Rhizosphere microbiome functional diversity and pathogen invasion resistance build up during plant development

Plant-microbiome interactions and their impacts on plant adaptation to climate change

Plants have co-evolved with a wide range of microbial communities over hundreds of millions of years, this has drastically influenced their adaptation to biotic and abiotic stress. The rapid development of multi-omics approaches has greatly improved our understanding of the diversity, composition, and functions of plant microbiomes, but how global climate change affects the assembly of plant microbiomes and their roles in regulating host plant adaptation to changing environmental conditions is not fully known. In this review, we summarize recent advancements in the community assembly of plant microbiomes, and their responses to climate change factors such as elevated CO2 levels, warming, and drought. We further delineate the research trends and hotspots in plant-microbiome interactions in the context of climate change, and summarize the key mechanisms by which plant microbiomes influence plant adaptation to the changing climate. We propose that future research is urgently needed to unravel the impact of key plant genes and signal molecules modulated by climate change on microbial communities, to elucidate the evolutionary response of plant-microbe interactions at the community level, and to engineer synthetic microbial communities to mitigate the effects of climate change on plant fitness.

Micro-/nanobubble oxygenation irrigation enhances soil phosphorus availability and yield by altering soil bacterial community abundance and core microbial populations

Micro-/nanobubble oxygenation irrigation, as a novel irrigation technique, has been widely utilized to enhance soil phosphorus availability and maize yield. Nevertheless, currently, most of the studies remain unclear about the precise mechanism through which micro-/nanobubble oxygenation improves soil phosphorus availability and maize yield. Therefore, we established two irrigation methods, conventional irrigation (CF) and micro-/nanobubble oxygenation irrigation (MB), to investigate the combined effects on enzyme activity, microbial communities, and soil phosphorus availability in the rhizosphere soil of maize.The results showed that compared to the CF treatment, the MB treatment significantly increased available phosphorus content and alkaline phosphatase activity in maize rhizosphere soil by 21.3% and 15.4%, respectively. Furthermore, MB significantly influenced bacterial diversity in the maize rhizosphere soil but did not considerably affect fungal diversity. Specifically, MB regulated the microbial community structure in the maize rhizosphere by altering the relative abundances of the bacterial phylum Firmicutes and the fungal phyla Mucoromycota, Chytridiomycota, and Basidiomycota. In addition, MB reduced the complexity of the bacterial network while increasing the interaction density among bacterial species. Meanwhile, MB enhanced the complexity of the fungal network. Structural equation modeling indicated that MB primarily promoted soil alkaline phosphatase activity by regulating bacterial community diversity, thereby enhancing soil phosphorus availability. In conclusion, the application of micro-/nanobubble oxygenation irrigation enhances the activity of alkaline phosphatasein the soil by modulating the microbial community within the rhizosphere, thereby facilitating increased phosphorus availability in the rhizosphere of maize.

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.

Host Metabolic Alterations Mediate Phyllosphere Microbes Defense upon Xanthomonas oryzae pv oryzae Infection

Rice bacterial leaf blight, caused by Xanthomonas oryzae pv oryzae (Xoo), is a significant threat to global food security. Although the microbiome plays an important role in protecting plant health, how the phyllosphere microbiome is recruited and the underlying disease resistance mechanism remain unclear. This study investigates how rice phyllosphere microbiomes respond to pathogen invasion through a comprehensive multiomics approach, exploring the mechanisms of microbial defense and host resistance. We discovered that Xoo infection significantly reshapes the physicosphere microbial community. The bacterial network became more complex, with increased connectivity and interactions following infection. Metabolite profiling revealed that l-ornithine was a key compound to recruiting three keystone microbes, Brevundimonas (YB12), Pantoea (YN26), and Stenotrophomonas (YN10). These microbes reduced the disease index by up to 67.6%, and these microbes demonstrated distinct defense mechanisms. Brevundimonas directly antagonized Xoo by disrupting cell membrane structures, while Pantoea and Stenotrophomonas enhanced plant immune responses by significantly increasing salicylic acid and jasmonic acid levels and activating defense-related enzymes. Our findings provide novel insights into plant-microbe interactions, demonstrating how host metabolic changes recruit and activate beneficial phyllosphere microbes to combat pathogenic invasion. This research offers promising strategies for sustainable agricultural practices and disease management.

Microbial communities in the phyllosphere and endosphere of Norway spruce under attack by Heterobasidion

Heterobasidion annosum species complex has been regarded as the most destructive disease agent of conifer trees in boreal forests. Tree microbiome can regulate the plant-pathogen interactions by influencing both host resistance and pathogen virulence. Such information would help to improve the future health of forests and explore strategies to enhance ecosystem stability. In this study, using next-generation sequencing technology, we investigated the microbial community in different tree regions (needles, upper stem, and lower stem) of Norway spruce with and without wood decay symptoms. The primary purpose was to uncover signature characteristic microbiome harbored by asymptomatic trees compared to diseased trees. Additionally, the study was to explore the inter-kingdom and intra-kingdom interactions in microbiome (bacteria and fungi) of symptomatic versus asymptomatic trees. The results showed that in upper stem, species richness (Chao1) of fungi and bacteria were both higher in asymptomatic trees than symptomatic trees (P < 0.05). Compared to symptomatic trees, asymptomatic trees harbored a higher abundance of Actinobacteriota, bacterial genera of Methylocella, Conexibacter, Jatrophihabitans, and fungal genera of Mollisia. Fungal communities from the same anatomic region differed between the symptomatic and asymptomatic trees. Bacterial communities from the two stem regions were also distinct between the symptomatic and asymptomatic trees. The symptomatic trees possessed a less stable microbial network with more positive correlations compared to the asymptomatic trees. In the lower stem, at intra-kingdom level, the distribution of correlation numbers was more even in the bacterial network compared to the fungal network. In conclusion, the Heterobasidion attack decreased the microbial community species richness and shifted the community structure and functional structure to varying degrees. The microbial network was enlarged and became more unstable at both inter-kingdom and intra-kingdom level due to the Heterobasidion infection.

Characterization of rhizosphere bacterial communities in oilseed rape cultivars with different susceptibility to Plasmodiophora brassicae infection

Rhizosphere microbiomes are constantly mobilized during plant-pathogen interactions, and this, in turn, affects their interactions. However, few studies have examined the activities of rhizosphere microbiomes in plants with different susceptibilities to soil-borne pathogens, especially those that cause clubroot disease. In this study, we compared the rhizosphere bacterial community in response to infection of Plasmodiophora brassicae among the four different clubroot susceptibility cultivars of oilseed rape (Brassica napus). Our results revealed obvious differences in the responses of rhizosphere bacterial community to the P. brassicae infection between the four cultivars of oilseed rape. Several bacterial genera that are associated with the nitrogen cycle, including Limnobacter, Thiobacillus, Anaeromyxobacter, Nitrosomonas, Tumebacillus, and Halomonas, showed significantly different changes between susceptible and resistant cultivars in the presence of P. brassicae infection. Moreover, increased connectedness and robustness were exhibited in the rhizosphere bacterial community co-occurrence network in clubroot-susceptible cultivars that were infected with P. brassicae, while only slight changes were observed in clubroot-resistant cultivars. Metagenomic analysis of microbial metabolism also indicated differences in the rhizosphere bacterial community between susceptible and resistant cultivars that were infected with P. brassicae. Functional analysis of the nitrogen cycle showed that genes related to nitrification (nxrB) were upregulated in susceptible cultivars, while genes related to assimilatory nitrate reduction (nasA, narB, and nirA) were upregulated in resistant cultivars that were infected with P. brassicae. These findings indicate that the synthesis and assimilation process of NO3 - content were promoted in susceptible and resistant cultivars, respectively. Our study revealed differences in the characteristics of rhizosphere bacterial communities in response to P. brassicae infection between clubroot-susceptible and clubroot-resistant cultivars as well as the potential impact of these differences on the plant-P. brassicae interaction.

Response of Yields, Soil Physiochemical Characteristics, and the Rhizosphere Microbiome to the Occurrence of Root Rot Caused by Fusarium solani in Ligusticum chuanxiong Hort

Ligusticum chuanxiong Hort. is considered an important medicinal herb with extremely high economic value and medicinal value due to its various effects, including anti-oxidation, sedative action, hepatoprotection, and invigorating blood circulation. However, L. chuanxiong cultivation is hampered by various plant diseases, especially the root rot caused by Fusarium solani, hindering the sustainable development of the L. chuanxiong industry. The occurrence of soil-borne diseases is closely linked to imbalances in the microbial community structure. Here, we studied the yields, rhizosphere microbiota, and soil physiochemical characteristics of healthy and diseased L. chuanxiong plants affected by root rot with high-throughput sequencing and microbial network analysis, aiming to explore the relationships between soil environmental factors, microbiomes, and plant health of L. chuanxiong. According to the results, L. chuanxiong root rot significantly decreased the yields, altered microbial community diversity and composition, enriched more pathogenic fungi, recruited some beneficial bacteria, and reduced microbial interaction network stability. The Mantel test showed that soil organic matter and pH were the major environmental factors modulating plant microbiome assembly. The root rot severity was significantly affected by soil physiochemical properties, including organic matter, cation exchange capacity, available nitrogen, phosphorus, potassium, and pH. Furthermore, two differential microbes that have great potential in the biocontrol of L. chuanxiong root rot were dug out in the obtained results, which were the genera Trichoderma and Bacillus. This study provided a theoretical basis for further studies revealing the microecological mechanism of L. chuanxiong root rot and the ecological prevention and control of L. chuanxiong root rot from a microbial ecology perspective.

Rhizosphere Engineering of Biocontrol Agents Enriches Soil Microbial Diversity and Effectively Controls Root-Knot Nematodes

The root-knot nematode (RKN) causes significant yield loss in tomatoes. Understanding the interaction of biocontrol agents (BCAs)-nematicides-soil microbiomes and RKNs is essential for enhancing the efficacy of biocontrol agents and nematicides to curb RKN damage to crops. The present study aimed to evaluate the in vitro effectiveness of BACa and nematicide against RKN and to apply the amplicon sequencing to assess the interaction of Bacillus velezensis (VB7) and Trichoderma koningiopsis (TK) against RKNs. Metagenomic analysis revealed the relative abundance of three phyla such as Proteobacteria (42.16%), Firmicutes (19.57%), and Actinobacteria (17.69%) in tomato rhizospheres. Those tomato rhizospheres treated with the combined application of B. velezensis VB7 + T. koningiopsis TK and RKN had a greater frequency of diversity and richness than the control. RKN-infested tomato rhizosphere drenched with bacterial and fungal antagonists had the maximum diversity index of bacterial communities. A strong correlation with a maximum number of interconnection edges in the phyla Proteobacteria, Firmicutes, and Actinobacteria was evident in soils treated with both B. velezensis VB7 and T. koningiopsis TK challenged against RKN in infected soil. The present study determined a much greater diversity of bacterial taxa observed in tomato rhizosphere soils treated with B. velezensis VB7 and T. koningiopsis TK than in untreated soil. It is suggested that the increased diversity and abundance of bacterial communities might be responsible for increased nematicidal properties in tomato plants. Hence, the combined applications of B. velezensis VB7 and T. koningiopsis TK can enhance the nematicidal action to curb RKN infecting tomatoes.

Impact of a Potent Strain of Plant Growth-Promoting Bacteria (PGPB), Bacillus subtilis S1 on Bacterial Community Composition, Enzymatic Activity, and Nitrogen Content in Cucumber Rhizosphere Soils

Antagonistic bacterial strains from Bacillus spp. have been widely studied and utilized in the biocontrol of phytopathogens and the promotion of plant growth, but their impacts on the rhizosphere microecology when applied to crop plants are unclear. Herein, the effects of applying the antagonistic bacterium Bacillus subtilis S1 as a biofertilizer on the rhizosphere microecology of cucumbers were investigated. In a pot experiment on cucumber seedlings inoculated with S1, 3124 bacterial operational taxonomic units (OTUs) were obtained from the rhizosphere soils using high-throughput sequencing of 16S rRNA gene amplicons, and the most abundant phylum was Proteobacteria that accounted for 49.48% in the bacterial community. S1 treatment significantly reduced the abundances of soil bacterial taxa during a period of approximately 30 days but did not affect bacterial diversity in the rhizosphere soils of cucumbers. The enzymatic activities of soil nitrite reductase (S-Nir) and dehydrogenase (S-DHA) were significantly increased after S1 fertilization. However, the activities of soil urease (S-UE), cellulase (S-CL), and sucrase (S-SC) were significantly reduced compared to the control group. Additionally, the ammonium- and nitrate-nitrogen contents of S1-treated soil samples were significantly lower than those of the control group. S1 fertilization reshaped the rhizosphere soil bacterial community of cucumber plants. The S-CL activity and nitrate-nitrogen content in rhizosphere soil affected by S1 inoculation play important roles in altering the abundance of rhizosphere soil microbiota.

Endophytic Microorganisms in Tomato Roots, Changes in the Structure and Function of the Community at Different Growing Stages

This study analyzed flower bud differentiation and fruiting stages to investigate how the structure of the plant endophytic microbial community in the roots of tomatoes changes with plant senescence. Based on high-throughput sequencing technology, the diversity and relative abundance of endophytic microorganisms (bacteria and fungi) in tomato stems at different growth stages were analyzed. At the same time, based on LEfSe analysis, the differences in endophytic microorganisms in tomato stems at different growth stages were studied. Based on PICRUSt2 function prediction and FUNGuild, we predicted the functions of endophytic bacterial and fungal communities in tomato stems at different growth stages to explore potential microbial functional traits. The results demonstrated that not only different unique bacterial genera but also unique fungal genera could be found colonizing tomato roots at different growth stages. In tomato seedlings, flower bud differentiation, and fruiting stages, the functions of colonizing endophytes in tomato roots could primarily contribute to the promotion of plant growth, stress resistance, and improvement in nutrient cycling, respectively. These results also suggest that different functional endophytes colonize tomato roots at different growth stages.

Metagenomic evaluation of peanut rhizosphere microbiome from the farms of Saurashtra regions of Gujarat, India

The narrow zone of soil around the plant roots with maximum microbial activity termed as rhizosphere. Rhizospheric bacteria promote the plant growth directly or indirectly by providing the nutrients and producing antimicrobial compounds. In this study, the rhizospheric microbiota of peanut plants was characterized from different farms using an Illumina-based partial 16S rRNA gene sequencing to evaluate microbial diversity and identify the core microbiome through culture-independent (CI) approach. Further, all rhizospheric bacteria that could grow on various nutrient media were identified, and the diversity of those microbes through culture-dependent method (CD) was then directly compared with their CI counterparts. The microbial population profiles showed a significant correlation with organic carbon and concentration of phosphate, manganese, and potassium in the rhizospheric soil. Genera like Sphingomicrobium, Actinoplanes, Aureimonas _A, Chryseobacterium, members from Sphingomonadaceae, Burkholderiaceae, Pseudomonadaceae, Enterobacteriaceae family, and Bacilli class were found in the core microbiome of peanut plants. As expected, the current study demonstrated more bacterial diversity in the CI method. However, a higher number of sequence variants were exclusively present in the CD approach compared to the number of sequence variants shared between both approaches. These CD-exclusive variants belonged to organisms that are more typically found in soil. Overall, this study portrayed the changes in the rhizospheric microbiota of peanuts in different rhizospheric soil and environmental conditions and gave an idea about core microbiome of peanut plant and comparative bacterial diversity identified through both approaches.

Trichoderma harzianum prevents red kidney bean root rot by increasing plant antioxidant enzyme activity and regulating the rhizosphere microbial community

Root rot is one of the main reasons for yield losses of red kidney bean (Phaseolus vulgaris) production. Pre-inoculation with Trichoderma harzianum can effectively lower the incidence of red kidney bean root rot. In this study, four treatments including CK (control), Fu13 (Fusarium oxysporum), T891 (T. harzianum) and T891 + Fu13 (T. harzianum + F. oxysporum) were arranged in a pot experiment to investigate how T891 affected the incidence and severity of root rot, plant growth, and changes of defense enzyme activity in red kidney bean plants. Community composition and diversity of the rhizosphere microbiota was evaluated through high-throughput sequencing, and co-occurrence network was analyzed. The results showed that when compared to the Fu13 treatment, pre-inoculation with T891 reduced the incidence and severity of red kidney bean root rot by 40.62 and 68.03% (p < 0.05), increased the root length, shoot length, total dry biomass by 48.63, 97.72, 122.17%. Upregulated activity of super-oxide dismutase (SOD), peroxidase (POD), catalase (CAT) by 7.32, 38.48, 98.31% (p < 0.05), and reduced malondialdehyde (MDA) by 23.70% (p < 0.05), respectively. Microbiological analyses also showed that F. oxysporum reduced alpha diversity resulting in alteration the composition of the rhizosphere microbial community in red kidney bean. T891 significantly reduced abundance of F. oxysporum, allowing the enrichment of potentially beneficial bacteria Porphyrobacter (ASV 46), Lysobacter (ASV 85), Microbacteriaceae (ASV 105), and Gemmatimonas (ASV 107), resulting in a more stable structure of the microbial network. The results of random forest analysis further revealed that ASV 46 (Porphyrobacter) was the primary influencing factor for the incidence of root rot after inoculation with T891, while ASV 85 (Lysobacter) was the primary influencing factor for the biomass of red kidney bean. In conclusion, T. harzianum promotes the growth of red kidney bean and inhibits root rot by improving plant antioxidant enzyme activity and regulating the rhizosphere microbial community.

Microbe-induced phenotypic variation leads to overyielding in clonal plant populations

Overyielding, the high productivity of multispecies plant communities, is commonly seen as the result of plant genetic diversity. Here we demonstrate that biodiversity-ecosystem functioning relationships can emerge in clonal plant populations through interaction with microorganisms. Using a model clonal plant species, we found that exposure to volatiles of certain microorganisms led to divergent plant phenotypes. Assembling communities out of plants associated with different microorganisms led to transgressive overyielding in both biomass and seed yield. Our results highlight the importance of belowground microbial diversity in plant biodiversity research and open new avenues for precision ecosystem management.

Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers?

Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.

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.

Review: Research progress on seasonal succession of phyllosphere microorganisms

Phyllosphere microorganisms have recently attracted the attention of scientists studying plant microbiomes. The origin, diversity, functions, and interactions of phyllosphere microorganisms have been extensively explored. Many experiments have demonstrated seasonal cycles of phyllosphere microbes. However, a comprehensive comparison of these separate investigations to characterize seasonal trends in phyllosphere microbes of woody and herbaceous plants has not been conducted. In this review, we explored the dynamic changes of phyllosphere microorganisms in woody and non-woody plants with the passage of the season, sought to find the driving factors, summarized these texts, and thought about future research trends regarding the application of phyllosphere microorganisms in agricultural production. Seasonal trends in phyllosphere microorganisms of herbaceous and woody plants have similarities and differences, but extensive experimental validation is needed. Climate, insects, hosts, microbial interactions, and anthropogenic activities are the diverse factors that influence seasonal variation in phyllosphere microorganisms.

Germination of pecan seeds changes the microbial community

Endophytes are core of the plant-associated microbiome, and seed endophytes are closely related to the plant growth and development. Seed germination is an important part of pecan's life activities, but the composition and changes of microbes during different germination processes have not yet been revealed in pecan seeds. In order to deeply explore the characteristics of endophytes during the germination process of pecan, high-throughput sequencing was performed on seeds at four different germination stages. Findings of present study was found that the diversity and composition of microorganisms were different in different germination stages, and the microbial richness and diversity were highest in the seed endocarp break stage. It was speculated that the change of endophytes in pecan seeds was related to the germination stage. By evaluating the relationship between microbial communities, the core microbiota Cyanobacteria, Proteobacteria and Actinobacteria (bacterial) and Anthophyta and Ascomycota (fungal) core microbiota were identified in germinating pecan seeds. Finally, biomarkers in different germination processes of pecan seeds were identified by LEfSe analysis, among which Proteobacteria, Gamma proteobacteria and, Cyanobacteria and Ascomycota and Sordariomycetes were most abundant. Thus, this study will help to explore the interaction mechanism between pecan seeds and endophytes in different germination processes, and provide materials for the research and development of pecan seed endophytes.

Fertilization Weakens the Ecological Succession of Dissolved Organic Matter in Paddy Rice Rhizosphere Soil at the Molecular Level

Dissolved organic matter (DOM) is involved in numerous biogeochemical processes, and understanding the ecological succession of DOM is crucial for predicting its response to farming (e.g., fertilization) practices. Although plentiful studies have examined how fertilization practice affects the content of soil DOM, it remains unknown how long-term fertilization drives the succession of soil DOM over temporal scales. Here, we investigated the succession of DOM in paddy rice rhizosphere soils subjected to different long-term fertilization treatments (CK: no fertilization; NPK: inorganic fertilization; OM: organic fertilization) along with plant growth. Our results demonstrated that long-term fertilization significantly promoted the molecular chemodiversity of DOM, but it weakened the correlation between DOM composition and plant development. Time-decay analysis indicated that the DOM composition had a shorter halving time under CK treatment (94.7 days), compared to NPK (337.4 days) and OM (223.8 days) treatments, reflecting a lower molecular turnover rate of DOM under fertilization. Moreover, plant development significantly affected the assembly process of DOM only under CK, not under NPK and OM treatments. Taken together, our results demonstrated that long-term fertilization, especially inorganic fertilization, greatly weakens the ecological succession of DOM in the plant rhizosphere, which has a profound implication for understanding the complex plant-DOM interactions.

Plant species identity and plant-induced changes in soil physicochemistry-but not plant phylogeny or functional traits - shape the assembly of the root-associated soil microbiome

The root-associated soil microbiome contributes immensely to support plant health and performance against abiotic and biotic stressors. Understanding the processes that shape microbial assembly in root-associated soils is of interest in microbial ecology and plant health research. In this study, 37 plant species were grown in the same soil mixture for 10 months, whereupon the root-associated soil microbiome was assessed using amplicon sequencing. From this, the contribution of direct and indirect plant effects on microbial assembly was assessed. Plant species and plant-induced changes in soil physicochemistry were the most significant factors that accounted for bacterial and fungal community variation. Considering that all plants were grown in the same starting soil mixture, our results suggest that plants, in part, shape the assembly of their root-associated soil microbiome via their effects on soil physicochemistry. With the increase in phylogenetic ranking from plant species to class, we observed declines in the degree of community variation attributed to phylogenetic origin. That is, plant-microbe associations were unique to each plant species, but the phylogenetic associations between plant species were not important. We observed a large degree of residual variation (> 65%) not accounted for by any plant-related factors, which may be attributed to random community assembly.

RIN enhances plant disease resistance via root exudate-mediated assembly of disease-suppressive rhizosphere microbiota

The RIPENING-INHIBITOR (RIN) transcriptional factor is a key regulator governing fruit ripening. While RIN also affects other physiological processes, its potential roles in triggering interactions with the rhizosphere microbiome and plant health are unknown. Here we show that RIN affects microbiome-mediated disease resistance via root exudation, leading to recruitment of microbiota that suppress the soil-borne, phytopathogenic Ralstonia solanacearum bacterium. Compared with the wild-type (WT) plant, RIN mutants had different root exudate profiles, which were associated with distinct changes in microbiome composition and diversity. Specifically, the relative abundances of antibiosis-associated genes and pathogen-suppressing Actinobacteria (Streptomyces) were clearly lower in the rhizosphere of rin mutants. The composition, diversity, and suppressiveness of rin plant microbiomes could be restored by the application of 3-hydroxyflavone and riboflavin, which were exuded in much lower concentrations by the rin mutant. Interestingly, RIN-mediated effects on root exudates, Actinobacteria, and disease suppression were evident from the seedling stage, indicating that RIN plays a dual role in the early assembly of disease-suppressive microbiota and late fruit development. Collectively, our work suggests that, while plant disease resistance is a complex trait driven by interactions between the plant, rhizosphere microbiome, and the pathogen, it can be indirectly manipulated using "prebiotic" compounds that promote the recruitment of disease-suppressive microbiota.

Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections

Soil-borne pathogens pose a major threat to food production worldwide, particularly under global change and with growing populations. Yet, we still know very little about how the soil microbiome regulates the abundance of soil pathogens and their impact on plant health. Here we combined field surveys with experiments to investigate the relationships of soil properties and the structure and function of the soil microbiome with contrasting plant health outcomes. We find that soil acidification largely impacts bacterial communities and reduces the capacity of soils to combat fungal pathogens. In vitro assays with microbiomes from acidified soils further highlight a declined ability to suppress Fusarium, a globally important plant pathogen. Similarly, when we inoculate healthy plants with an acidified soil microbiome, we show a greatly reduced capacity to prevent pathogen invasion. Finally, metagenome sequencing of the soil microbiome and untargeted metabolomics reveals a down regulation of genes associated with the synthesis of sulfur compounds and reduction of key traits related to sulfur metabolism in acidic soils. Our findings suggest that changes in the soil microbiome and disruption of specific microbial processes induced by soil acidification can play a critical role for plant health.

Changes in Bulk and Rhizosphere Soil Microbial Diversity Communities of Native Quinoa Due to the Monocropping in the Peruvian Central Andes

Quinoa (Chenopodium quinoa) is a highly nutritious crop that is resistant to adverse conditions. Due to the considerable increase in its commercial production in Andean soils, the plant is suffering the negative effects of monocropping, which reduces its yield. We used for the first time a high-throughput Illumina MiSeq sequencing approach to explore the composition, diversity, and functions of fungal and bacterial communities of the bulk and rhizosphere in soils of native C. quinoa affected by monocropping in the central Andes of Peru. The results showed that the bacterial and fungal community structure among the treatments was significantly changed by the monocropping and the types of soil (rhizosphere and bulk). Also, in soils subjected to monocropping, there was an increase in Actinobacteria and a decrease in Proteobacteria, and the reduction in the presence of Ascomycota and the increase in Basidiomycota. By alpha-diversity indices, lower values of bacteria and fungi were observed in the monoculture option compared to the soil not affected by monocropping, and sometimes significant differences were found between both. We detected differentially abundant phytopathogenic fungi and bacteria with growth-stimulating effects on plants. Also, we denoted a decrease in the abundance of the functional predictions in bacteria in the monocropped soils. This research will serve as a starting point to explore the importance and effects of microorganisms in degraded soils and their impact on the growth and quality of quinoa crops.

Unraveling the functional genes present in rhizosphere microbiomes of Solanum lycopersicum

The microbiomes living in the rhizosphere soil of the tomato plant contribute immensely to the state of health of the tomato plant alongside improving sustainable agriculture. With the aid of shotgun metagenomics sequencing, we characterized the putative functional genes (plant-growth-promoting and disease-resistant genes) produced by the microbial communities dwelling in the rhizosphere soil of healthy and powdery mildew-diseased tomato plants. The results identified twenty-one (21) plant growth promotion (PGP) genes in the microbiomes inhabiting the healthy rhizosphere (HR) which are more predomiant as compared to diseased rhizosphere (DR) that has nine (9) genes and four (4) genes in bulk soil (BR). Likewise, we identified some disease-resistant genes which include nucleotide binding genes and antimicrobial genes. Our study revealed fifteen (15) genes in HR which made it greater in comparison to DR that has three (3) genes and three (3) genes in bulk soil. Further studies should be conducted by isolating these microorganisms and introduce them to field experiments for cultivation of tomatoes.

Looking beyond Virus Detection in RNA Sequencing Data: Lessons Learned from a Community-Based Effort to Detect Cellular Plant Pathogens and Pests

High-throughput sequencing (HTS), more specifically RNA sequencing of plant tissues, has become an indispensable tool for plant virologists to detect and identify plant viruses. During the data analysis step, plant virologists typically compare the obtained sequences to reference virus databases. In this way, they are neglecting sequences without homologies to viruses, which usually represent the majority of sequencing reads. We hypothesized that traces of other pathogens might be detected in this unused sequence data. In the present study, our goal was to investigate whether total RNA-seq data, as generated for plant virus detection, is also suitable for the detection of other plant pathogens and pests. As proof of concept, we first analyzed RNA-seq datasets of plant materials with confirmed infections by cellular pathogens in order to check whether these non-viral pathogens could be easily detected in the data. Next, we set up a community effort to re-analyze existing Illumina RNA-seq datasets used for virus detection to check for the potential presence of non-viral pathogens or pests. In total, 101 datasets from 15 participants derived from 51 different plant species were re-analyzed, of which 37 were selected for subsequent in-depth analyses. In 29 of the 37 selected samples (78%), we found convincing traces of non-viral plant pathogens or pests. The organisms most frequently detected in this way were fungi (15/37 datasets), followed by insects (13/37) and mites (9/37). The presence of some of the detected pathogens was confirmed by independent (q)PCRs analyses. After communicating the results, 6 out of the 15 participants indicated that they were unaware of the possible presence of these pathogens in their sample(s). All participants indicated that they would broaden the scope of their bioinformatic analyses in future studies and thus check for the presence of non-viral pathogens. In conclusion, we show that it is possible to detect non-viral pathogens or pests from total RNA-seq datasets, in this case primarily fungi, insects, and mites. With this study, we hope to raise awareness among plant virologists that their data might be useful for fellow plant pathologists in other disciplines (mycology, entomology, bacteriology) as well.

The contrasting responses of abundant and rare microbial community structures and co-occurrence networks to secondary forest succession in the subalpine region

Knowledge of variations in abundant and rare soil microbial communities and interactions during secondary forest succession is lacking. Soil samples were gathered from different secondary successional stages (grassland, shrubland, and secondary forest) to study the responses of abundant and rare bacterial and fungal communities, interactions and driving factors to secondary forest succession by Illumina sequencing of the 16S and ITS rRNA genes. The results showed that the α-diversities (Shannon index) of abundant bacteria and fungi revealed no significant changes during secondary forest succession, but increased significantly for rare bacteria. The abundant and rare bacterial and fungal β-diversities changed significantly during secondary forest succession. Network analysis showed no obvious changes in the topological properties (nodes, links, and average degree) of abundant microbial networks during secondary forest succession. In contrast, these properties of the rare microbial networks in the secondary forest were higher than those in the grassland and shrubland, indicating that rare microbial networks are more responsive to secondary forest succession than abundant microorganisms. Additionally, rare microbial networks revealed more microbial interactions and greater network complexity than abundant microbial networks due to their higher numbers of nodes and links. The keystone species differed between the abundant and rare microbial networks and consisted of 1 and 48 keystone taxa in the abundant and rare microbial networks, respectively. Soil TP was the most important influencing factor of abundant and rare bacterial communities. Successional stages and plant richness had the most important influences on abundant and rare fungal communities, respectively. C:P, SM and N:P were mainly related to abundant and rare microbial network topological properties. Our study indicates that abundant and rare microbial communities, interactions and driving factors respond differently to secondary forest succession.

A Synthetic Microbial Community of Plant Core Microbiome Can Be a Potential Biocontrol Tool

Microbes are accepted as the foremost drivers of the rhizosphere ecology that influences plant health in direct or indirect ways. In recent years, the rapid development of gene sequencing technology has greatly facilitated the study of plant microbiome structure and function, and various plant-associated microbiomes have been categorized. Additionally, there is growing research interest in plant-disease-related microbes, and some specific microflora beneficial to plant health have been identified. This Review discusses the plant-associated microbiome's biological control pathways and functions to modulate plant defense against pathogens. How do plant microbiomes enhance plant resistance? How does the plant core microbiome-associated synthetic microbial community (SynCom) improve plant health? This Review further points out the primary need to develop smart agriculture practices using SynComs against plant diseases. Finally, this Review provides ideas for future opportunities in plant disease control and mining new microbial resources.

Microbes to support plant health: understanding bioinoculant success in complex conditions

A promising, sustainable way to enhance plant health and productivity is by leveraging beneficial microbes. Beneficial microbes are natural soil residents with proven benefits for plant performance and health. When applied in agriculture to improve crop yield and performance, these microbes are commonly referred to as bioinoculants. Yet, despite their promising properties, bioinoculant efficacy can vary dramatically in the field, hampering their applicability. Invasion of the rhizosphere microbiome is a critical determinant for bioinoculant success. Invasion is a complex phenomenon that is shaped by interactions with the local, resident microbiome and the host plant. Here, we explore all of these dimensions by cross-cutting ecological theory and molecular biology of microbial invasion in the rhizosphere. We refer to the famous Chinese philosopher and strategist Sun Tzu, who believed that solutions for problems require deep understanding of the problems themselves, to review the major biotic factors determining bioinoculant effectiveness.

Ecological corridors homogenize plant root endospheric mycobiota

Ecological corridors promote species coexistence in fragmented habitats where dispersal limits species fluxes. The corridor concept was developed and investigated with macroorganisms in mind, while microorganisms, the invisible majority of biodiversity, were disregarded. We analyzed the effect of corridors on the dynamics of endospheric fungal assemblages associated with plant roots at the scale of 1 m over 2 years (i.e. at five time points) by combining an experimental corridor-mesocosm with high-throughput amplicon sequencing. We showed that plant root endospheric mycobiota were sensitive to corridor effects when the corridors were set up at a small spatial scale. The endospheric mycobiota of connected plants had higher species richness, lower beta-diversity, and more deterministic assembly than the mycobiota of isolated plants. These effects became more pronounced with the development of host plants. Biotic corridors composed of host plants may thus play a key role in the spatial dynamics of microbial communities and may influence microbial diversity and related ecological functions.

Differences in soil physicochemical properties and rhizosphere microbial communities of flue-cured tobacco at different transplantation stages and locations

Rhizosphere microbiota play an important role in regulating soil physical and chemical properties and improving crop production performance. This study analyzed the relationship between the diversity of rhizosphere microbiota and the yield and quality of flue-cured tobacco at different transplant times (D30 group, D60 group and D90 group) and in different regions [Linxiang Boshang (BS) and Linxiang ZhangDuo (ZD)] by high-throughput sequencing technology. The results showed that there were significant differences in the physicochemical properties and rhizosphere microbiota of flue-cured tobacco rhizosphere soil at different transplanting times, and that the relative abundance of Bacillus in the rhizosphere microbiota of the D60 group was significantly increased. RDA and Pearson correlation analysis showed that Bacillus, Streptomyces and Sphingomonas were significantly correlated with soil physical and chemical properties. PIGRUSt2 function prediction results showed that compared with the D30 group, the D60 group had significantly increased metabolic pathways such as the superpathway of pyrimidine deoxyribonucleoside salvage, allantoin degradation to glyoxylate III and pyrimidine deoxyribonucleotides de novo biosynthesis III metabolic pathways. The D90 group had significantly increased metabolic pathways such as ubiquitol-8 biosynthesis (prokaryotic), ubiquitol-7 biosynthesis (prokaryotic) and ubiquitol-10 biosynthesis (prokaryotic) compared with the D60 group. In addition, the yield and quality of flue-cured tobacco in the BS region were significantly higher than those in the ZD region, and the relative abundance of Firmicutes and Bacillus in the rhizosphere microbiota of flue-cured tobacco in the BS region at the D60 transplant stage was significantly higher than that in the ZD region. In addition, the results of the hierarchical sample metabolic pathway abundance map showed that the PWY-6572 metabolic pathway was mainly realized by Paenibacillus, and that the relative abundance of flue-cured tobacco rhizosphere microbiota (Paenibacillus) participating in PWY-6572 in the D60 transplant period in the BS region was significantly higher than that in the ZD region. In conclusion, different transplanting periods of flue-cured tobacco have important effects on soil physical and chemical properties and rhizosphere microbial communities. There were significant differences in the rhizosphere microbiota and function of flue-cured tobacco in different regions, which may affect the performance and quality of this type of tobacco.

Tool and techniques study to plant microbiome current understanding and future needs: an overview

Microorganisms are present in the universe and they play role in beneficial and harmful to human life, society, and environments. Plant microbiome is a broad term in which microbes are present in the rhizo, phyllo, or endophytic region and play several beneficial and harmful roles with the plant. To know of these microorganisms, it is essential to be able to isolate purification and identify them quickly under laboratory conditions. So, to improve the microbial study, several tools and techniques such as microscopy, rRNA, or rDNA sequencing, fingerprinting, probing, clone libraries, chips, and metagenomics have been developed. The major benefits of these techniques are the identification of microbial community through direct analysis as well as it can apply in situ. Without tools and techniques, we cannot understand the roles of microbiomes. This review explains the tools and their roles in the understanding of microbiomes and their ecological diversity in environments.

Cross-kingdom synthetic microbiota supports tomato suppression of Fusarium wilt disease

The role of rhizosphere microbiota in the resistance of tomato plant against soil-borne Fusarium wilt disease (FWD) remains unclear. Here, we showed that the FWD incidence was significantly negatively correlated with the diversity of both rhizosphere bacterial and fungal communities. Using the microbiological culturomic approach, we selected 205 unique strains to construct different synthetic communities (SynComs), which were inoculated into germ-free tomato seedlings, and their roles in suppressing FWD were monitored using omics approach. Cross-kingdom (fungi and bacteria) SynComs were most effective in suppressing FWD than those of Fungal or Bacterial SynComs alone. This effect was underpinned by a combination of molecular mechanisms related to plant immunity and microbial interactions contributed by the bacterial and fungal communities. This study provides new insight into the dynamics of microbiota in pathogen suppression and host immunity interactions. Also, the formulation and manipulation of SynComs for functional complementation constitute a beneficial strategy in controlling soil-borne disease.

Nodule-associated diazotrophic community succession is driven by developmental phases combined with microhabitat of Sophora davidii

Nodule-associated nitrogen-fixing microorganisms (diazotrophs) residing in legume root nodules, and they have the potential to enhance legume survival. However, the succession characteristics and mechanisms of leguminous diazotrophic communities remain largely unexplored. We performed a high-throughput nifH amplicon sequencing with samples of root nodules and soil in the three developmental phases (young nodules, active nodules and senescent nodules) of the Sophora davidii (Franch.) Skeels root nodules, aiming to investigate the dynamics of nodule-endophytic diazotrophs during three developmental phases of root nodules. The results demonstrated the presence of diverse diazotrophic bacteria and successional community shifting dominated by Mesorhizobium and Bradyrhizobium inside the nodule according to the nodule development. The relative abundance decreased for Mesorhizobium, while decreased first and then increased for Bradyrhizobium in nodule development from young to active to senescent. Additionally, strains M. amorphae BT-30 and B. diazoefficiens B-26 were isolated and selected to test the interaction between them in co-cultured conditions. Under co-culture conditions: B. diazoefficiens B-26 significantly inhibited the growth of M. amorphae BT-30. Intriguingly, growth of B. diazoefficiens B-26 was significantly promoted by co'culture with M. amorphae BT-30 and could utilize some carbon and nitrogen sources that M. amorphae BT-30 could not. Additionally, the composition of microbial community varied in root nodules, in rhizosphere and in bulk soil. Collectively, our study highlights that developmental phases of nodules and the host microhabitat were the key driving factors for the succession of nodule-associated diazotrophic community.

Resource availability drives bacteria community resistance to pathogen invasion via altering bacterial pairwise interactions

Microbial interactions within resident communities are a major determinant of resistance to pathogen invasion. Yet, interactions vary with environmental conditions, raising the question of how community composition and environments interactively shape invasion resistance. Here, we use resource availability (RA) as a model parameter altering the resistance of model bacterial communities to invasion by the plant pathogenic bacterium Ralstonia solanacearum. We found that at high RA, interactions between resident bacterial species were mainly driven by the direct antagonism, in terms of the means of invader inhibition. Consequently, the competitive resident communities with a higher production of antibacterial were invaded to a lesser degree than facilitative communities. At low RA, bacteria produced little direct antagonist potential, but facilitative communities reached a relatively higher community productivity, which showed higher resistance to pathogen invasion than competitive communities with lower productivities. This framework may lay the basis to understand complex microbial interactions and biological invasion as modulated by the dynamic changes of environmental resource availability.

Rhizosphere microorganisms of Crocus sativus as antagonists against pathogenic Fusarium oxysporum

Introduction

Several microorganisms in the plant root system, especially in the rhizosphere, have their own compositions and functions. Corm rot is the most severe disease of Crocus sativus, leading to more than 50% mortality in field production.

Methods

In this study, metagenomic sequencing was used to analyze microbial composition and function in the rhizosphere of C. sativus for possible microbial antagonists against pathogenic Fusarium oxysporum.

Results

The microbial diversity and composition were different in the C. sativus rhizosphere from different habitats. The diversity index (Simpson index) was significantly lower in the C. sativus rhizospheric soil from Chongming (Rs_CM) and degenerative C. sativus rhizospheric soil from Chongming (RsD_CM) than in others. Linear discriminant analysis effect size results showed that differences among habitats were mainly at the order (Burkholderiales, Micrococcales, and Hypocreales) and genus (Oidiodendron and Marssonina) levels. Correlation analysis of the relative lesion area of corm rot showed that Asanoa was the most negatively correlated bacterial genus (ρ = -0.7934, p< 0.001), whereas Moniliophthora was the most negatively correlated fungal genus (ρ = -0.7047, p< 0.001). The relative lesion area result showed that C. sativus from Qiaocheng had the highest resistance, followed by Xiuzhou and Jiande. C. sativus groups with high disease resistance had abundant pathogen resistance genes, such as chitinase and β-1,3-glucanase genes, from rhizosphere microorganisms. Further, 13 bacteria and 19 fungi were isolated from C. sativus rhizosphere soils, and antagonistic activity against pathogenic F. oxysporum was observed on potato dextrose agar medium. In vivo corm experiments confirmed that Trichoderma yunnanense SR38, Talaromyces sp. SR55, Burkholderia gladioli SR379, and Enterobacter sp. SR343 displayed biocontrol activity against corm rot disease, with biocontrol efficiency of 20.26%, 31.37%, 39.22%, and 14.38%, respectively.

Discussion

This study uncovers the differences in the microbial community of rhizosphere soil of C. sativus with different corm rot disease resistance and reveals the role of four rhizospheric microorganisms in providing the host C. sativus with resistance against corm rot. The obtained biocontrol microorganisms can also be used for application research and field management.

Bacillus aryabhattai LAD impacts rhizosphere bacterial community structure and promotes maize plant growth

BACKGROUND

Plant growth-promoting rhizobacteria may significantly impact the soil microbial community and the growth of plant roots and have critical roles in soil ecosystem functioning. However, the interactions between rhizobacteria and plants are extremely complicated and remain understudied.

RESULTS

In this study, a Bacillus strain was isolated from a long-term maize colonization soil and identified as Bacillus aryabhattai strain LAD. Laboratory tests showed that B. aryabhattai LAD had phosphate-solubilizing and nitrogen-fixing functions that benefit plant growth. The effects of LAD cultures on the root system development of corn seedlings and the structure of rhizosphere bacterial communities were studied. The most significant stimulations of LAD culture on plant growth were observed at a cell density of 10²  CFU mL^-1 . Treatment with LAD culture in hydroponics caused an increase of 107%, 197%, and 25% in the shoot length, total root length, and main root thickness respectively. The LAD treatment also significantly affected the rhizosphere microbial abundance and community structure. The rhizobacterial abundance and species richness in the corn seedlings treated with LAD culture were significantly lower than those in the control group. However, the LAD-treated samples had higher relative abundances of plant growth-promoting rhizobacteria like Bacillus and Burkholderia than the control samples did, suggesting that LAD treatment may facilitate the mutualistic relation between the rhizosphere microbiome and the plant.

CONCLUSION

These results collectively demonstrated that LAD is capable of shaping the rhizosphere microbial community structure and functions as a plant growth-promoting agent, which makes it a strong candidate for application as bio-fertilizer in agricultural systems. © 2022 Society of Chemical Industry.

Small changes in rhizosphere microbiome composition predict disease outcomes earlier than pathogen density variations

Even in homogeneous conditions, plants facing a soilborne pathogen tend to show a binary outcome with individuals either remaining fully healthy or developing severe to lethal disease symptoms. As the rhizosphere microbiome is a major determinant of plant health, we postulated that such a binary outcome may result from an early divergence in the rhizosphere microbiome assembly that may further cascade into varying disease suppression abilities. We tested this hypothesis by setting up a longitudinal study of tomato plants growing in a natural but homogenized soil infested with the soilborne bacterial pathogen Ralstonia solanacearum. Starting from an originally identical species pool, individual rhizosphere microbiome compositions rapidly diverged into multiple configurations during the plant vegetative growth. This variation in community composition was strongly associated with later disease development during the later fruiting state. Most interestingly, these patterns also significantly predicted disease outcomes 2 weeks before any difference in pathogen density became apparent between the healthy and diseased groups. In this system, a total of 135 bacterial OTUs were associated with persistent healthy plants. Five of these enriched OTUs (Lysinibacillus, Pseudarthrobacter, Bordetella, Bacillus, and Chryseobacterium) were isolated and shown to reduce disease severity by 30.4-100% when co-introduced with the pathogen. Overall, our results demonstrated that an initially homogenized soil can rapidly diverge into rhizosphere microbiomes varying in their ability to promote plant protection. This suggests that early life interventions may have significant effects on later microbiome states, and highlights an exciting opportunity for microbiome diagnostics and plant disease prevention.

Soil conditions on bacterial wilt disease affect bacterial and fungal assemblage in the rhizosphere

Natural soil has the ability to suppress the soil-borne pathogen to a certain extent, and the assemblage of soil microbiome plays a crucial role in maintaining such ability. Long-term monoculture accelerates the forms of soil microbiome and leads to either disease conducive or suppressive soils. Here, we explored the impact of soil conditions on bacterial wilt disease (healthy or diseased) under long-term tobacco monoculture on the assemblage of bacterial and fungal communities in bulk and rhizosphere soils during the growth periods. With Illumina sequencing, we compared the bacterial and fungal composition of soil samples from tobacco bacterial wilt diseased fields and healthy fields in three growth periods. We found that Proteobacteria and Ascomycota were the most abundant phylum for bacteria and fungi, respectively. Factors of soil conditions and tobacco growth periods can significantly influence the microbial composition in bulk soil samples, while the factor of soil conditions mainly determined the microbial composition in rhizosphere soil samples. Next, rhizosphere samples were further analyzed with LEfSe to determine the discriminative taxa affected by the factor of soil conditions. For bacteria, the genus Ralstonia was found in the diseased soils, whereas the genus Flavobacterium was the only shared taxon in healthy soils; for fungi, the genus Chaetomium was the most significant taxon in healthy soils. Besides, network analysis confirmed that the topologies of networks of healthy soils were higher than that of diseased soils. Together, our results suggest that microbial assemblage in the rhizosphere will be largely affected by soil conditions especially after long-term monoculture.

Rhizospheric microorganisms: The gateway to a sustainable plant health

Plant health is essential for food security, and constitutes a major predictor to safe and sustainable food systems. Over 40% of the global crops' productions are lost to pests, insects, diseases, and weeds, while the routinely used chemical-based pesticides to manage the menace also have detrimental effects on the microbial communities and ecosystem functioning. The rhizosphere serves as the microbial seed bank where microorganisms transform organic and inorganic substances in the rhizosphere into accessible plant nutrients as plants harbor diverse microorganisms such as fungi, bacteria, nematodes, viruses, and protists among others. Although, the pathogenic microbes initiate diseases by infiltrating the protective microbial barrier and plants' natural defense systems in the rhizosphere. Whereas, the process is often circumvented by the beneficial microorganisms which antagonize the pathogens to instill disease resistance. The management of plant health through approaches focused on disease prevention is instrumental to attaining sustainable food security, and safety. Therefore, an in-depth understanding of the evolving and succession of root microbiomes in response to crop development as discussed in this review opens up new-fangled possibilities for reaping the profit of beneficial root–microbiomes' interactions toward attaining sustainable plant health.

Insights into Pyrroloquinoline Quinone (PQQ) Effects on Soil Nutrients and Pathogens from Pepper Monocropping Soil under Anaerobic and Aerobic Conditions

Imbalances of soil available nutrients and soilborne diseases have seriously restricted the productivity of crops and jeopardized food security worldwide. Pyrroloquinoline quinone (PQQ), a redox cofactor in some bacteria involved in glucose metabolism and phosphorus mineralization, could be anticipated to alter soil ecosystems to a certain extent. However, there is limited information on PQQ defending soilborne pathogens and regulating soil main nutrients. Here, a pot experiment based on mono-cropping soils of pepper was conducted to examine the effects of PQQ amendment on reconstructing soil microbial communities and soil nutrients under aerobic/anaerobic conditions comprising three treatments, namely, control, PQQ (aerobic), and FL-PQQ (anaerobic). The results revealed that soil microbial community composition and soil nutrients were distinctly altered by PQQ regimes. Compared to control, PQQ treatment significantly increased the content of soil available phosphorus (AP), while FL_PQQ treatment strongly improved the content of soil available nitrogen (AN). In terms of pathogens, relative to control, both PQQ treatments suppressed the abundances of pathogens, of which FL_PQQ treatment significantly decreased the abundance of the pathotrophic fungal by 64% and the abundance of Fusarium oxysporum by 57%, largely attributed to the increase of organic acid generators (Oxobacter, Hydrogenispora) and potential antagonists (Bacillus, Talaromyces). Structural equation modeling (SEM) showed that PQQ regimes suppressed pathogens by indirectly regulating soil physicochemical properties and microbial communities. Overall, we proposed that PQQ application both in aerobic/anaerobic conditions could improve soil available nutrients and suppress soil pathogens in pepper monocropping soils.

IMPORTANCE The attention to PQQ (pyrroloquinoline quinone) effect on soil nutrients and pathogens was less paid in monocropping soils. However, the underlying microbial interacting mechanism remains unclear. Adopting a novel external bio-additive, the effects of PQQ on soil main nutrients and the pathotrophic fungal under aerobic and anaerobic regimes will be investigated, which would help to improve soil quality health. Our main conclusion was that PQQ would help to remediate monocropping obstacle soils in terms of soil nutrients and soil pathogens by associating with the microbial community, and anaerobic PQQ application more favored amelioration of continuous obstacle soils. These results will benefit the health and sustainable development of pepper production as well as other greenhouse vegetable production.

Protist feeding patterns and growth rate are related to their predatory impacts on soil bacterial communities

Predatory protists are major consumers of soil micro-organisms. By selectively feeding on their prey, they can shape soil microbiome composition and functions. While different protists are known to show diverging impacts, it remains impossible to predict a priori the effect of a given species. Various protist traits including phylogenetic distance, growth rate and volume have been previously linked to the predatory impact of protists. Closely-related protists,however, also showed distinct prey choices which could mirror specificity in their dietary niche. We, therefore, aimed to estimate the dietary niche breadth and overlap of eight protist isolates on 20 bacterial species in plate assays. To assess the informative value of previously suggested and newly proposed (feeding-related) protist traits, we related them to the impacts of predation of each protist on a protist-free soil bacterial community in a soil microcosm via 16S rRNA gene amplicon sequencing. We could demonstrate that each protist showed a distinct feeding pattern in vitro. Further, the assayed protist feeding patterns and growth rates correlated well with the observed predatory impacts on the structure of soil bacterial communities. We thus conclude that in vitro screening has the potential to inform on the specific predatory impact of selected protists.

Effects of Imazethapyr on Soybean Root Growth and Soil Microbial Communities in Sloped Fields

The herbicide imazethapyr was previously recommended for controlling weeds in soybean fields. However, the effects of imazethapyr on soil microbial communities and their relationship with crop root growth in sloped soils remain unclear. In this study, a field experiment was conducted on a sloped field to explore the effects of imazethapyr on crop root growth, microbial communities, microbial co-occurrence networks, and the interactions between microbes and crop root growth. The field experiment included two factors: slope and imazethapyr. The slope factor included three different slope gradients: 5° (S1), 10° (S2), and 15° (S3). The imazethapyr factor included two treatments: with (I1) and without (I0) imazethapyr. Thus, six total combinations of slope and imazethapyr treatments were tested in this study: S1I1, S2I1, S3I1, S1I0, S2I0, and S3I0. The results show that, compared to the I0 treatments, the I1 treatments significantly increased the soybean root length, surface area, and volume by 11.7~26.5 m, 171.7~324.2 cm2, and 1.8~3.1 cm3, respectively, across all the slopes. The Proteobacteria, Actinobacteriota, and Bacteroidota bacterial phyla and Ascomycota and Basidiomycota fungal phyla were found to be the top phyla represented bacterial and fungal communities. These five phyla were scattered in co-occurrence networks of bacterial and fungal communities, suggesting these phyla play critical roles in enhancing the stability of co-occurrence networks. Compared to the I0 treatments, the I1 treatments increased nodes from Proteobacteria, Actinobacteriota, and Bacteroidota phyla by 6.4%, 9.1%, and 11.2%, respectively, in the bacterial co-occurrence network. Similarly, in the fungal co-occurrence network, the I1 treatments improved nodes from Ascomycota and Basidiomycota phyla by 1.8% and 5.8%, respectively. Compared to the I0 treatments, the I1 treatments increased positive relations by 8.3% and 3.2%, respectively, in the bacterial and fungal co-occurrence networks. Moreover, the I1 treatments increased the relative abundance of root-promoting biomarkers and suppressed root-limiting biomarkers. However, the application of imazethapyr reduced the diversity and richness of bacterial and fungal communities in general. Furthermore, the nodes and links of bacterial co-occurrence networks in the I0 treatments were 9.2% and 78.8% higher than these in the I1 treatments. Similarly, the I1 treatments also decreased 17.9% of fungal community links compared to the I0 treatments. Our data also show that compared to the I0 treatments, the I1 treatments decreased almost all gene families encoding nitrogen and carbon cycling pathways. In conclusion, the application of imazethapyr increased soybean root growth by increasing root-promoting biomarkers and improved the stability and cooperation of co-occurrence networks of bacterial and fungal communities. However, the application of imazethapyr had some negative impacts on microbial communities, such as reducing the diversity of bacterial and fungal communities and nitrogen and carbon cycling pathways.

Assembly of root-associated bacterial community in cadmium contaminated soil following five-year consecutive application of soil amendments: Evidences for improved soil health

Soil amendments have been extensively used to remediate heavy metal contaminated soils by immobilizing or altering edaphic properties to reduce the bioavailability of heavy metals. However, the potential influences of long-term soil amendments applications on microbial communities and polluted soil health are still in its infancy despite that have been applied for decades. We used amplicon sequencing and q-PCR array to characterize the root-associated microbial community compositions and rhizosphere functional genes in a five-year field experiment with consecutive application of four amendments (lime, biochar, pig manure, and a commercial Mg-Ca-Si conditioner). Compared with the control, soil amendments reduced the available Cd (CaCl₂ extractable Cd) in soils and strongly affected bacterial community compositions in four root-associated niches. Five rare keystone bacterial species were found belonging to the family Gallionellaceae (1), Haliangiaceae (1), Anaerolineaceae (2), and Xanthobacteraceae (1), which significantly correlated with soil pH and the functional genes nifH and phoD. Random forest analysis showed that rhizosphere soil pH and microbial functions, and root-associated keystone bacterial community compositions mainly influenced the Cd concentrations in rice grains. Altogether, our field data revealed five-year consecutive application of soil amendments regulated root-associated microbial community assembly and enhanced microbial functions, thereby improved rhizosphere health of Cd-contaminated soils.

Exploring rhizo-microbiome transplants as a tool for protective plant-microbiome manipulation

The development of strategies for effectively manipulating and engineering beneficial plant-associated microbiomes is a major challenge in microbial ecology. In this sense, the efficacy and potential implications of rhizosphere microbiome transplant (RMT) in plant disease management have only scarcely been explored in the literature. Here, we initially investigated potential differences in rhizosphere microbiomes of 12 Solanaceae eggplant varieties and accessed their level of resistance promoted against bacterial wilt disease caused by the pathogen Ralstonia solanacearum, in a 3-year field trial. We elected 6 resistant microbiomes and further tested the broad feasibility of using RMT from these donor varieties to a susceptible model Solanaceae tomato variety MicroTom. Overall, we found the rhizosphere microbiome of resistant varieties to enrich for distinct and specific bacterial taxa, of which some displayed significant associations with the disease suppression. Quantification of the RMT efficacy using source tracking analysis revealed more than 60% of the donor microbial communities to successfully colonize and establish in the rhizosphere of recipient plants. RTM from distinct resistant donors resulted in different levels of wilt disease suppression, reaching up to 47% of reduction in disease incidence. Last, we provide a culture-dependent validation of potential bacterial taxa associated with antagonistic interactions with the pathogen, thus contributing to a better understanding of the potential mechanism associated with the disease suppression. Our study shows RMT from appropriate resistant donors to be a promising tool to effectively modulate protective microbiomes and promote plant health. Together we advocate for future studies aiming at understanding the ecological processes and mechanisms mediating rates of coalescence between donor and recipient microbiomes in the plant rhizosphere.

Ecological Dynamics and Microbial Treatments against Oomycete Plant Pathogens

In this review, we explore how ecological concepts may help assist with applying microbial biocontrol agents to oomycete pathogens. Oomycetes cause a variety of agricultural diseases, including potato late blight, apple replant diseases, and downy mildew of grapevine, which also can lead to significant economic damage in their respective crops. The use of microbial biocontrol agents is increasingly gaining interest due to pressure from governments and society to reduce chemical plant protection products. The success of a biocontrol agent is dependent on many ecological processes, including the establishment on the host, persistence in the environment, and expression of traits that may be dependent on the microbiome. This review examines recent literature and trends in research that incorporate ecological aspects, especially microbiome, host, and environmental interactions, into biological control development and applications. We explore ecological factors that may influence microbial biocontrol agents’ efficacy and discuss key research avenues forward.

Patterns in the Microbial Community of Salt-Tolerant Plants and the Functional Genes Associated with Salt Stress Alleviation

Salinity is an important abiotic stress affecting plant growth. We have known that plants can recruit beneficial microbes from the surrounding soil. However, the ecological functions of the core microbiome in salt-tolerant plants, together with their driving factors, remain largely unexplored. Here, we employed both amplicon and shotgun metagenomic sequencing to investigate the microbiome and function signatures of bulk soil and rhizocompartment samples from three salt-tolerant plants (legumes Glycine soja and Sesbania cannabina and nonlegume Sorghum bicolor). Strong filtration effects for microbes and functional genes were found in the rhizocompartments following a spatial gradient. The dominant bacteria belonged to Ensifer for legumes and Bacillus for S. bicolor. Although different salt-tolerant plants harbored distinct bacterial communities, they all enriched genes involved in cell motility, Na⁺ transport, and plant growth-promoting function (e.g., nitrogen fixation and phosphate solubilization) in rhizoplane soils, implying that the microbiome assembly of salt-tolerant plants might depend on the ecological functions of microbes rather than microbial taxa. Moreover, three metagenome-assembled genomes affiliated to Ensifer were obtained, and their genetic basis for salt stress alleviation were predicted. Soil pH, electrical conductivity, and total nitrogen were the most important driving factors for explaining the above microbial and functional gene selection. Correspondingly, the growth of an endophyte, Ensifer meliloti CL09, was enhanced by providing root exudates, suggesting that root exudates might be one of factors in the selection of rhizosphere and endosphere microbiota. Overall, this study reveals the ecological functions of the populations inhabiting the root of salt-tolerant plants. IMPORTANCE Salinity is an important but little-studied abiotic stressor affecting plant growth. Although several previous reports have examined salt-tolerant plant microbial communities, we still lack a comprehensive understanding about the functional characteristics and genomic information of this population. The results of this study revealed the root-enriched and -depleted bacterial groups, and found three salt-tolerant plants harbored different bacterial populations. The prediction of three metagenome-assembled genomes confirmed the critical role of root dominant species in helping plants tolerate salt stress. Further analysis indicated that plants enriched microbiome from soil according to their ecological functions but not microbial taxa. This highlights the importance of microbial function in enhancing plant adaptability to saline soil and implies that we should pay more attention to microbial function and not only to taxonomic information. Ultimately, these results provide insight for future agriculture using the various functions of microorganisms on the saline soil.

Fungi-Bacteria Associations in Wilt Diseased Rhizosphere and Endosphere by Interdomain Ecological Network Analysis

In the plant rhizosphere and endosphere, some fungal and bacterial species regularly co-exist, however, our knowledge about their co-existence patterns is quite limited, especially during invasion by bacterial wilt pathogens. In this study, the fungal communities from soil to endophytic compartments were surveyed during an outbreak of tobacco wilt disease caused by Ralstonia solanacearum. It was found that the stem endophytic fungal community was significantly altered by pathogen invasion in terms of community diversity, structure, and composition. The associations among fungal species in the rhizosphere and endosphere infected by R. solanacearum showed more complex network structures than those of healthy plants. By integrating the bacterial dataset, associations between fungi and bacteria were inferred by Inter-Domain Ecological Network (IDEN) approach. It also revealed that infected samples, including both the rhizosphere and endosphere, had more complex interdomain networks than the corresponding healthy samples. Additionally, the bacterial wilt pathogenic Ralstonia members were identified as the keystone genus within the IDENs of both root and stem endophytic compartments. Ralstonia members was negatively correlated with the fungal genera Phoma, Gibberella, and Alternaria in infected roots, as well as Phoma, Gibberella, and Diaporthe in infected stems. This suggested that those endophytic fungi may play an important role in resisting the invasion of R. solanacearum.

Characterizing rhizosphere microbiota of peanut (Arachis hypogaea L.) from pre-sowing to post-harvest of crop under field conditions

The rhizosphere, a narrow zone of soil near plant roots, is a hot spot for microbial activity. Rhizosphere microbiota directly or indirectly benefit plants by supplementing nutrients, producing beneficial chemicals, or suppressing pathogens. Plants attract and modulate bacteria within the rhizosphere by releasing exudates. Plants also tend to select the rhizosphere microbiota based on their needs; a phenomenon termed as “rhizosphere effect”. In this study, we characterized the rhizosphere microbiota of peanut plants across the crop development cycle from pre-sowing of seeds to post-harvest of crop under field conditions. The rhizosphere and bulk soil samples from different crop developmental stages were also compared. The composition of bulk soil microbiota resembled microbiota of pre-sowing and post-harvest soil and was markedly different from rhizosphere soil samples. Rhizosphere samples were enriched with multiple organisms mostly from the Proteobacteria, Firmicutes and Bacteroidota phyla. Differences in diversity were observed among the rhizosphere samples but not in bulk soil across different crop development stages. Pseudomonas_M indica was highly enriched during the germination of seeds. Furthermore, Plant Growth Promoting (PGP) bacteria like Bacillus were enriched during the middle stages of crop development but there was a decline in PGP organisms in the matured crop stage. We also observed a significant association of pH and Electrical Conductivity (EC) with the profiles of microbial community. Overall, this study portrayed the changes in rhizosphere microbiota of peanut during different developmental stages of crop and may help to design stage specific bio-strategies such as bio-fertilizer to improve crop yield.

Plant developmental stage drives the differentiation in ecological role of the maize microbiome

BACKGROUND

Plants live with diverse microbial communities which profoundly affect multiple facets of host performance, but if and how host development impacts the assembly, functions and microbial interactions of crop microbiomes are poorly understood. Here we examined both bacterial and fungal communities across soils, epiphytic and endophytic niches of leaf and root, and plastic leaf of fake plant (representing environment-originating microbes) at three developmental stages of maize at two contrasting sites, and further explored the potential function of phylloplane microbiomes based on metagenomics.

RESULTS

Our results suggested that plant developmental stage had a much stronger influence on the microbial diversity, composition and interkingdom networks in plant compartments than in soils, with the strongest effect in the phylloplane. Phylloplane microbiomes were co-shaped by both plant growth and seasonal environmental factors, with the air (represented by fake plants) as its important source. Further, we found that bacterial communities in plant compartments were more strongly driven by deterministic processes at the early stage but a similar pattern was for fungal communities at the late stage. Moreover, bacterial taxa played a more important role in microbial interkingdom network and crop yield prediction at the early stage, while fungal taxa did so at the late stage. Metagenomic analyses further indicated that phylloplane microbiomes possessed higher functional diversity at the early stage than the late stage, with functional genes related to nutrient provision enriched at the early stage and N assimilation and C degradation enriched at the late stage. Coincidently, more abundant beneficial bacterial taxa like Actinobacteria, Burkholderiaceae and Rhizobiaceae in plant microbiomes were observed at the early stage, but more saprophytic fungi at the late stage.

CONCLUSIONS

Our results suggest that host developmental stage profoundly influences plant microbiome assembly and functions, and the bacterial and fungal microbiomes take a differentiated ecological role at different stages of plant development. This study provides empirical evidence for host exerting strong effect on plant microbiomes by deterministic selection during plant growth and development. These findings have implications for the development of future tools to manipulate microbiome for sustainable increase in primary productivity. Video Abstract.

Rice recruits Sphingomonas strain HJY-rfp via root exudate regulation to increase chlorpyrifos tolerance and boost residual catabolism

Inoculation with pollution-degrading endophytes boosts the catabolism of residual contaminants and promotes the pollution adaptation of host plants. We investigated the interaction pattern between Sphingomonas strain HJY-rfp, a chlorpyrifos-degrading endophytic bacterium, and rice (Oryza sativa) under pesticide stress using hydroponic cultivation. We observed a notable trend of endophytic root colonization in rice plants treated with 10 mg l-1 chlorpyrifos solution, and after 24 h the migration of HJY-rfp enhanced the chlorpyrifos degradation rate in leaves and stems by 53.36% and 40.81%, respectively. Critically, the rice root exudate profile (organic acids and amino acids) changed under chlorpyrifos stress, and variations in the contents of several components affected the chemotactic behaviour of HJY-rfp. HJY-rfp colonization dramatically activated defensive enzymes, which enabled efficient scavenging of reactive oxygen species, and led to 9.8%, 22.5%, and 41.9% increases in shoot length, fresh weight, and accumulation of total chlorophyll, respectively, in rice suffering from oxidative damage by chlorpyrifos. Endophytic colonization caused up-regulation of detoxification genes that have shown a significant positive correlation with chlorpyrifos degradation in vivo. Collectively, our results demonstrate that agrochemical stress causes plants to actively recruit specific symbiotic microbes to detoxify contaminants and survive better under pollution conditions.

Changes in protist communities in drainages across the Pearl River Delta under anthropogenic influence

Drainages in the Pearl River Delta urban agglomeration (PRDUA) host vital aquatic ecosystems and face enormous pressures from human activities in one of the largest urban agglomerations in the world. Despite being crucial components of aquatic ecosystems, the interactions and assembly processes of the protistan community are rarely explored in areas with serious anthropogenic disturbance. To elucidate the mechanisms of these processes, we used environmental DNA sequencing of 18S rDNA to investigate the influence of environmental factors and species interactions on the protistan community and its assembly in drainages of the PRDUA during summer. The protistan community showed a high level of diversity and a marked spatial pattern in this region. Community assembly was driven primarily by stochastic processes based on the Sloan neutral community model, explaining 74.28%, 75.82%, 73.67%, 74.40% and 51.24% of community variations in the BJ (Beijiang), XJ (Xijiang), PRD (Pearl River Delta), PRE (Pearl River Estuary) areas and in total, respectively. Meanwhile, environmental variables including temperature, pH, dissolved oxygen, transparency, nutrients and land use were strongly correlated with the composition and assembly of the protistan community, explaining 40.40% of variation in the protistan community. Furthermore, the bacterial community was simultaneously analysed by the 16S rDNA sequencing. Co-occurrence network analysis revealed that species interactions within bacteria (81.41% positive) or protists (82.80% positive), and those between bacteria and protists (50% positive and 50% negative) impacted the protistan community assembly. In summary, stochastic processes dominated, whereas species interactions and environmental factors also played important roles in shaping the protistan communities in drainages across the PRDUA. This study provides insights into the ecological patterns, assembly processes and species interactions underlying protistan dynamics in urban aquatic ecosystems experiencing serious anthropogenic disturbance.