species in a temperate forest. We selected four sites at two altitudes, and we marked five individuals per plant species at each site. Soil rhizosphere samples were collected from each SV plant species, during the rainy and dry seasons. Soil samples from the rhizosphere of each plant species were analyzed for AMF spores, organic matter (OM), pH, soil moisture, and available phosphorus, and nitrogen. Three ecological filters influenced the AMF community assembly: host plant identity, abiotic factors, and AMF species co-occurrence. This assembly consisted of 61 AMF species, with different β-diversity values among plant species across seasons and altitudes. Canonical correspondence analysis revealed that AMF community composition is linked to OM and available P and N, with only a few AMF species co-occurring, while most do not. Our study highlights how ecological filters shape AMF structure, which is essential for understanding how soil and environmental factors affect AMF in SV plant species across seasons and altitudes.

Mycorrhizal and endophytic fungi structure forest below-ground symbiosis through contrasting but interdependent assembly processes

BACKGROUND

Interactions between plants and diverse root-associated fungi are essential drivers of forest ecosystem dynamics. The symbiosis is potentially dependent on multiple ecological factors/processes such as host/symbiont specificity, background soil microbiome, inter-root dispersal of symbionts, and fungus-fungus interactions within roots. Nonetheless, it has remained a major challenge to reveal the mechanisms by which those multiple factors/processes determine the assembly of root-associated fungal communities. Based on the framework of joint species distribution modeling, we examined 1,615 root-tips samples collected in a cool-temperate forest to reveal how root-associated fungal community structure was collectively formed through filtering by host plants, associations with background soil fungi, spatial autocorrelation, and symbiont-symbiont interactions. In addition, to detect fungi that drive the assembly of the entire root-associated fungal community, we inferred networks of direct fungus-fungus associations by a statistical modeling that could account for implicit environmental effects.

RESULTS

The fine-scale community structure of root-associated fungi were best explained by the statistical model including the four ecological factors/processes. Meanwhile, among partial models, those including background soil fungal community structure and within-root fungus-fungus interactions showed the highest performance. When fine-root distributions were examined, ectomycorrhizal fungi tended to show stronger associations with background soil community structure and spatially autocorrelated patterns than other fungal guilds. In contrast, the distributions of root-endophytic fungi were inferred to depend greatly on fungus-fungus interactions. An additional statistical analysis further suggested that some endophytic fungi, such as Phialocephala and Leptodontidium, were placed at the core positions within the web of direct associations with other root-associated fungi.

CONCLUSION

By applying emerging statistical frameworks to intensive datasets of root-associated fungal communities, we demonstrated background soil fungal community structure and fungus-fungus associations within roots, as well as filtering by host plants and spatial autocorrelation in ecological processes, could collectively drive the assembly of root-associated fungi. We also found that basic assembly rules could differ between mycorrhizal and endophytic fungi, both of which were major components of forest ecosystems. Consequently, knowledge of how multiple ecological factors/processes differentially drive the assembly of multiple fungal guilds is indispensable for comprehensively understanding the mechanisms by which terrestrial ecosystem dynamics are organized by plant-fungal symbiosis.

Exploring the rhizosphere of perennial wheat: potential for plant growth promotion and biocontrol applications

Perennial grains, which remain productive for multiple years, rather than growing for only one season before harvest, have deep, dense root systems that can support a richness of beneficial microorganisms, which are mostly underexplored. In this work we isolated forty-three bacterial strains associated with the rhizosphere of the OK72 perennial wheat line, developed from a cross between winter common wheat and Thinopyrum ponticum. Identified using 16S rDNA sequencing, these bacteria were assessed for plant growth-promoting traits such as indole-3-acetic acid, siderophores and ACC-deaminase acid production, biofilm formation, and the ability to solubilize phosphate and proteins. Twenty-five strains exhibiting in vitro significant plant growth promoting traits, belong to wheat keystone genera Pseudomonas, Microbacterium, Variovorax, Pedobacter, Dyadobacter, Plantibacter, and Flavobacterium. Seven strains, including Aeromicrobium and Okibacterium genera, were able to promote root growth in a commercial annual wheat cultivar while strains from Pseudomonas genus inhibited the growth of Aspergillus flavus and Fusarium species, using direct antagonism assays. The same strains produced a high amount of 1-undecanol a volatile organic compound, which may aid in suppressing fungal growth. The study highlights the potential of these bacteria to form new commercial consortia, enhancing the health and productivity of annual wheat crops within sustainable agricultural practices.

Effect of different vegetation restoration patterns on community structure and co-occurrence networks of soil fungi in the karst region

Introduction

The Grain for Green Project (GGP) by the Chinese government was an important vegetation restoration project in ecologically fragile and severely degraded karst regions. Soil fungi play a facilitating role in the cycling of nutrients both above and below the ground, which is crucial for maintaining ecosystem function and stability. In karst regions, their role is particularly critical due to the unique geological and soil characteristics, as they mitigate soil erosion, enhance soil fertility, and promote vegetation growth. However, little is known about how the implementation of this project shifts the co-occurrence network topological features and assembly processes of karst soil fungi, which limits our further understanding of karst vegetation restoration.

Methods

By using MiSeq high-throughput sequencing combined with null model analysis technology, we detected community diversity, composition, co-occurrence networks, and assembly mechanisms of soil fungi under three GGP patterns (crop, grassland, and plantation) in the southwestern karst region.

Results

Ascomycota and Basidiomycota were the main fungal phyla in all the karst soils. Returning crop to plantation and grassland had no significant effect on α diversity of soil fungi (P > 0.05), but did significantly affect the β diversity (P = 0.001). Soil moisture and total nitrogen (TN) were the main factors affecting the community structure of soil fungi. Compared with crop, soil fungi networks in grassland and plantation exhibited a higher nodes, edges, degree, and relatively larger network size, indicating that vegetation restoration enhanced fungal interactions. The soil fungi networks in grassland and plantation were more connected than those in crop, implying that the interaction between species was further strengthened after returning the crop to plantation and grassland. In addition, null-model analysis showed that the assembly process of soil fungal communities from crop to grassland and plantation shifted from an undominant process to dispersal limitation.

Discussion

These data indicated that GGP in karst region changed the composition and assembly mechanisms of the soil fungal community and enhanced the interaction between fungal species, which can contribute to a better understanding of the fungal mechanisms involved in the restoration of degraded karst soils through vegetation recovery.

From Microbes to Microbiomes: Applications for Plant Health and Sustainable Agriculture

Plant-microbe interaction research has had a transformative trajectory, from individual microbial isolate studies to comprehensive analyses of plant microbiomes within the broader phytobiome framework. Acknowledging the indispensable role of plant microbiomes in shaping plant health, agriculture, and ecosystem resilience, we underscore the urgent need for sustainable crop production strategies in the face of contemporary challenges. We discuss how the synergies between advancements in 'omics technologies and artificial intelligence can help advance the profound potential of plant microbiomes. Furthermore, we propose a multifaceted approach encompassing translational considerations, transdisciplinary research initiatives, public-private partnerships, regulatory policy development, and pragmatic expectations for the practical application of plant microbiome knowledge across diverse agricultural landscapes. We advocate for strategic collaboration and intentional transdisciplinary efforts to unlock the benefits offered by plant microbiomes and address pressing global issues in food security. By emphasizing a nuanced understanding of plant microbiome complexities and fostering realistic expectations, we encourage the scientific community to navigate the transformative journey from discoveries in the laboratory to field applications. As companies specializing in agricultural microbes and microbiomes undergo shifts, we highlight the necessity of understanding how to approach sustainable agriculture with site-specific management solutions. While cautioning against overpromising, we underscore the excitement of exploring the many impacts of microbiome-plant interactions. We emphasize the importance of collaborative endeavors with societal partners to accelerate our collective capacity to harness the diverse and yet-to-be-discovered beneficial activities of plant microbiomes.

Endophytic fungi: A future prospect for breast cancer therapeutics and drug development

Globally, breast cancer is a primary contributor to cancer-related fatalities and illnesses among women. Consequently, there is a pressing need for safe and effective treatments for breast cancer. Bioactive compounds from endophytic fungi that live in symbiosis with medicinal plants have garnered significant interest in pharmaceutical research due to their extensive chemical composition and prospective medicinal attributes. This review underscores the potentiality of fungal endophytes as a promising resource for the development of innovative anticancer agents specifically tailored for breast cancer therapy. The diversity of endophytic fungi residing in medicinal plants, success stories of key endophytic bioactive metabolites tested against breast cancer and the current progress with regards to in vivo studies and clinical trials on endophytic fungal metabolites in breast cancer research forms the underlying theme of this article. A thorough compilation of putative anticancer compounds sourced from endophytic fungi that have demonstrated therapeutic potential against breast cancer, spanning the period from 1990 to 2022, has been presented. This review article also outlines the latest trends in endophyte-based drug discovery, including the use of artificial intelligence, machine learning, multi-omics approaches, and high-throughput strategies. The challenges and future prospects associated with fungal endophytes as substitutive sources for developing anticancer drugs targeting breast cancer are also being highlighted.

Microbial allies: exploring fungal endophytes for biosynthesis of terpenoid indole alkaloids

Terpenoid indole alkaloids (TIAs) are natural compounds found in medicinal plants that exhibit various therapeutic activities, such as antimicrobial, anti-inflammatory, antioxidant, anti-diabetic, anti-helminthic, and anti-tumor properties. However, the production of these alkaloids in plants is limited, and there is a high demand for them due to the increasing incidence of cancer cases. To address this research gap, researchers have focused on optimizing culture media, eliciting metabolic pathways, overexpressing genes, and searching for potential sources of TIAs in organisms other than plants. The insufficient number of essential genes and enzymes in the biosynthesis pathway is the reason behind the limited production of TIAs. As the field of natural product discovery from biological species continues to grow, endophytes are being investigated more and more as potential sources of bioactive metabolites with a variety of chemical structures. Endophytes are microorganisms (fungi, bacteria, archaea, and actinomycetes), that exert a significant influence on the metabolic pathways of both the host plants and the endophytic cells. Bio-prospection of fungal endophytes has shown the discovery of novel, high-value bioactive compounds of commercial significance. The discovery of therapeutically significant secondary metabolites has been made easier by endophytic entities' abundant but understudied diversity. It has been observed that fungal endophytes have better intermediate processing ability due to cellular compartmentation. This paper focuses on fungal endophytes and their metabolic ability to produce complex TIAs, recent advancements in this area, and addressing the limitations and future perspectives related to TIA production.

Unboxing PGPR-mediated management of abiotic stress and environmental cleanup: what lies inside?

Abiotic stresses including heavy metal toxicity, drought, salt and temperature extremes disrupt the plant growth and development and lowers crop output. Presence of environmental pollutants further causes plants suffering and restrict their ability to thrive. Overuse of chemical fertilizers to reduce the negative impact of these stresses is deteriorating the environment and induces various secondary stresses to plants. Therefore, an environmentally friendly strategy like utilizing plant growth-promoting rhizobacteria (PGPR) is a promising way to lessen the negative effects of stressors and to boost plant growth in stressful conditions. These are naturally occurring inhabitants of various environments, an essential component of the natural ecosystem and have remarkable abilities to promote plant growth. Furthermore, multifarious role of PGPR has recently been widely exploited to restore natural soil against a range of contaminants and to mitigate abiotic stress. For instance, PGPR may mitigate metal phytotoxicity by boosting metal translocation inside the plant and changing the metal bioavailability in the soil. PGPR have been also reported to mitigate other abiotic stress and to degrade environmental contaminants remarkably. Nevertheless, despite the substantial quantity of information that has been produced in the meantime, there has not been much advancement in either the knowledge of the processes behind the alleged positive benefits or in effective yield improvements by PGPR inoculation. This review focuses on addressing the progress accomplished in understanding various mechanisms behind the protective benefits of PGPR against a variety of abiotic stressors and in environmental cleanups and identifying the cause of the restricted applicability in real-world.

Forest-to-Cropland Conversion Reshapes Microbial Hierarchical Interactions and Degrades Ecosystem Multifunctionality at a National Scale

Conversion from natural lands to cropland, primarily driven by agricultural expansion, could significantly alter soil microbiome worldwide; however, influences of forest-to-cropland conversion on microbial hierarchical interactions and ecosystem multifunctionality have not been fully understood. Here, we examined the effects of forest-to-cropland conversion on intratrophic and cross-trophic microbial interactions and soil ecosystem multifunctionality and further disclosed their underlying drivers at a national scale, using Illumina sequencing combined with high-throughput quantitative PCR techniques. The forest-to-cropland conversion significantly changed the structure of soil microbiome (including prokaryotic, fungal, and protistan communities) while it did not affect its alpha diversity. Both intrakingdom and interkingdom microbial networks revealed that the intratrophic and cross-trophic microbial interaction patterns generally tended to be more modular to resist environmental disturbance introduced from forest-to-cropland conversion, but this was insufficient for the cross-trophic interactions to maintain stability; hence, the protistan predation behaviors were still disturbed under such conversion. Moreover, key soil microbial clusters were declined during the forest-to-cropland conversion mainly because of the increased soil total phosphorus level, and this drove a great degradation of the ecosystem multifunctionality (by 207%) in cropland soils. Overall, these findings comprehensively implied the negative effects of forest-to-cropland conversion on the agroecosystem, from microbial hierarchical interactions to ecosystem multifunctionality.

Nitrogen addition changed soil fungal community structure and increased the biomass of functional fungi in Korean pine plantations in temperate northeast China

Nitrogen (N) deposition is a global environmental issue that can have significant impacts on the community structure and function in ecosystems. Fungi play a key role in soil biogeochemical cycles and their community structures are tightly linked to the health and productivity of forest ecosystems. Based on high-throughput sequencing and ergosterol extraction, we examined the changes in community structure, composition, and biomass of soil ectomycorrhizal (ECM) and saprophytic (SAP) fungi in 0-10 cm soil layer after 8 years of continuous N addition and their driving factors in a temperate Korean pine plantation in northeast China. Our results showed that N addition increased fungal community richness, with the highest richness and Chao1 index under the low N treatment (LN: 20 kg N ha-1 yr-1). Based on the FUN Guild database, we found that the relative abundance of ECM and SAP fungi increased first and then decreased with increasing N deposition concentration. The molecular ecological network analysis showed that the interaction between ECM and SAP fungi was enhanced by N addition, and the interaction was mainly positive in the ECM fungal network. N addition increased fungal biomass, and the total fungal biomass (TFB) was the highest under the MN treatment (6.05 ± 0.3 mg g-1). Overall, we concluded that N addition changed soil biochemical parameters, increased fungal activity, and enhanced functional fungal interactions in the Korean pine plantation over an 8-year simulated N addition. We need to consider the effects of complex soil conditions on soil fungi and emphasize the importance of regulating soil fungal community structure and biomass for managing forest ecosystems. These findings could deepen our understanding of the effects of increased N deposition on soil fungi in temperate forests in northern China, which can provide the theoretical basis for reducing the effects of increased N deposition on forest soil.

Disease-induced changes in bacterial and fungal communities from plant below- and aboveground compartments

The plant microbes are an integral part of the host and play fundamental roles in plant growth and health. There is evidence indicating that plants have the ability to attract beneficial microorganisms through their roots in order to defend against pathogens. However, the mechanisms of plant microbial community assembly from below- to aboveground compartments under pathogen infection remain unclear. In this study, we investigated the bacterial and fungal communities in bulk soil, rhizosphere soil, root, stem, and leaf of both healthy and infected (Potato virus Y disease, PVY) plants. The results indicated that bacterial and fungal communities showed different recruitment strategies in plant organs. The number and abundance of shared bacterial ASVs between bulk and rhizosphere soils decreased with ascending migration from below- to aboveground compartments, while the number and abundance of fungal ASVs showed no obvious changes. Field type, plant compartments, and PVY infection all affected the diversity and structures of microbial community, with stronger effects observed in the bacterial community than the fungal community. Furthermore, PVY infection, rhizosphere soil pH, and water content (WC) contributed more to the assembly of the bacterial community than the fungal community. The analysis of microbial networks revealed that the bacterial communities were more sensitive to PVY infection than the fungal communities, as evidenced by the lower network stability of the bacterial community, which was characterized by a higher proportion of positive edges. PVY infection further increased the bacterial network stability and decreased the fungal network stability. These findings advance our understanding of how microbes respond to pathogen infections and provide a rationale and theoretical basis for biocontrol technology in promoting sustainable agriculture. KEY POINTS: • Different recruitment strategies between plant bacterial and fungal communities. • Bacterial community was more sensitive to PVY infection than fungal community. • pH and WC drove the microbial community assembly under PVY infection.

The addition of discrimination inhibitors stimulations discrimination potential and N2O emissions were linked to predation among microorganisms in long term nitrogen application and straw returning systems

Introduction

Ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) have been proven to be key microorganisms driving the ammonia oxidation process. However, under different fertilization practices, there is a lack of research on the impact of interaction between predators and AOA or AOB on nitrogen cycling at the multi-trophic level.

Methods

In this study, a network-oriented microscopic culture experiment was established based on four different long-term fertilization practices soils. We used the nitrification inhibitors 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxide-3-oxyl (PTIO) and 3, 4-Dimethylpyrazole phosphate (DMPP) inhibited AOA and AOB, respectively, to explore the impact of interaction between protists and AOA or AOB on nitrogen transformation.

Results

The results showed that long-term nitrogen application promoted the potential nitrification rate (PNR) and nitrous oxide (N2O) emission, and significantly increased the gene abundance of AOB, but had no obvious effect on AOA gene abundance. DMPP significantly reduced N2O emission and PNR, while PTIO had no obvious effect on them. Accordingly, in the multi-trophic microbial network, Cercozoa and Proteobacteria were identified as keystone taxa of protists and AOB, respectively, and were significantly positively correlated with N2O, PNR and nitrate nitrogen. However, Nitrososphaerota archaeon as the keystone species of AOA, had an obvious negative linkage to these indicators. The structural equation model (SEM) showed that AOA and AOB may be competitors to each other. Protists may promote AOB diversity through direct trophic interaction with AOA.

Conclusion

The interaction pattern between protists and ammonia-oxidizing microorganisms significantly affects potential nitrification rate and N2O emission, which has important implications for soil nitrogen cycle.

Potato Microbiome: Relationship with Environmental Factors and Approaches for Microbiome Modulation

Every land plant exists in a close relationship with microbial communities of several niches: rhizosphere, endosphere, phyllosphere, etc. The growth and yield of potato-a critical food crop worldwide-highly depend on the diversity and structure of the bacterial and fungal communities with which the potato plant coexists. The potato plant has a specific part, tubers, and the soil near the tubers as a sub-compartment is usually called the "geocaulosphere", which is associated with the storage process and tare soil microbiome. Specific microbes can help the plant to adapt to particular environmental conditions and resist pathogens. There are a number of approaches to modulate the microbiome that provide organisms with desired features during inoculation. The mechanisms of plant-bacterial communication remain understudied, and for further engineering of microbiomes with particular features, the knowledge on the potato microbiome should be summarized. The most recent approaches to microbiome engineering include the construction of a synthetic microbial community or management of the plant microbiome using genome engineering. In this review, the various factors that determine the microbiome of potato and approaches that allow us to mitigate the negative impact of drought and pathogens are surveyed.

Dynamics of Endophytic Fungal Communities Associated with Cultivated Medicinal Plants in Farmland Ecosystem

Microorganisms are an important component of global biodiversity and play an important role in plant growth and development and the protection of host plants from various biotic and abiotic stresses. However, little is known about the identities and communities of endophytic fungi inhabiting cultivated medicinal plants in the farmland ecosystem. The diversity and community composition of the endophytic fungi of cultivated medicinal plants in different hosts, tissue niches, and seasonal effects in the farmland of Northern China were examined using the next-generation sequencing technique. In addition, the ecological functions of the endophytic fungal communities were investigated by combining the sequence classification information and fungal taxonomic function annotation. A total of 1025 operational taxonomic units (OTUs) of endophytic fungi were obtained at a 97% sequence similarity level; they were dominated by Dothideomycetes and Pleosporales. Host factors (species identities and tissue niches) and season had significant effects on the community composition of endophytic fungi, and endophytic fungi assembly was shaped more strongly by host than by season. In summer, endophytic fungal diversity was higher in the root than in the leaf, whereas opposite trends were observed in winter. Network analysis showed that network connectivity was more complex in the leaf than in the root, and the interspecific relationship between endophytic fungal OTUs in the network structure was mainly positive rather than negative. The functional predications of fungi revealed that the pathotrophic types of endophytic fungi decreased and the saprotrophic types increased from summer to winter in the root, while both pathotrophic and saprotrophic types of endophytic fungi increased in the leaf. This study improves our understanding of the community composition and ecological distribution of endophytic fungi inhabiting scattered niches in the farmland ecosystem. In addition, the study provides insight into the biodiversity assessment and management of cultivated medicinal plants.

Diversity and biogeography of plant phyllosphere bacteria are governed by latitude-dependent mechanisms

Predicting and managing the structure and function of plant microbiomes requires quantitative understanding of community assembly and predictive models of spatial distributions at broad geographic scales. Here, we quantified the relative contribution of abiotic and biotic factors to the assembly of phyllosphere bacterial communities, and developed spatial distribution models for keystone bacterial taxa along a latitudinal gradient, by analyzing 16S rRNA gene sequences from 1453 leaf samples taken from 329 plant species in China. We demonstrated a latitudinal gradient in phyllosphere bacterial diversity and community composition, which was mostly explained by climate and host plant factors. We found that host-related factors were increasingly important in explaining bacterial assembly at higher latitudes while nonhost factors including abiotic environments, spatial proximity and plant neighbors were more important at lower latitudes. We further showed that local plant-bacteria associations were interconnected by hub bacteria taxa to form metacommunity-level networks, and the spatial distribution of these hub taxa was controlled by hosts and spatial factors with varying importance across latitudes. For the first time, we documented a latitude-dependent importance in the driving factors of phyllosphere bacteria assembly and distribution, serving as a baseline for predicting future changes in plant phyllosphere microbiomes under global change and human activities.

More Than the Sum of Its Parts: Unlocking the Power of Network Structure for Understanding Organization and Function in Microbiomes

Plant and soil microbiomes are integral to the health and productivity of plants and ecosystems, yet researchers struggle to identify microbiome characteristics important for providing beneficial outcomes. Network analysis offers a shift in analytical framework beyond "who is present" to the organization or patterns of coexistence between microbes within the microbiome. Because microbial phenotypes are often significantly impacted by coexisting populations, patterns of coexistence within microbiomes are likely to be especially important in predicting functional outcomes. Here, we provide an overview of the how and why of network analysis in microbiome research, highlighting the ways in which network analyses have provided novel insights into microbiome organization and functional capacities, the diverse network roles of different microbial populations, and the eco-evolutionary dynamics of plant and soil microbiomes.

Into the void: ECM fungal communities involved in the succession from rockroses to oak stands

Oak forests accompanied by Cistus species are a common landscape in the Mediterranean basin. It is argued that Cistus dominated fields serve as recruitment areas for Quercus seedlings, as they help in the transmission of the fungal community through vegetative succession in these ecosystems. To test these assumptions, we analyzed the fungal community in terms of its richness and composition, taking into account the effects of host (Oaks vs. Cistus) and forest structure, mainly based on age. Edaphic variables related to the different structures were also analyzed to examine how they evolve through succession and relate to shifts in the fungal community. No differences in fungal richness were observed between old Cistus stands and younger Quercus, while a brief increase in ECM richness was observed. Community composition also showed a greater overlap between old Cistus and young Quercus stands. We suggest that the most important step in fungal transfer from one host to another is the shift from the oldest Cistus fields to the youngest Quercus stands, with the genera Amanita, Cortinarius, Lactarius, Inocybe, Russula, and Tomentella probably playing a major role. In summary, our work has also revealed the network of fungal community structure in the succession of Cistus to Oak stands, it would suggest that the fungi share niches and significantly enhance the ecological setting of the transition from Cistus to Oak stands.

Variation and stability of rhizosphere bacterial communities of Cucumis crops in association with root-knot nematodes infestation

Introduction

Root-knot nematodes (RKN) disease is a devastating disease in Cucumis crops production. Existing studies have shown that resistant and susceptible crops are enriched with different rhizosphere microorganisms, and microorganisms enriched in resistant crops can antagonize pathogenic bacteria. However, the characteristics of rhizosphere microbial communities of Cucumis crops after RKN infestation remain largely unknown.

Methods

In this study, we compared the changes in rhizosphere bacterial communities between highly RKN-resistant Cucumis metuliferus (cm3) and highly RKN-susceptible Cucumis sativus (cuc) after RKN infection through a pot experiment.

Results

The results showed that the strongest response of rhizosphere bacterial communities of Cucumis crops to RKN infestation occurred during early growth, as evidenced by changes in species diversity and community composition. However, the more stable structure of the rhizosphere bacterial community in cm3 was reflected in less changes in species diversity and community composition after RKN infestation, forming a more complex and positively co-occurrence network than cuc. Moreover, we observed that both cm3 and cuc recruited bacteria after RKN infestation, but the bacteria enriched in cm3 were more abundant including beneficial bacteria Acidobacteria, Nocardioidaceae and Sphingomonadales. In addition, the cuc was enriched with beneficial bacteria Actinobacteria, Bacilli and Cyanobacteria. We also found that more antagonistic bacteria than cuc were screened in cm3 after RKN infestation and most of them were Pseudomonas (Proteobacteria, Pseudomonadaceae), and Proteobacteria were also enriched in cm3 after RKN infestation. We hypothesized that the cooperation between Pseudomonas and the beneficial bacteria in cm3 could inhibit the infestation of RKN.

Discussion

Thus, our results provide valuable insights into the role of rhizosphere bacterial communities on RKN diseases of Cucumis crops, and further studies are needed to clarify the bacterial communities that suppress RKN in Cucumis crops rhizosphere.

Cadmium inhibits powdery mildew colonization and reconstructs microbial community in leaves of the hyperaccumulator plant Sedum alfredii

Understanding the influence of the heavy metal cadmium (Cd) on the phyllosphere microbiome of hyperaccumulator plants is crucial for enhancing phytoremediation. The characteristics of the phyllosphere of Sedum alfredii Hance, a hyperaccumulator plant, were investigated using 16S rRNA and internal transcribed spacer amplicon sequencing of powdery mildew-infected leaves treated or untreated with Cd. The results showed that the colonization of powdery mildew caused severe chlorosis and necrosis in S. alfredii leaves, and the relative abundance of Leotiomycetes in infected leaves increased dramatically and significantly decreased phyllosphere microbiome diversity. However, S. alfredii preferentially accumulated higher concentrations of Cd in the leaves of infected plants than in uninfected plants by powdery mildew, which in turn significantly inhibited powdery mildew colonization in leaves; the relative abundance of the fungal class Leotiomycetes in infected leaves decreased, and alpha and beta diversities of the phyllosphere microbiome significantly increased with Cd treatment in the infected plants. In addition, the inter-kingdom networks in the microbiota of the infected leaves treated with Cd presented many nodes and edges, and the highest inter-kingdom modularity compared to the untreated infected leaves, indicating a highly connected microbial community. These results suggest that Cd significantly inhibits powdery mildew colonization by altering the composition of the phyllosphere microbiome in S. alfredii leaves, paving the way for efficient heavy metal phytoremediation and providing a new perspective on defense strategies against heavy metals.

Microbial Interactions Related to N2O Emissions and Temperature Sensitivity from Rice Paddy Fields

The soil microbiome is a driver of nitrous oxide (N₂O) emissions in terrestrial ecosystems. Identifying the core microbiome of N₂O emissions and its temperature sensitivity from trillions of soil microorganisms is a great challenge and is essential to improving the predictability of soil-climate feedback related to increasing temperature. Here, the integrated soil microbiome covering archaeal, bacterial, fungal, algal, and microfaunal communities was studied to disengage the potential linkage with its N₂O emissions and its temperature sensitivity in paddy fields by hunting for core species pairs. The results showed that between-group interactions of core bacterial and archaeal members and the within-group interactions of core bacterial members jointly contributed to the N₂O emissions and its temperature sensitivity. The contribution of between-group interactions (32 to 33%) was greater than that of within groups (10 to 18%). These results suggested that N₂O emissions and their fluctuations related to climate warming are affected by the within- and between-group interactions of the soil microbiome. Our results help advance the knowledge on the importance of microbial keystone species and network associations in controlling N₂O production and their responses to increasing temperature. IMPORTANCE Soil microorganisms drive emissions of nitrous oxide from soils; this is a powerful greenhouse gas and the dominant ozone-depleting agent. N₂O emissions can be partly predicted from soil properties and specific microbial groups, whereas a possible role of below-ground microbial interactions has largely been overlooked. Here, the integrated soil microbiome covering archaeal, bacterial, fungal, algal, and microfaunal communities was studied to disengage the potential linkage with the N₂O emissions and temperature sensitivity of the microbiome in paddy fields by hunting for core species pairs. The results showed that between-group interactions of core bacterial and archaeal members and the within-group interactions of core bacterial members jointly contributed to the N₂O emissions. The contribution of between-group interactions (32 to 33%) was greater than that of within-group interactions (10 to 18%). Our results help advance the knowledge on the importance of microbial keystone species and interactions in controlling N₂O production and their responses to increasing temperature.

Core endophytic mycobiome in Ulmus minor and its relation to Dutch elm disease resistance

The core microbiota of plants exerts key effects on plant performance and resilience to stress. The aim of this study was to identify the core endophytic mycobiome in U. minor stems and disentangle associations between its composition and the resistance to Dutch elm disease (DED). We also defined its spatial variation within the tree and among distant tree populations. Stem samples were taken i) from different heights of the crown of a 168-year-old elm tree, ii) from adult elm trees growing in a common garden and representing a gradient of resistance to DED, and iii) from trees growing in two distant natural populations, one of them with varying degrees of vitality. Endophyte composition was profiled by high throughput sequencing of the first internal transcribed spacer region (ITS1) of the ribosomal DNA. Three families of yeasts (Buckleyzymaceae, Trichomeriaceae and Bulleraceae) were associated to DED-resistant hosts. A small proportion (10%) of endophytic OTUs was almost ubiquitous throughout the crown while tree colonization by most fungal taxa followed stochastic patterns. A clear distinction in endophyte composition was found between geographical locations. By combining all surveys, we found evidence of a U. minor core mycobiome, pervasive within the tree and ubiquitous across locations, genotypes and health status.

From guest to host: parasite Cistanche deserticola shapes and dominates bacterial and fungal community structure and network complexity

BACKGROUND

Rhizosphere and plant microbiota are assumed to play an essential role in deciding the well-being of hosts, but effects of parasites on their host microbiota have been rarely studied. Also, the characteristics of the rhizosphere and root microbiota of parasites and hosts under parasitism is relatively unknown. In this study, we used Cistanche deserticola and Haloxylon ammodendron from cultivated populations as our model parasites and host plants, respectively. We collected samples from BULK soil (BULK), rhizosphere soil of H. ammodendron not parasitized (NCD) and parasitized (RHA) to study how the parasite influenced the rhizosphere microbiota of the host. We also collected samples from the rhizosphere soil and roots of C. deserticola (RCD and ECD) and Haloxylon ammodendron (RHA and EHA) to explore the difference between the microbiota of the parasite and its host under parasitism.

RESULTS

The parasite reduced the compositional and co-occurrence network complexities of bacterial and fungal microbiota of RHA. Additionally, the parasite increased the proportion of stochastic processes mainly belonging to dispersal limitation in the bacterial microbiota of RHA. Based on the PCoA ordinations and permutational multivariate analysis of variance, the dissimilarity between microbiota of C. deserticola and H. ammodendron were rarely evident (bacteria, R² = 0.29971; fungi, R² = 0.15631). Interestingly, four hub nodes of H. ammodendron in endosphere fungal microbiota were identified, while one hub node of C. deserticola in endosphere fungal microbiota was identified. It indicated that H. ammodendron played a predominant role in the co-occurrence network of endosphere fungal microbiota. Source model of plant microbiome suggested the potential source percentage from the parasite to the host (bacteria: 52.1%; fungi: 16.7%) was lower than host-to-parasite (bacteria: 76.5%; fungi: 34.3%), illustrating that microbial communication was bidirectional, mainly from the host to the parasite.

CONCLUSIONS

Collectively, our results suggested that the parasite C. deserticola shaped the diversity, composition, co-occurrence network, and community assembly mechanisms of the rhizosphere microbiota of H. ammodendron. Additionally, the microbiota of C. deserticola and H. ammodendron were highly similar and shared. Our findings on parasite and host microbiota provided a novel line of evidence supporting the influence of parasites on the microbiota of their hosts.

Crop rotations increased soil ecosystem multifunctionality by improving keystone taxa and soil properties in potatoes

Continuous cropping of the same crop leads to soil degradation and a decline in crop production, and these impacts could be mitigated through rotation cropping. Although crop rotation enhances soil fertility, microbial community diversity, and potato yield, its effects on the soil ecosystem multifunctionality (EMF) remain unclear. In the present research, we comparatively examined the effects of potato continuous cropping (PP) and rotation cropping [potato-oat rotation (PO) and potato-forage maize rotation (PFM)] on the soil EMF as well as the roles of keystone taxa, microbes abundance, and chemical properties in EMF improvement. It was demonstrated that soil EMF is increased in rotation cropping (PO and PFM) than PP. Soil pH was higher in rotation cropping (PO and PFM) than in PP, while total phosphorus (TP) and available phosphorus (AP) were significantly decreased than that in PP. Rotation cropping (PO and PFM) markedly changed the bacterial and fungal community compositions, and improved the potential plant-beneficial fungi, e.g., Schizothecium and Chaetomium, while reducing the abundances of the potentially phytopathogenic fungi, e.g., Alternaria, Fusarium, Verticillium dahiae, Gibberella, Plectosphaerella, Colletotrichum, Phoma, and Lectera in comparison with PP. Also, co-occurrence patterns for bacteria and fungi were impacted by crop rotation, and keystone taxa, e.g., Nitrospira.1, Lysinibacillus, Microlunatus.1, Sphingomonas.3, Bryobacter.1, Micromonospora, and Schizothecium, were enriched in PO and PFM than PP. The structural equation model (SEM) further demonstrated that cropping systems increased soil ecosystem multifunctionality through regulating SOM and keystone taxa (Schizothecium1), and keystone taxa were mediated by soil pH. This study suggested that rotation cropping might contribute to the improvement of soil ecosystem multifunctionality as well as the development of disease-suppressive soils in comparison with potato continuous cropping.

Plant and fungal species interactions differ between aboveground and belowground habitats in mountain forests of eastern China

Plant and fungal species interactions drive many essential ecosystem properties and processes; however, how these interactions differ between aboveground and belowground habitats remains unclear at large spatial scales. Here, we surveyed 494 pairwise fungal communities in leaves and soils by Illumina sequencing, which were associated with 55 woody plant species across more than 2,000-km span of mountain forests in eastern China. The relative contributions of plant, climate, soil and space to the variation of fungal communities were assessed, and the plant-fungus network topologies were inferred. Plant phylogeny was the strongest predictor for fungal community composition in leaves, accounting for 19.1% of the variation. In soils, plant phylogeny, climatic factors and soil properties explained 9.2%, 9.0% and 8.7% of the variation in soil fungal community, respectively. The plant-fungus networks in leaves exhibited significantly higher specialization, modularity and robustness (resistance to node loss), but less complicated topology (e.g., significantly lower linkage density and mean number of links) than those in soils. In addition, host/fungus preference combinations and key species, such as hubs and connectors, in bipartite networks differed strikingly between aboveground and belowground samples. The findings provide novel insights into cross-kingdom (plant-fungus) species co-occurrence at large spatial scales. The data further suggest that community shifts of trees due to climate change or human activities will impair aboveground and belowground forest fungal diversity in different ways.

Biochar-mediated changes in the microbial communities of rhizosphere soil alter the architecture of maize roots

Aeolian sandy soil is a key resource for supporting food production on a global scale; however, the growth of crops in Aeolian sandy soil is often impaired due to its poor physical properties and lack of nutrients and organic matter. Biochar can be used to enhance the properties of Aeolian sandy soil and create an environment more suitable for crop growth, but the long-term effects of biochar on Aeolian sandy soil and microbial communities need to be clarified. Here, a field experiment was conducted in which biochar was applied to a maize (Zea mays L.) field in a single application at different rates: CK, 0 Mg ha-1; C1, 15.75 Mg ha-1; C2, 31.50 Mg ha-1; C3, 63.00 Mg ha-1; and C4, 126.00 Mg ha-1. After 7 years of continuous maize cropping, verify the relationship between root architecture and soil microbial communities under biochar application using a root scanner and 16S/ITS rRNA gene sequencing. The application of biochar promoted the growth of maize. Specifically, total root length, total root surface area, total root volume, and root biomass were 13.99-17.85, 2.52-4.69, 23.61-44.41, and 50.61-77.80% higher in treatments in which biochar was applied (C2, C3, and C4 treatments) compared with the control treatment, respectively. Biochar application increased the diversity of bacterial communities, the ACE index, and Chao 1 index of C1, C2, C3, and C4 treatments increased by 5.83-8.96 and 5.52-8.53%, respectively, compared with the control treatment, and significantly changed the structure of the of bacterial communities in rhizosphere soil. However, there was no significant change in the fungal community. The growth of maize roots was more influenced by rhizosphere bacteria and less by fungal community. A microbial co-occurrence network revealed strong associations among rhizosphere microorganisms. The core taxa (Module hubs taxa) of the bulk soil microbial co-occurrence network were closely related to the total length and total surface area of maize roots, and the core taxa (Connectors taxa) of the rhizosphere soil were closely related to total root length. Overall, our findings indicate that the application of biochar promotes the growth of maize roots in aeolian sandy soil through its effects on bacterial communities in rhizosphere soil.

Succession of soil bacterial communities and network patterns in response to conventional and biodegradable microplastics: A microcosmic study in Mollisol

Significant soil contamination of microplastics (MPs) by the application of agricultural mulching films has aroused global concern, however, the effects of conventional and biodegradable MPs on the dynamics of soil microbial communities and network patterns have not been sufficiently reported. In this study, we conducted a soil microcosmic experiment by adding low-density polyethylene and biodegradable MPs (PE and BD) into a black soil at the dosages of 0 % (CK), 0.1 % (low-dose, w/w), 1 % (medium-dose, w/w) and 5 % (high-dose, w/w), and soils were sampled on the 15th, 30th, 60th and 90th day of soil incubation for high-throughput sequencing. The results showed that the incubation time was the most influential factor driving the variations in bacterial community structures, and significant effects of MP dosages and types were also detected. With the increase in MP dosage, bacterial diversity markedly increased and decreased at the beginning (D15) and end of sampling day (D90), respectively. Compared to CK, BD induced a larger community dissimilarity than PE and tended to enrich environmentally friendly taxa, while PE likely promoted the growth of hazardous taxa. Moreover, BD simplified interspecies interactions compared to the networks of PE and CK, and Nitrospira was identified as a keystone species in both PE and BD networks. These findings provide new insights into the influences of conventional and biodegradable MPs on the succession patterns of soil bacterial communities, and further studies are needed to explore the soil metabolic potentials affected by the presence of MPs.

Longitudinal transmission of bacterial and fungal communities from seed to seed in rice

Vertical transmission of microbes is crucial for the persistence of host-associated microbial communities. Although vertical transmission of seed microbes has been reported from diverse plants, ecological mechanisms and dynamics of microbial communities from parent to progeny remain scarce. Here we reveal the veiled ecological mechanism governing transmission of bacterial and fungal communities in rice across two consecutive seasons. We identify 29 bacterial and 34 fungal members transmitted across generations. Abundance-based regression models allow to classify colonization types of the microbes. We find that they are late colonizers dominating each community at the ripening stage. Ecological models further show that the observed temporal colonization patterns are affected by niche change and neutrality. Source-sink modeling reveals that parental seeds and stem endosphere are major origins of progeny seed microbial communities. This study gives empirical evidence for ecological mechanism and dynamics of bacterial and fungal communities as an ecological continuum during seed-to-seed transmission.

Islands Within Islands: Bacterial Phylogenetic Structure and Consortia in Hawaiian Lava Caves and Fumaroles

Lava caves, tubes, and fumaroles in Hawai‘i present a range of volcanic, oligotrophic environments from different lava flows and host unexpectedly high levels of bacterial diversity. These features provide an opportunity to study the ecological drivers that structure bacterial community diversity and assemblies in volcanic ecosystems and compare the older, more stable environments of lava tubes, to the more variable and extreme conditions of younger, geothermally active caves and fumaroles. Using 16S rRNA amplicon-based sequencing methods, we investigated the phylogenetic distinctness and diversity and identified microbial interactions and consortia through co-occurrence networks in 70 samples from lava tubes, geothermal lava caves, and fumaroles on the island of Hawai‘i. Our data illustrate that lava caves and geothermal sites harbor unique microbial communities, with very little overlap between caves or sites. We also found that older lava tubes (500–800 yrs old) hosted greater phylogenetic diversity (Faith's PD) than sites that were either geothermally active or younger (<400 yrs old). Geothermally active sites had a greater number of interactions and complexity than lava tubes. Average phylogenetic distinctness, a measure of the phylogenetic relatedness of a community, was higher than would be expected if communities were structured at random. This suggests that bacterial communities of Hawaiian volcanic environments are phylogenetically over-dispersed and that competitive exclusion is the main driver in structuring these communities. This was supported by network analyses that found that taxa (Class level) co-occurred with more distantly related organisms than close relatives, particularly in geothermal sites. Network “hubs” (taxa of potentially higher ecological importance) were not the most abundant taxa in either geothermal sites or lava tubes and were identified as unknown families or genera of the phyla, Chloroflexi and Acidobacteria. These results highlight the need for further study on the ecological role of microbes in caves through targeted culturing methods, metagenomics, and long-read sequence technologies.

Contrasting Responses of Rhizosphere Fungi of Scutellaria tsinyunensis , an Endangered Plant in Southwestern China

Scutellaria tsinyunensis is an endangered species in southwest China, distributed sporadically in mountainous areas at an elevation of approximately 200 to 900 m. Rhizosphere soil properties and fungal communities play critical roles in plant survival and expansion. Nevertheless, understanding of soil properties and fungal communities in the S. tsinyunensis distribution areas is extremely limited. The present study examined soil properties and fungal communities in nearly all extant S. tsinyunensis populations at two altitudinal gradients (low and high groups). Our findings indicated that soil characteristics (i.e., soil pH, water content, and available phosphorus) were affected distinctively by altitudes (P < 0.05). In addition, the low altitude group harbored higher fungal richness and diversity than the high altitude. Co-occurrence network analysis identified six key genera that proved densely connected interactions with many genera. Further analysis represented that the low altitude group harbored three beneficial genera belonging to Ascomycota (Archaeorhizomyces, Dactylella, and Helotiales), whereas the high altitude showed more pathogenic fungi (Apiosporaceae, Colletotrichum, and Fusarium). Correlation analysis found that soil water content was highly correlated with Hydnodontaceae and Lophiostoma. Besides, plants’ canopy density was negatively correlated with four pathogenic fungi, indicating that the high abundance of the pathogen at high altitudes probably inhibited the survival of S. tsinyunensis. To sum up, this comprehensive analysis generates novel insights to explore the contrasting responses of S. tsinyunensis rhizosphere fungal communities and provides profound references for S. tsinyunensis habitat restoration and species conservation.

IMPORTANCE Our study highlighted the importance of rhizosphere fungal communities in an endangered plant, S. tsinyunensis. Comparative analysis of soil samples in nearly all extant S. tsinyunensis populations identified that soil properties, especially soil water content, might play essential roles in the survival and expansion of S. tsinyunensis. Our findings proved that a series of fungal communities (e.g., Archaeorhizomyces, Dactylella, and Helotiales) could be essential indicators for S. tsinyunensis habitat restoration and protection for the first time. In addition, further functional and correlation analyses revealed that pathogenic fungi might limit the plant expansion into high altitudes. Collectively, our findings displayed a holistic picture of the rhizosphere microbiome and environmental factors associated with S. tsinyunensis.

Agricultural Management Drive Bacterial Community Assembly in Different Compartments of Soybean Soil-Plant Continuum

Flowering stage of soybean is an important agronomic trait, which is important for soybean yield, quality and adaptability, and is the external expression of integrating external environmental factors and endogenous signals of the plant itself. Cropping system can change soil properties and fertility, which in turn determine plant growth and yield. The microbial community is the key regulator of plant health and production performance. Currently, there is limited understanding of the effects of cropping systems on microbial community composition, ecological processes controlling community assembly in different soil-plant continuum compartments of soybean. Here, we hope to clarify the structure and assembly process of different soybean compartments bacterial community at flowering stage through our work. The results showed that intercropping decreased the species diversity of rhizosphere and phyllosphere, and phylloaphere microbes mainly came from rhizosphere. FAPROTAX function prediction showed that indicator species sensitive to intercropping and crop rotation were involved in nitrogen/phosphorus cycle and degradation process, respectively. In addition, compared to the continuous cropping, intercropping increased the stochastic assembly processes of bacterial communities in plant-associated compartments, while crop rotation increased the complexity and stability of the rhizosphere network and the deterministic assembly process. Our study highlights the importance of intercropping and crop rotation, as well as rhizosphere and phyllosphere compartments for future crop management and sustainable agricultural regulation of crop microbial communities.

Multitrophic diversity and biotic associations influence subalpine forest ecosystem multifunctionality

Biodiversity across multiple trophic levels is required to maintain multiple ecosystem functions. Yet, it remains unclear how multitrophic diversity and species interactions regulate ecosystem multifunctionality. Here, combining data from nine different trophic groups (including trees, shrubs, herbs, leaf mites, small mammals, bacteria, pathogenic fungi, saprophytic fungi and symbiotic fungi) and 13 ecosystem functions related to supporting, provisioning and regulating services, we used a multitrophic perspective to evaluate the effects of elevation, diversity and network complexity on scale-dependent subalpine forest multifunctionality. Our results demonstrate that elevation and soil pH significantly modified species composition and richness across multitrophic groups and influenced multiple functions simultaneously. We provide evidence that species richness across multiple trophic groups had stronger effects on multifunctionality than species richness at any single trophic level. Moreover, biotic associations, indicating the complexity of trophic networks, were positively associated with multifunctionality. The relative effects of diversity on multifunctionality increased at the scale of the larger community compared to a scale accounting for neighbouring interactions. Our results highlight the paramount importance of scale- and context- dependent multitrophic diversity and interactions for a better understanding of mountain ecosystem multifunctionality in a changing world. This article is protected by copyright. All rights reserved.

Environmental stress-discriminatory taxa are associated with high C and N cycling functional potentials in dryland grasslands

Increasing environmental stress strongly affects soil microbial communities, but the responses of the microbial assembly and the functional potential of the dominant microbial community in the presence of environmental stress in drylands are still poorly understood. Here, we undertook a broad appraisal of the abundance, diversity, similarity, community assembly, network properties and functions of soil microbiomes in 82 dryland grasslands along environmental gradients. We found that the bacterial and fungal diversity and community similarity showed different sensitivities to environmental stress (decreased mean annual precipitation (MAP) and soil nutrient levels and increased soil pH), and MAP was the most important factor influencing microbial community patterns. In addition, the dominant subcommunity of both bacteria and fungi was more sensitive to environmental stress than the nondominant subcommunity. Although increasing environmental stress decreased microbial phylogenetic clustering, it had no effects on the stochastic and deterministic assembly process balance. Moreover, we identified 101 bacterial and 34 fungal environmental stress-discriminatory taxa that were sensitive to environmental stress, and these bacterial markers showed a high correlation with the abundance of carbon (C) and nitrogen (N) cycling-related genes, whereas the taxa classified as connectors in the network were mainly correlated with C degradation genes. Our study shows that the different responses of bacteria and fungi to environmental stress bring challenges to predicting microbial function, but a relatively small number of taxa play an important role in driving C and N cycling-related functional genes, indicating that identifying an organism's phenotypic characteristics or traits of key taxa may improve our knowledge of the microbial response to ongoing global changes.

Nematode Predation and Competitive Interactions Affect Microbe-Mediated Phosphorus Dynamics

Nematode predation plays an essential role in determining changes in the rhizosphere microbiome. These changes affect the local nutrient balance and cycling of essential nutrients by selectively structuring interactions across functional taxa in the system. Currently, it is largely unknown to what extent nematode predation induces shifts in the microbiome associated with different rates of soil phosphorous (P) mineralization. Here, we performed an 7-year field experiment to investigate the importance of nematode predation influencing P availability and cycling. These were tracked via the changes in the alkaline phosphomonoesterase (ALP)-producing bacterial community and ALP activity in the rhizosphere of rapeseed. Here, we found that the nematode addition led to high predation pressure and thereby caused shifts in the abundance and composition of the ALP-producing bacterial community. Further analyses based on cooccurrence networks and metabolomics consistently showed that nematode addition induced competitive interactions between potentially keystone ALP-producing bacteria and other members within the community. Structural equation modeling revealed that the outcome of this competition induced by stronger predation pressure of nematodes was significantly associated with higher diversity of ALP-producing bacteria, thereby enhancing ALP activity and P availability. Taken together, our results provide evidence for the importance of predator-prey and competitive interactions in soil biology and their direct influences on nutrient cycling dynamics.

Distinct Co-occurrence Relationships and Assembly Processes of Active Methane-Oxidizing Bacterial Communities Between Paddy and Natural Wetlands of Northeast China

Studies of methane-oxidizing bacteria are updating our views of their composition and function in paddy and natural wetlands. However, few studies have characterized differences in the methane-oxidizing bacterial communities between paddy and natural wetlands. Here, we conducted a ¹³C stable isotope-probing experiment and high-throughput sequencing to determine the structure profiling, co-occurrence relationships, and assembly processes of methanotrophic communities in four wetlands of Northeast China. There was a clear difference in community structure between paddy and natural wetlands. LEfSe analyses revealed that Methylobacter, FWs, and Methylosinus were enriched in natural wetlands, while Methylosarcina were prevailing in paddy, all identified as indicative methanotrophs. We observed distinct co-occurrence relationships between paddy and natural wetlands: more robust and complex connections in natural wetlands than paddy wetlands. Furthermore, the relative importance of stochastic processes was greater than that of deterministic processes, as stochastic processes explained >50% of the variation in communities. These results demonstrated that the co-occurrence relationships and assembly processes of active methanotrophic communities in paddy and natural wetlands were distinct. Overall, the results of this study enhance our understanding of the communities of methane-oxidizing bacteria in paddy and natural wetlands of Northeast China.

Endophytic Fungi: Key Insights, Emerging Prospects, and Challenges in Natural Product Drug Discovery

Plant-associated endophytes define an important symbiotic association in nature and are established bio-reservoirs of plant-derived natural products. Endophytes colonize the internal tissues of a plant without causing any disease symptoms or apparent changes. Recently, there has been a growing interest in endophytes because of their beneficial effects on the production of novel metabolites of pharmacological significance. Studies have highlighted the socio-economic implications of endophytic fungi in agriculture, medicine, and the environment, with considerable success. Endophytic fungi-mediated biosynthesis of well-known metabolites includes taxol from Taxomyces andreanae, azadirachtin A and B from Eupenicillium parvum, vincristine from Fusarium oxysporum, and quinine from Phomopsis sp. The discovery of the billion-dollar anticancer drug taxol was a landmark in endophyte biology/research and established new paradigms for the metabolic potential of plant-associated endophytes. In addition, endophytic fungi have emerged as potential prolific producers of antimicrobials, antiseptics, and antibiotics of plant origin. Although extensively studied as a “production platform” of novel pharmacological metabolites, the molecular mechanisms of plant–endophyte dynamics remain less understood/explored for their efficient utilization in drug discovery. The emerging trends in endophytic fungi-mediated biosynthesis of novel bioactive metabolites, success stories of key pharmacological metabolites, strategies to overcome the existing challenges in endophyte biology, and future direction in endophytic fungi-based drug discovery forms the underlying theme of this article.

Seasonal Dynamics and Persistency of Endophyte Communities in Kalidium schrenkianum Shifts Under Radiation Stress

Endophytes are essential components of plant microbiota. Studies have shown that environmental factors and seasonal alternation can change the microbial community composition of plants. However, most studies have mainly emphasized the transitive endophyte communities and seasonal alternation but paid less attention to their persistence through multiple seasons. Kalidium schrenkianum is a perennial halophyte growing in an arid habitat with radiation stress (137Cs) in northwest China. In this study, K. schrenkianum growing under different environmental stresses were selected to investigate the dynamics and persistency of endophytic microbial communities amid seasons in a year. The results showed that Gammaproteobacteria and unassigned Actinobacteria were the most dominant bacterial communities, while the most dominant fungal communities were Dothideomycetes, unassigned Fungi, and Sodariomycetes. The bacterial community diversity in roots was higher than that in aerial tissues, and root communities had higher diversity in summer and autumn. In contrast, the fungal community diversity was higher in aerial tissues comparing to roots, and the highest diversity was in spring. Season was a determinant factor in the microbial community composition in the roots but not in the aerial tissues. RaupCrick index suggested that the bacterial communities were mainly shaped by stochastic processes. Our research investigated the community traits and members with temporal persistency. For example, bacterial taxa Afipia, Delftia, Stenotrophomonas, Xanthomonadaceae_B_OTU_211, and fungal taxa Neocamarosporium F_OTU_388, F_OTU_404, F_OTU_445, and unassigned Fungi F_OTU_704, F_OTU_767 showed higher frequencies than predicted in all the four seasons tested with neutral community model. The networks of co-occurrence associations presented in two or more seasons were visualized which suggested potential time-continuous core modules in most communities. In addition, the community dynamics and persistency also showed different patterns by radiation levels. Our findings would enhance our understanding of the microbial community assembly under environmental stress, and be promising to improve the development of integrated concept of core microbiome in future.

Skin bacterial metacommunities of San Francisco Bay Area salamanders are structured by host genus and habitat quality

Host-associated microbial communities can influence physiological processes of macroorganisms, including contributing to infectious disease resistance. For instance, some bacteria that live on amphibian skin produce antifungal compounds that inhibit two lethal fungal pathogens, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal). Therefore, differences in microbiome composition among host species or populations within a species can contribute to variation in susceptibility to Bd/Bsal. This study applies 16S rRNA sequencing to characterize the skin bacterial microbiomes of three widespread terrestrial salamander genera native to the western United States. Using a metacommunity structure analysis, we identified dispersal barriers for these influential bacteria between salamander families and localities. We also analyzed the effects of habitat characteristics such as percent natural cover and temperature seasonality on the microbiome. We found that certain environmental variables may influence the skin microbial communities of some salamander genera more strongly than others. Each salamander family had a somewhat distinct community of putative anti-Bd skin bacteria, suggesting that salamanders may select for a functional assembly of cutaneous symbionts that could differ in its ability to protect these amphibians from disease. Our observations raise the need to consider host identity and environmental heterogeneity during the selection of probiotics to treat wildlife diseases.

Distinct Responses of Rare and Abundant Microbial Taxa to In Situ Chemical Stabilization of Cadmium-Contaminated Soil

Soil microorganisms, which intricately link to ecosystem functions, are pivotal for the ecological restoration of heavy metal-contaminated soil. Despite the importance of rare and abundant microbial taxa in maintaining soil ecological function, the taxonomic and functional changes in rare and abundant communities during in situ chemical stabilization of cadmium (Cd)-contaminated soil and their contributions to the restoration of ecosystem functions remain elusive. Here, a 3-year field experiment was conducted to assess the effects of five soil amendments (CaCO₃ as well as biochar and rice straw, individually or in combination with CaCO₃) on rare and abundant microbial communities. The rare bacterial community exhibited a narrower niche breadth to soil pH and Cd speciation than the abundant community and was more sensitive to environmental changes altered by different soil amendments. However, soil amendments had comparable impacts on rare and abundant fungal communities. The assemblies of rare and abundant bacterial communities were dominated by variable selection and stochastic processes (dispersal limitation and undominated processes), respectively, while assemblies of both rare and abundant fungal communities were governed by dispersal limitation. Changes in soil pH, Cd speciation, and soil organic matter (SOM) by soil amendments may play essential roles in community assembly of rare bacterial taxa. Furthermore, the restored ecosystem multifunctionality by different amendments was closely related to the recovery of specific keystone species, especially rare bacterial taxa (Gemmatimonadaceae and Haliangiaceae) and rare fungal taxa (Ascomycota). Together, our results highlight the distinct responses of rare and abundant microbial taxa to soil amendments and their linkage with ecosystem multifunctionality.

IMPORTANCE Understanding the ecological roles of rare and abundant species in the restoration of soil ecosystem functions is crucial to remediation of heavy metal-polluted soil. Our study assessed the efficiencies of five commonly used soil amendments on recovery of ecosystem multifunctionality and emphasized the relative contributions of rare and abundant microbial communities to ecosystem multifunctionality. We found great discrepancies in community composition, assembly, niche breadth, and environmental responses between rare and abundant communities during in situ chemical stabilization of Cd-contaminated soil. Application of different soil amendments triggered recovery of specific key microbial species, which were highly related to ecosystem multifunctionality. Together, our results highlighted the importance of rare bacterial as well as rare and abundant fungal communities underpinning restoration of soil ecosystem multifunctionality during the Cd stabilization process.

Synergistic and Offset Effects of Fungal Species Combinations on Plant Performance

In natural and agricultural ecosystems, survival and growth of plants depend substantially on residing microbes in the endosphere and rhizosphere. Although numerous studies have reported the presence of plant-growth promoting bacteria and fungi in below-ground biomes, it remains a major challenge to understand how sets of microbial species positively or negatively affect plants' performance. By conducting a series of single- and dual-inoculation experiments of 13 plant-associated fungi targeting a Brassicaceae plant species (Brassica rapa var. perviridis), we here systematically evaluated how microbial effects on plants depend on presence/absence of co-occurring microbes. The comparison of single- and dual-inoculation experiments showed that combinations of the fungal isolates with the highest plant-growth promoting effects in single inoculations did not have highly positive impacts on plant performance traits (e.g., shoot dry weight). In contrast, pairs of fungi with small/moderate contributions to plant growth in single-inoculation contexts showed the greatest effects on plants among the 78 fungal pairs examined. These results on the offset and synergistic effects of pairs of microbes suggest that inoculation experiments of single microbial species/isolates can result in the overestimation or underestimation of microbial functions in multi-species contexts. Because keeping single-microbe systems under outdoor conditions is impractical, designing sets of microbes that can maximize performance of crop plants is an important step for the use of microbial functions in sustainable agriculture.