Rootstocks Shape the Rhizobiome: Rhizosphere and Endosphere Bacterial Communities in the Grafted Tomato System

Viruses Facilitate Energy Acquisition Potential by Their Bacterial Hosts in Rhizosphere of Grafted Plants

Viruses alter the ecological and evolutionary trajectories of bacterial host communities. Plant grafting is a technique that integrates two species or varietiies and have consequences on the rhizosphere functioning. The grafting effects on the taxonomic and functional assembly of viruses and their bacterial host in the plant rhizosphere remain largely elusive. Using shotgun metagenome sequencing, we recover a total of 1441 viral operational taxonomic units from the rhizosphere of grafted and ungrafted plants after 8-year continuous monoculture. In the grafted and ungrafted rhizosphere, the Myoviridae, Zobellviridae and Kyanoviridae emerged as the predominant viral families, collectively representing around 40% of the viral community in each respective environment. Grafting enriched the members in viral family Kyanoviridae, Tectiviridae, Peduoviridae and Suoliviridae, and auxiliary metabolic genes related to pyruvate metabolism and energy acquisition (e.g., gloB, DNMT1 and dcyD). The virus-bacterial interactions increased the rapid growth potential of bacteria, which explains the strong increase in abundance of specific bacterial hosts (i.e., Chitinophagaceae, Cyclobacteriaceae and Spirosomaceae) in the grafted-plant rhizosphere. Overall, these results deepen our understanding of microbial community assembly and ecological services from the perspective of virus-host interactions.

Microbial Interactions Influence the Chemical Defense of Wild and Cultivated Tomato Species

Tomato, a globally significant crop, faces continuous threats from pests and pathogens, necessitating alternative approaches to reduce chemical inputs. Beneficial soil microbes, such as arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR), offer promising solutions by enhancing plant growth and pest tolerance. However, domestication may have weakened tomatoes' interactions with these microbes, potentially compromising their innate immunity, a hypothesis that remains largely unexplored. To address this gap, we examined the effects of AMF and PGPR inoculation on growth, herbivory resistance, and metabolic responses in the domesticated Solanum lycopersicum 'Moneymaker' and three wild tomato relatives. Our findings reveal that microbial inoculation significantly influences both domesticated and wild tomatoes, with PGPR generally enhancing and AMF reducing plant growth across species. Using targeted and untargeted metabolomics, we found that soil microbes substantially alter plant chemistry above- and belowground in a species-specific manner. Notably, herbivore responses were more affected by AMF presence than by tomato species. These results highlight that while domestication has profoundly shaped tomato traits, microbial interactions can modulate these phenotypes. Thus, selecting microbial strains best suited to modern cultivars is crucial for optimizing plant growth and resilience against pests.

Rootstocks and drought stress impact the composition and functionality of grapevine rhizosphere bacterial microbiota

The microbiota, a component of the plant holobiont, plays an active role in the response to biotic and abiotic stresses. Nowadays, with recurrent drought and global warming, a growing challenge in viticulture is being addressed by different practices, including the use of adapted rootstocks. However, the relationships between these practices, abiotic stress and the composition and functions of the rhizosphere microbiota remain to be deciphered. This study aimed to unravel the impact of five rootstocks, water management and the combination of both on the rhizosphere bacterial microbiota in grapevines using shotgun metagenomics approach. The results showed that drought impacted the diversity, composition and functionality of the rhizosphere bacterial community. The genera Mycolicibacterium, Mycobacterium and Rhodococcus, and the bacterial functions, including DNA damage repair, fatty acid synthesis, sugar and amino acid transport, oxidative stress reduction, toxin synthesis and detoxification of exogenous compounds were significantly enriched under drought conditions. Rootstocks also significantly affected the rhizosphere bacterial richness but its influence on diversity and functionality compared to water management was weaker. Some taxa and function could be linked to water managements applied. The interaction between rootstocks and water management further influenced the rhizosphere composition, especially under drought conditions, where distinct clustering was observed for specific rootstocks. The results highlight the importance of conducting multifactorial studies to better understand their impact on shaping functional rhizosphere bacterial communities. This study paves the way for future research on beneficial bacterial inoculation and genetic engineering of rootstock to cope with drought stress.

Mechanisms of heavy metal-induced rhizosphere changes and crop metabolic evolution: The role of carbon materials

To investigate the effects of modified carbon-based materials on soil environmental remediation and crop physiological regulation, this research relied on rice pots with lead (Pb) and cadmium (Cd) composite contamination. Dolomite, montmorillonite, attapulgite and sepiolite modified biochar with different doses have been developed to explore the mechanisms on heavy metal passivation, nutrient improvement, microbial activation, and crop growth. The results indicated that the modified materials effectively reduced heavy metal bioavailability and accumulation in plant tissues through adsorption complexation. Specifically, under montmorillonite and sepiolite modified treatments, the Grains-Pb content significantly decreased by 29.23-30.31% and 27.49-30.58%, compared to the control group (CK). Meantime, carbon-based materials increased available nutrient levels, providing a biological substrate for soil microorganisms metabolism. The content of ammonium nitrogen (NH4+-N) and available phosphorus (AP) in different proportions of montmorillonite modified biochar increased by 10.99-13.98% and 55.76-77.86%, respectively, compared to CK. Furthermore, sepiolite modified biochar enhanced bacterial community diversity, significantly improving the tolerance and resistance of bacterial communities such as Proteobacteria and Acidobacteria to heavy metals. Meanwhile, carbon-based materials enhanced community stability and network complexity, improving microbial stress resistance to adverse environments. In summary, montmorillonite and sepiolite modified biochar regulated microbial community interaction mechanisms by mitigating the physiological toxicity of heavy metals. This process enhanced soil available nutrients and ecological function stability, which had significant implications for improving crop growth and quality.

Exploring the role of grafting in abiotic stress management: Contemporary insights and automation trends

Grafting is a technique that involves attaching a rootstock to the aerial part of another genotype or species (scion), leading to improved crop performance and sustainable growth. The ability to tolerate abiotic stresses depends on cell membrane stability, a reduction in electrolyte leakage, and the species of scion and rootstock chosen. This external mechanism, grafting, serves as a beneficial tool in influencing crop performance by combining nutrient uptake and translocation to shoots, promoting sustainable plant growth, and enhancing the potential yield of both fruit and vegetable crops. Grafting helps to enhance crop production and improve the capacity of plants to utilize water when undergoing abiotic stress, particularly in genotypes that produce high yields upon rootstocks that are capable of decreasing the impact of drought stress on the shoot. The rootstock plays a pivotal role in establishing a grafted plant by forming a union between the graft and the rootstock. This process is characterized by its integrative, reciprocal nature, enabling plants to tolerate abiotic stress conditions. Grafting has been shown to alleviate the overproduction of lipid peroxidation and reactive oxygen species in the leaves and roots and enhance drought tolerance in plants by maintaining antioxidant enzyme activities and stress-responsive gene expression. Phytohormones, such as cytokinin, auxin, and gibberellin, play a critical role in maintaining rootstock-scion interactions. This review unveils the role of grafting in mitigating various environmental stressors, establishment of a robust graft junction, physiology of rootstock-scion communication, the mechanism underlying rootstock influence, hormonal regulations and the utilization of agri-bots in perfect healing and further cultivation of vegetable crops through grafting.

Effect of plant-derived microbial soil legacy in a grafting system-a turn for the better

BACKGROUND

Plant-soil feedback arises from microbial legacies left by plants in the soil. Grafting is a common technique used to prevent yield declines in monocultures. Yet, our understanding of how grafting alters the composition of soil microbiota and how these changes affect subsequent crop performance remains limited. Our experiment involved monoculturing ungrafted and grafted watermelons to obtain conditioned soils, followed by growing the watermelons on the conditioned soils to investigate plant-soil feedback effects.

RESULTS

Ungrafted plants grew better in soil previously conditioned by a different plant (heterospecific soil) while grafted plants grew better in soil conditioned by the same plant (conspecific soil). We demonstrated experimentally that these differences in growth were linked to changes in microorganisms. Using a supervised machine learning algorithm, we showed that differences in the relative abundance of certain genera, such as Rhizobium, Chryseobacterium, Fusarium, and Aspergillus, significantly influenced the conspecific plant-soil feedback. Metabolomic analyses revealed that ungrafted plants in heterospecific soil enriched arginine biosynthesis, whereas grafted plants in conspecific soil increased sphingolipid metabolism. Elsewhere, the metagenome-assembled genomes (MAGs) of ungrafted plants identified in heterospecific soil include Chryseobacterium and Lysobacter, microorganisms having been prominently identified in earlier research as contributors to plant growth. Metabolic reconstruction revealed the putative ability of Chryseobacterium to convert D-glucono-1,5-lactone to gluconic acid, pointing to distinct disease-suppressive mechanisms and hence distinct microbial functional legacies between grafted and ungrafted plants.

CONCLUSIONS

Our findings show a deep impact of the soil microbial reservoir on plant growth and suggest the necessity to protect and improve this microbial community in agricultural soils. The work also suggests possibilities of optimizing microbiota-mediated benefits through grafting herein, a way that "engineered" soil microbial communities for better plant growth. Video Abstract.

The impact of kaolin mining activities on bacterial diversity and community structure in the rhizosphere soil of three local plants

Introduction

Thus far, the impact of kaolin mining activities on the surrounding native plants and rhizosphere microecology has not been fully understood.

Methods

In this study, we used 16S rRNA high-throughput sequencing to examine the impact of kaolin mining on the rhizosphere bacterial communities and functions of three local plant species: Conyza bonariensis, Artemisia annua, and Dodonaea viscosa.

Results

The results showed that kaolin mining significantly reduced the diversity of rhizosphere bacteria in these plants, as indicated by the Shannon, Simpson, Chao1, and observed species indices (p < 0.05). Kaolin mining had an impact on the recruitment of three rhizosphere bacteria native to the area: Actinoplanes, RB41, and Mycobacterium. These bacteria were found to be more abundant in the rhizosphere soil of three local plants than in bulk soil, yet the mining of kaolin caused a decrease in their abundance (p < 0.05). Interestingly, Ralstonia was enriched in the rhizosphere of these plants found in kaolin mining areas, suggesting its resilience to environmental stress. Furthermore, the three plants had different dominant rhizosphere bacterial populations in kaolin mining areas, such as Nocardioides, Pseudarthrobacter, and Sphingomonas, likely due to the unique microecology of the plant rhizosphere. Kaolin mining activities also caused a shift in the functional diversity of rhizosphere bacteria in the three local plants, with each plant displaying different functions to cope with kaolin mining-induced stress, such as increased abundance of the GlpM family and glucan-binding domain.

Discussion

This study is the first to investigate the effects of kaolin mining on the rhizosphere microecology of local plants, thus contributing to the establishment of soil microecological health monitoring indicators to better control soil pollution in kaolin mining areas.

Bacillus B2 promotes root growth and enhances phosphorus absorption in apple rootstocks by affecting MhMYB15

Due to the chelation of phosphorus in the soil, it becomes unavailable for plant growth and development. The mechanisms by which phosphorus-solubilizing bacteria activate immobilized phosphorus to promote the growth and development of woody plants, as well as the intrinsic molecular mechanisms, are not clear. Through the analysis of microbial communities in the rhizosphere 16S V3-V4 and a homologous gene encoding microbial alkaline phosphomonoesterase (phoD) in phosphate-efficient (PE) and phosphate-inefficient apple rootstocks, it was found that PE significantly enriched beneficial rhizobacteria. The best phosphorus-solubilizing bacteria, Bacillus sp. strain 7DB1 (B2), was isolated, purified, and identified from the rhizosphere soil of PE rootstocks. Incubating with Bacillus B2 into the rhizosphere of apple rootstocks significantly increased the soluble phosphorus and flavonoid content in the rhizosphere soil. Simultaneously, this process stimulates the root development of the rootstocks and enhances plant phosphorus uptake. After root transcriptome sequencing, candidate transcription factor MhMYB15, responsive to Bacillus B2, was identified through heatmap and co-expression network analysis. Yeast one-hybrid, electrophoretic mobility shift assay, and LUC assay confirmed that MhMYB15 can directly bind to the promoter regions of downstream functional genes, including chalcone synthase MhCHS2 and phosphate transporter MhPHT1;15. Transgenic experiments with MhMYB15 revealed that RNAi-MhMYB15 silenced lines failed to induce an increase in flavonoid content and phosphorus levels in the roots under the treatment of Bacillus B2, and plant growth was slower than the control. In conclusion, MhMYB15 actively responds to Bacillus B2, regulating the accumulation of flavonoids and the uptake of phosphorus, thereby influencing plant growth and development.

Impacts of the Ban on the Soil-Applied Fumigant Methyl Bromide

The loss of the soil fumigant methyl bromide (MeBr) and adoption of soil fumigant alternatives has been challenging for farmers, particularly for those crops in which pathogens previously controlled by MeBr have emerged as significant problems, but it has resulted in some unanticipated benefits for the scientific community and the environment. Applauded as one of the most effective environmental agreements to date, the universally accepted Montreal Protocol on Ozone Depleting Substances has had a significant impact on the environment, reducing the release of halogenated compounds from anthropogenic sources enough to mitigate global warming by an estimated 1.1°C by 2021. The funding associated with various MeBr transition programs has increased collaboration across scientific disciplines, commodity groups, industry, and regulatory agencies. Chemical alternatives and improved application strategies, including the development of gas-retentive agricultural films, coupled with sound efficacy data and grower ingenuity have resulted in the sustained production of many of the impacted crops; although there has been some loss of acreage and value, particularly for Florida fumigated crops, for some, value has continued to increase, allowing production to continue. The loss of a single, broad-spectrum tool for pest control has led to a deeper understanding of the specific pest complexes impacting these at-risk crops, as well as the development of new, biologically based management tools for their control while increasing our understanding of the role of the soil microbiome in pest control and crop production.

Global insights into endophytic bacterial communities of terrestrial plants: Exploring the potential applications of endophytic microbiota in sustainable agriculture

Endophytic microorganisms are indispensable symbionts during plant growth and development and often serve functions such as growth promotion and stress resistance in plants. Therefore, an increasing number of researchers have applied endophytes for multifaceted phytoremediation (e.g., organic pollutants and heavy metals) in recent years. With the availability of next-generation sequencing technologies, an increasing number of studies have shifted the focus from culturable bacteria to total communities. However, information on the composition, structure, and function of bacterial endophytic communities is still not widely synthesized. To explore the general patterns of variation in bacterial communities between plant niches, we reanalyzed data from 1499 samples in 30 individual studies from different continents and provided comprehensive insights. A group of bacterial genera were commonly found in most plant roots and shoots. Our analysis revealed distinct variations in the diversity, composition, structure, and function of endophytic bacterial communities between plant roots and shoots. These variations underscore the sophisticated mechanisms by which plants engage with their endophytic microbiota, optimizing these interactions to bolster growth, health, and resilience against stress. Highlighting the strategic role of endophytic bacteria in promoting sustainable agricultural practices and environmental stewardship, our study not only offers global insights into the endophytic bacterial communities of terrestrial plants but also underscores the untapped potential of these communities as invaluable resources for future research.

Bacterial community structure and co-occurrence networks in the rhizosphere and root endosphere of the grafted apple

BACKGROUND

Compared with aerial plant tissues (such as leaf, stem, and flower), root-associated microbiomes play an indisputable role in promoting plant health and productivity. We thus explored the similarities and differences between rhizosphere and root endosphere bacterial community in the grafted apple system.

RESULTS

Using pot experiments, three microhabitats (bulk soil, rhizosphere and root endosphere) samples were obtained from two-year-old apple trees grafted on the four different rootstocks. We then investigated the bacterial community composition, diversity, and co-occurrence network in three microhabitats using the Illumina sequencing methods. Only 63 amplicon sequence variants (ASVs) out of a total of 24,485 were shared in the rhizosphere and root endosphere of apple grafted on the four different rootstocks (M9T337, Malus hupehensis Rehd., Malus robusta Rehd., and Malus baccata Borkh.). The core microbiome contained 8 phyla and 25 families. From the bulk soil to the rhizosphere to the root endosphere, the members of the phylum and class levels demonstrated a significant enrichment and depletion pattern. Co-occurrence network analysis showed the network complexity of the rhizosphere was higher than the root endosphere. Most of the keystone nodes in both networks were classified as Proteobacteria, Actinobacteriota and Bacteroidetes and were low abundance species.

CONCLUSION

The hierarchical filtration pattern existed not only in the assembly of root endosphere bacteria, but also in the core microbiome. Moreover, most of the core ASVs were high-abundance species, while the keystone ASVs of the network were low-abundance species.

A QTL of eggplant shapes the rhizosphere bacterial community, co-responsible for resistance to bacterial wilt

Resistant crop cultivars can recruit beneficial rhizobacteria to resist disease. However, whether this recruitment is regulated by quantitative trait loci (QTL) is unclear. The role of QTL in recruiting specific bacteria against bacterial wilt (BW) is an important question of practical significance to disease management. Here, to identify QTL controlling BW resistance, Super-BSA was performed in F2 plants derived from resistant eggplant cultivar R06112 × susceptible cultivar S55193. The QTL was narrowed down through BC1F1-BC3F1 individuals by wilting symptoms and KASP markers. Rhizosphere bacterial composition of R06112, S55193, and resistant individuals EB158 (with the QTL) and susceptible individuals EB327 (without QTL) from BC2F1 generation were assessed by Illumina sequencing-based analysis, and the activation of plant immunity by the bacterial isolates was analyzed. Evidence showed that BW-resistant is controlled by one QTL located at the 270 kb region on chromosome 10, namely EBWR10, and nsLTPs as candidate genes confirmed by RNA-Seq. EBWR10 has a significant effect on rhizobacteria composition and significantly recruits Bacillus. pp. A SynCom of three isolated Bacillus. pp trains significantly reduced the disease incidence, changed activities of CAT, PPO, and PAL and concentration of NO, H2O2, and O2-, activated SA and JA signaling-dependent ISR, and displayed immune activation against Ralstonia solanacearum in eggplant. Our findings demonstrate for the first time that the QTL can recruit beneficial rhizobacteria, which jointly promote the suppression of BW. This method charts a path to develop the QTL in resistant cultivar-driven probiotics to ameliorate plant diseases.

Microbiome-Mediated Strategies to Manage Major Soil-Borne Diseases of Tomato

The tomato (Solanum lycopersicum L.) is consumed globally as a fresh vegetable due to its high nutritional value and antioxidant properties. However, soil-borne diseases can severely limit tomato production. These diseases, such as bacterial wilt (BW), Fusarium wilt (FW), Verticillium wilt (VW), and root-knot nematodes (RKN), can significantly reduce the yield and quality of tomatoes. Using agrochemicals to combat these diseases can lead to chemical residues, pesticide resistance, and environmental pollution. Unfortunately, resistant varieties are not yet available. Therefore, we must find alternative strategies to protect tomatoes from these soil-borne diseases. One of the most promising solutions is harnessing microbial communities that can suppress disease and promote plant growth and immunity. Recent omics technologies and next-generation sequencing advances can help us develop microbiome-based strategies to mitigate tomato soil-borne diseases. This review emphasizes the importance of interdisciplinary approaches to understanding the utilization of beneficial microbiomes to mitigate soil-borne diseases and improve crop productivity.

16S metabarcoding analysis reveals the influence of organic and conventional farming practices on bacterial communities from the rhizospheric of Coffea arabica L

Coffea sp. is cultivated in many tropical countries. Brazil has always adopted intensive agricultural practices, but organic coffee farming is an alternative system based on the non-use of agrochemicals and the rational management of soils. Metabarcoding 16S analysis using next-generation sequencing has been developed to identify and compare the diversity of the Coffea arabica L. rhizospheric bacterial community in two farming areas in São Paulo, Brazil. Dourado uses conventional farming, while Ribeirão Corrente uses organic. We found broad taxonomic composition, with sequences from 24 phyla, 55 classes, 61 orders, 146 families, and 337genus. The three most abundant phyla were Proteobacteria (38.27%), Actinobacteria (15.56%), and Acidobacteria (16.10%). In organic farming, the top 3 were the family Sphingomonadaceae, order Rhizobiales, genus Nocardioides, and Gp6. The genus Gp2 and the phylum Candidatus Saccharibacteria were the most abundant OTUs exclusively present in conventional farming. In the organic farming practice, Proteobacteria, Actinobacteria, and Acidobacteria were also present among the exclusive OTUs; we also found OTUs belonging to Bacteroidetes, Firmicutes, and Verrucomicrobia. Our study indicates a positive effect of organic farming on microbial communities. Fertilization may directly affect soil microbiota, suggesting that a large and active microbial community low in functional diversity might not adapt to new climatic conditions. A diverse community could provide better resilience to environmental changes, improving the productivity of this important crop.

Influence of Grafting on Rootstock Rhizosphere Microbiome Assembly in Rosa sp. 'Natal Brier'

The root microbiome is vital in plant development and health and is highly influenced by crop cultural practices. Rose (Rosa sp.) is the most popular cut flower worldwide. Grafting in rose production is a standard practice to increase yield, improve flower quality, or reduce root-associated pests and diseases. 'Natal Brier' is a standard rootstock used in most commercial operations in Ecuador and Colombia, leading countries in producing and exporting ornamentals. It is known that the rose scion genotype affects root biomass and the root exudate profile of grafted plants. However, little is known about the influence of the rose scion genotype on the rhizosphere microbiome. We examined the influence of grafting and scion genotype on the rhizosphere microbiome of the rootstock 'Natal Brier'. The microbiomes of the non-grafted rootstock and the rootstock grafted with two red rose cultivars were assessed using 16S rRNA and ITS sequencing. Grafting changed microbial community structure and function. Further, analysis of grafted plant samples revealed that the scion genotype highly influences the rootstock microbiome. Under the presented experimental conditions, the rootstock 'Natal Brier' core microbiome consisted of 16 bacterial and 40 fungal taxa. Our results highlight that the scion genotype influences root microbe's recruitment, which might also influence the functionality of assembled microbiomes.

Interactions between rootstocks and compost influence the active rhizosphere bacterial communities in citrus

BACKGROUND

While the rootstock genotype (belowground part of a plant) can impact rhizosphere microbial communities, few studies have examined the relationships between rootstock genotype-based recruitment of active rhizosphere bacterial communities and the availability of root nutrients for plant uptake. Rootstocks are developed to provide resistance to disease or tolerance of abiotic stresses, and compost application is a common practice to also control biotic and abiotic stresses in crops. In this field study, we examined: (i) the effect of four citrus rootstocks and/or compost application on the abundance, diversity, composition, and predicted functionality of active rhizosphere bacterial communities, and (ii) the relationships between active rhizosphere bacterial communities and root nutrient concentrations, with identification of bacterial taxa significantly correlated with changes in root nutrients in the rhizosphere.

RESULTS

The rootstock genotype determined differences in the diversity of active rhizosphere bacterial communities and also impacted how compost altered the abundance, diversity, composition, and predicted functions of these active communities. Variations in the active bacterial rhizobiome were strongly linked to root nutrient cycling, and these interactions were root-nutrient- and rootstock-specific. Direct positive relationships between enriched taxa in treated soils and specific root nutrients were detected, and potentially important taxa for root nutrient uptake were identified. Significant differences in specific predicted functions were related to soil nutrient cycling (carbon, nitrogen, and tryptophan metabolisms) in the active bacterial rhizobiome among rootstocks, particularly in soils treated with compost.

CONCLUSIONS

This study illustrates that interactions between citrus rootstocks and compost can influence active rhizosphere bacterial communities, which impact root nutrient concentrations. In particular, the response of the rhizobiome bacterial abundance, diversity, and community composition to compost was determined by the rootstock. Specific bacterial taxa therefore appear to be driving changes in root nutrient concentrations in the active rhizobiome of different citrus rootstocks. Several potential functions of active bacterial rhizobiomes recruited by different citrus rootstocks did not appear to be redundant but rather rootstock-specific. Together, these findings have important agronomic implications as they indicate the potential for agricultural production systems to maximize benefits from rhizobiomes through the choice of selected rootstocks and the application of compost. Video Abstract.

The Hydroponic Rockwool Root Microbiome: Under Control or Underutilised?

Land plants have an ancient and intimate relationship with microorganisms, which influences the composition of natural ecosystems and the performance of crops. Plants shape the microbiome around their roots by releasing organic nutrients into the soil. Hydroponic horticulture aims to protect crops from damaging soil-borne pathogens by replacing soil with an artificial growing medium, such as rockwool, an inert material made from molten rock spun into fibres. Microorganisms are generally considered a problem to be managed, to keep the glasshouse clean, but the hydroponic root microbiome assembles soon after planting and flourishes with the crop. Hence, microbe–plant interactions play out in an artificial environment that is quite unlike the soil in which they evolved. Plants in a near-ideal environment have little dependency on microbial partners, but our growing appreciation of the role of microbial communities is revealing opportunities to advance practices, especially in agriculture and human health. Hydroponic systems are especially well-suited to active management of the root microbiome because they allow complete control over the root zone environment; however, they receive much less attention than other host–microbiome interactions. Novel techniques for hydroponic horticulture can be identified by extending our understanding of the microbial ecology of this unique environment.

Evaluating the hologenome concept by analyzing the root-endosphere microbiota of chimeric plants

The hologenome concept considers the entity formed by a host and its microbiota, the holobiont, as new level of hierarchical organization subject to neutral and selective forces. We used grafted plants to formally evaluate the hologenome concept. We analyzed the root-endosphere microbiota of two independent watermelon and grapevine plant systems, including ungrafted and reciprocal-grafting combinations. Grafted and ungrafted hosts harbor markedly different microbiota compositions. Furthermore, the results indicate a non-random assembly of bacterial communities inhabiting the root endosphere of chimeric plants with interactive effect of both the rootstock and scion on the recruitment of microorganisms. Because chimeric plants did not have a random microbiota, the null hypothesis that holobionts assemble randomly and hologenome concept is an intellectual construction only can be rejected. The study supports the relevance of hologenome as biological level of organization and opens new avenues for a better fundamental understanding of plants as holobionts.

Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects

Global food production, food supply chains and food security are increasingly stressed by human population growth and loss of arable land, becoming more vulnerable to anthropogenic and environmental perturbations. Numerous mutualistic and antagonistic species are interconnected with the cultivation of crops and livestock and these can be challenging to identify on the large scales of food production systems. Accurate identifications to capture this diversity and rapid scalable monitoring are necessary to identify emerging threats (i.e. pests and pathogens), inform on ecosystem health (i.e. soil and pollinator diversity), and provide evidence for new management practices (i.e. fertiliser and pesticide applications). Increasingly, environmental DNA (eDNA) is providing rapid and accurate classifications for specific organisms and entire species assemblages in substrates ranging from soil to air. Here, we aim to discuss how eDNA is being used for monitoring of agricultural ecosystems, what current limitations exist, and how these could be managed to expand applications into the future. In a systematic review we identify that eDNA-based monitoring in food production systems accounts for only 4 % of all eDNA studies. We found that the majority of these eDNA studies target soil and plant substrates (60 %), predominantly to identify microbes and insects (60 %) and are biased towards Europe (42 %). While eDNA-based monitoring studies are uncommon in many of the world's food production systems, the trend is most pronounced in emerging economies often where food security is most at risk. We suggest that the biggest limitations to eDNA for agriculture are false negatives resulting from DNA degradation and assay biases, as well as incomplete databases and the interpretation of abundance data. These require in silico, in vitro, and in vivo approaches to carefully design, test and apply eDNA monitoring for reliable and accurate taxonomic identifications. We explore future opportunities for eDNA research which could further develop this useful tool for food production system monitoring in both emerging and developed economies, hopefully improving monitoring, and ultimately food security.

Soil and Soilless Tomato Cultivation Promote Different Microbial Communities That Provide New Models for Future Crop Interventions

The cultivation of soilless tomato in greenhouses has increased considerably, but little is known about the assembly of the root microbiome compared to plants grown in soil. To obtain such information, we constructed an assay in which we traced the bacterial and fungal communities by amplicon-based metagenomics during the cultivation chain from nursery to greenhouse. In the greenhouse, the plants were transplanted either into agricultural soil or into coconut fiber bags (soilless). At the phylum level, bacterial and fungal communities were primarily constituted in all microhabitats by Proteobacteria and Ascomycota, respectively. The results showed that the tomato rhizosphere microbiome was shaped by the substrate or soil in which the plants were grown. The microbiome was different particularly in terms of the bacterial communities. In agriculture, enrichment has been observed in putative biological control bacteria of the genera Pseudomonas and Bacillus and in potential phytopathogenic fungi. Overall, the study describes the different shaping of microbial communities in the two cultivation methods.

Microbial diversity composition of apple tree roots and resistance of apple Valsa canker with different grafting rootstock types

Background

The composition and diversity of root microbial community are affected by plant genotypes and soil environment, which in turn affect plant growth and development. Grafting rootstock types of the apple tree can affect phenotypes in cultivation practice, but it is not clear whether grafting rootstock types can affect the composition and diversity of root microbial community and the resistance of apple tree to apple Valsa canker.

Methods

To explore root microbial differences and the correlation, 16S rRNA and ITS genes were sequenced using Novaseq technology.

Results

The results showed that the influence of grafting rootstock types on the composition of the root fungal community was greater than that of bacteria. And the bacterial community richness was higher in the healthy (OTUs: 1693) and dwarfing rootstock (OTUs: 1526) than in the disease (OTUs: 1181) and standard rootstock (OTUs: 1412), while the fungal community richness was the opposite. Moreover, the bacterial abundance of root zone, rhizosphere, and root endophytic microorganisms with the same grafting rootstock type exhibited a decreasing trend. Results of Nested PCR assay on soil and root tissue of Valsa mali showed that the content of V. mali in dwarfing rootstocks are lower than standard rootstocks. These results suggest that apple trees grafting with dwarfing rootstocks are more resistant to V. mali than standard rootstocks.

Conclusions

Under different grafting types, the effect on the composition of fungal community in apple tree root was greater than that of bacteria. The bacterial community in dwarfing rootstocks is more abundant and diverse, including more beneficial microorganisms. Therefore, dwarfing rootstock is more conducive to the resistance to apple Valsa canker from biological control.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02517-x.

Impact analysis of hydraulic loading rate on constructed wetland: Insight into the response of bulk substrate and root-associated microbiota

Constructed wetland (CW) is an environment-friendly and low-cost technology for nutrients removal from domestic wastewater. For a well-tuned CW, hydraulic loading rate (HLR) is one of the critical factors, particularly under the challenging circumstance of more frequent heavy rainfall events brought by global warming. In this study, a comprehensive investigation was conducted to explore the influence of different HLRs on the CW's bulk substrate and root-associated microbiota aiming to yield new insight for CW management from a hybrid perspective of environmental microbiology and engineering science. The response of the microbial community and associated nutrients removal performance under different HLR settings were analyzed after a one-year operation. Results showed that the bulk substrate and rhizosphere genera involved in desulfurization and denitrification, such as Ferritrophicum, Sulfurimonas, and Sulfurisoma, were enriched in the higher HLR condition and associated with the higher total nitrogen (TN) and nitrate nitrogen (NO₃^--N) removal compared to the lower HLR condition. Co-occurrence network analysis demonstrated a more complex network under the higher HLR condition. Besides, it was observed that more stochastic in microbial assembly under the higher HLR condition. Surprisingly, zoonotic pathogens were observed and showed a greater prevalence under the higher HLR condition, indicating the potential correlation between HLR and pathogen intrusion. Collectively, this study revealed that the microbiota could be significantly altered under different HLR conditions, thereby resulting in differences in nutrients removal performance.

Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review

Agricultural productivity is highly influenced by its associated microbial community. With advancements in omics technology, metagenomics is known to play a vital role in microbial world studies by unlocking the uncultured microbial populations present in the environment. Metagenomics is a diagnostic tool to target unique signature loci of plant and animal pathogens as well as beneficial microorganisms from samples. Here, we reviewed various aspects of metagenomics from experimental methods to techniques used for sequencing, as well as diversified computational resources, including databases and software tools. Exhaustive focus and study are conducted on the application of metagenomics in agriculture, deciphering various areas, including pathogen and plant disease identification, disease resistance breeding, plant pest control, weed management, abiotic stress management, post-harvest management, discoveries in agriculture, source of novel molecules/compounds, biosurfactants and natural product, identification of biosynthetic molecules, use in genetically modified crops, and antibiotic-resistant genes. Metagenomics-wide association studies study in agriculture on crop productivity rates, intercropping analysis, and agronomic field is analyzed. This article is the first of its comprehensive study and prospects from an agriculture perspective, focusing on a wider range of applications of metagenomics and its association studies.

Contrasting effects of genotype and root size on the fungal and bacterial communities associated with apple rootstocks

The endophytic microbiome of plants is believed to have a significant impact on its physiology and disease resistance, however, the role of host genotype in determining the composition of the endophytic microbiome of apple root systems remains an open question that has important implications for defining breeding objectives. In the current study, the bacterial and fungal microbiota associated with four different apple rootstocks planted in April, 2018 in the same soil environment and harvested in May, 2019 were evaluated to determine the role of genotype on the composition of both the bacterial and fungal communities. Results demonstrated a clear impact of genotype and root size on microbial composition and diversity. The fungal community was more affected by plant genotype whereas the bacterial community was shaped by root size. Fungal and bacterial abundance was equal between different-sized roots however, significantly higher microbial counts were detected in rhizosphere samples compared to root endosphere samples. This study provides information that can be used to develop a comprehensive and readily applicable understanding of the impact of genotype and environmental factors on the establishment of plant microbiome, as well as its potential function and impact on host physiology.

The structure and assembly mechanisms of plastisphere microbial community in natural marine environment

The microbial colonization profiles on microplastics (MPs) in marine environments have recently sparked global interest. However, many studies have characterized plastisphere microbiomes without considering the ecological processes that underly microbiome assembly. Here, we carried out a three-timepoint exposure experiment at 1-, 4-, and 8-week and investigated the colonization dynamics for polyethylene, polypropylene, polystyrene, polyvinyl chloride, and acrylonitrile-butadiene-styrene MP pellets in natural coastal water. Using high-throughput sequencing of 16S rRNA, we found diversity and evenness were higher (p < 0.05) in the plastisphere communities than those in seawater, and microorganisms colonizing were co-influenced by environmental factors, polymer types, and exposure duration. Functional potential and co-occurrence network analysis revealed that MP exposure enriched the xenobiotic biodegradation potential and reduced the complexity of the MP microbial network. Simultaneously, null-model analyses indicated that stochastic processes contributed a bigger role than deterministic processes in shaping plastisphere microbial community structure with dispersal limitations contributing to a greater extent to microbial succession trajectories. These results implied the plastic surface had a more important role as a raft onto which microbes attach rather than selectively recruiting plastic-specific microbial colonizers. Our work strengthened the understanding of the ecological mechanisms by which microbial community patterns are controlled during colonization by plastic-associated microbes.

Rhizosphere and Endosphere Bacterial Communities Survey by Metagenomics Approach

The diversity of microbes associated with plant roots is in the order of tens of thousands of species. It is estimated that only 0.1-1.0% of the living bacteria present in soils can be cultured under standard conditions. The microbial marker-gene sequence data and the next-generation sequencing technologies have enabled systemic studies of root-associated microbiomes. Molecular techniques can be used to generate comprehensive taxonomic profiles of the microorganisms present in roots. The aim of this chapter is to provide a standard method for the obtention of rhizosphere and endosphere fractions, and a generic workflow of the Quantitative Insights Into Microbial Ecology version 2 (QIIME2) software to analysis of 16S rRNA marker-gene.

Responses of Root Endophytes to Phosphorus Availability in Peach Rootstocks With Contrasting Phosphorus-Use Efficiencies

Phosphorus (P) is an important macronutrient for all lives, but it is also a finite resource. Therefore, it is important to understand how to increase the P availability and plant uptake. The endophytes can help host plants to improve P uptake and will be apparently affected by plant genotypes. To investigate the mechanism of root endophytes in promoting P uptake of peach rootstocks, we analyzed the variations of the root endophytic fungal and bacterial communities of peach rootstocks with different P efficiencies under high or low level of P addition. Results showed that Proteobacteria was the dominant bacterial phylum in the roots of all rootstocks under the two levels of P addition. At low P level, the abundance of Actinoplanes in phosphorus-inefficiency root system was apparently higher than that at high P level. Actinoplanes produced important secondary metabolites, improving the stress resistance of plants. Under high P condition, the abundance of Ferrovibrio was higher in Qing Zhou Mi Tao than in Du Shi. Fe oxides considerably reduced the availability of applied P, which partially explained why the P utilization in Qing Zhou Mi Tao is inefficient. Further, Ascomycota was the dominant fungal phylum in the roots of all rootstocks under different levels of P addition. The fungi community of roots varied in different rootstocks at each P level, but was similar for the same rootstock at different P levels, which indicated that genotype had a greater effect than P addition on the fungal community of peach rootstocks.

Responses of cucumber (Cucumis sativus L.) rhizosphere microbial community to some agronomic management practices

The microbial communities associated to the rhizosphere (the rhizomicrobiome) have a substantial impact on plant growth and yield. Understanding the effects of agricultural management on the rhizomicrobiome is very important for selecting efficient practices. By sequencing the V4 region of 16S rRNA for bacteria and the ITS1 regions and fungi, we investigated the influences of agronomic practices, including cucumber grafting on cucurbit hybrid (Cucurbita moschata × C. maxima), cucumber-garlic intercropping, and treatment with fungicide iprodione-carbendazim on cucumber rhizosphere microbial communities during plant growth. Soil dehydrogenase activity (DHA) and plant vegetative parameters were assessed as an indicator of overall soil microbial activity. We found that both treatments and growth stage induced significant shifts in microbial community structure. Grafting had the highest number of differentially abundant OTUs compared to control samples, followed by intercropping and fungicide treatment, while plant development stage affected both alpha and beta diversities indices and composition of the rhizomicrobiome. DHA was more dependent on plant growth stages than on treatments. Among the assessed factors, grafting and plant developmental stage resulted in the greatest changes in the microbial community composition. Grafting also increased the plant growth parameters, suggesting that this method should be further investigated in vegetable production systems.

The effect of plant domestication on host control of the microbiota

Macroorganisms are colonized by microbial communities that exert important biological and ecological functions, the composition of which is subject to host control and has therefore been described as "an ecosystem on a leash". However, domesticated organisms such as crop plants are subject to both artificial selection and natural selection exerted by the agricultural ecosystem. Here, we propose a framework for understanding how host control of the microbiota is influenced by domestication, in which a double leash acts from domesticator to host and host to microbes. We discuss how this framework applies to a plant compartment that has demonstrated remarkable phenotypic changes during domestication: the seed.

Revealing Microbiome Structure and Assembly Process in Three Rhizocompartments of Achyranthes bidentata Under Continuous Monoculture Regimes

The complex composition and interaction of root-associated microbes are critical to plant health and performance. In this study, we presented a detailed characterization of three rhizocompartment (rhizosphere, rhizoplane, and root) microbiomes of Achyranthes bidentata under different years of consecutive monoculture by deep sequencing in order to determine keystone microorganisms via co-occurrence network analysis. The network analysis showed that multiple consecutive monoculture (MCM, represented 5Y and 10Y) soils generated some distinct beneficial bacterial taxa such as Bacillus, Fictibacillus, Bradyrhizobium, Shinella, and Herbaspirillum. For fungi, Mortierella substituted for Fusarium in occupying an important position in different rhizocompartments under A. bidentate monoculture. Quantitative PCR analysis confirmed a significant increase in Bacillus, Pseudomonas, and Burkholderia spp. The results of the inoculation assay showed that addition of beneficial bacteria Bacillus subtilis 74 and Bacillus halodurans 75 significantly increased the root length and fresh weight of A. bidentata. Furthermore, three types of phytosterones, as the main allochemicals, were identified both in the rhizosphere soil and in culture medium under sterile conditions by LC-MS/MS. When looking at in vitro interactions, it was found that phytosterones displayed a positive interaction with dominant beneficial species (Bacillus amyloliquefaciens 4 and B. halodurans 75) and had a negative effect on the presence of the pathogenic fungi Fusarium solani and Fusarium oxysporum. Overall, this study demonstrated that consecutive monoculture of A. bidentata can alter the bacterial and fungal community by secreting root exudates, leading to recruitment of beneficial microbes and replacement of plant-specific pathogenic fungi with plant beneficial fungi.

Root-associated (rhizosphere and endosphere) microbiomes of the Miscanthus sinensis and their response to the heavy metal contamination

The plant root-associated microbiomes, including both the rhizosphere and the root endosphere microbial community, are considered as a critical extension of the plant genome. Comparing to the well-studied rhizosphere microbiome, the understanding of the root endophytic microbiome is still in its infancy. Miscanthus sinensis is a pioneering plant that could thrive on metal contaminated lands and holds the potential for phytoremediation applications. Characterizing its root-associated microbiome, especially the root endophytic microbiome, could provide pivotal knowledge for phytoremediation of mine tailings. In the current study, M. sinensis residing in two Pb/Zn tailings and one uncontaminated site were collected. The results demonstrated that the metal contaminant fractions exposed strong impacts on the microbial community structures. Their influences on the microbial community, however, gradually decreases from the bulk soil through the rhizosphere soil and finally to the endosphere, which resulting in distinct root endophytic microbial community structures compared to both the bulk and rhizosphere soil. Diverse members affiliated with the order Rhizobiales was identified as the core microbiome residing in the root of M. sinensis. In addition, enrichment of plant-growth promoting functions within the root endosphere were predicted, suggesting the root endophytes may provide critical services to the host plant. The current study provides new insights into taxonomy and potential functions of the root-associated microbiomes of the pioneer plant, M. sinensis, which may facilitate future phytoremediation practices.

Bioprospecting of Beneficial Bacteria Traits Associated With Tomato Root in Greenhouse Environment Reveals That Sampling Sites Impact More Than the Root Compartment

Tomato is subject to several diseases that affect both field- and greenhouse-grown crops. To select cost-effective potential biocontrol agents, we used laboratory throughput screening to identify bacterial strains with versatile characteristics suitable for multipurpose uses. The natural diversity of tomato root-associated bacterial communities was bioprospected under a real-world environment represented by an intensive tomato cultivation area characterized by extraseasonal productions in the greenhouse. Approximately 400 tomato root-associated bacterial isolates, in majority Gram-negative bacteria, were isolated from three compartments: the soil close to the root surface (rhizosphere, R), the root surface (rhizoplane, RP), and the root interior (endorhizosphere, E). A total of 33% of the isolates produced siderophores and were able to solubilize phosphates and grow on NA with 8% NaCl. A total of 30% of the root-associated bacteria showed antagonistic activity against all the tomato pathogens tested, i.e., Clavibacter michiganesis pv. michiganensis, Pseudomonas syringae pv. tomato, Pseudomonas corrugata and Xanthomonas euvesicatoria pv. perforans, and Fusarium oxysporum f. sp. lycopersici. We found that the sampling site rather than the root compartment of isolation influenced bacterial composition in terms of analyzed phenotype. This was demonstrated through a diversity analysis including general characteristics and PGPR traits, as well as biocontrol activity in vitro. Analysis of 16S rRNA gene (rDNA) sequencing of 77 culturable endophytic bacteria that shared multiple beneficial activity revealed a predominance of bacteria in Bacillales, Enterobacteriales, and Pseudomonadales. Their in vitro antagonistic activity showed that Bacillus species were significantly more active than the isolates in the other taxonomic group. In planta activity against phytopathogenic bacteria of a subset of Bacillus and Pseudomonas isolates was also assessed.

Interactive Effects of Scion and Rootstock Genotypes on the Root Microbiome of Grapevines (Vitis spp. L.)

Diversity and community structure of soil microorganisms are increasingly recognized as important contributors to sustainable agriculture and plant health. In viticulture, grapevine scion cultivars are grafted onto rootstocks to reduce the incidence of the grapevine pest phylloxera. However, it is unknown to what extent this practice influences root-associated microbial communities. A field survey of bacteria in soil surrounding the roots (rhizosphere) of 4 cultivars × 4 rootstock combinations was conducted to determine whether rootstock and cultivar genotypes are important drivers of rhizosphere community diversity and composition. Differences in α-diversity was highly dependent on rootstock–cultivar combinations, while bacterial community structure primarily clustered according to cultivar differences, followed by differences in rootstocks. Twenty-four bacterial indicator genera were significantly more abundant in one or more cultivars, while only thirteen were found to be specifically associated with one or more rootstock genotypes, but there was little overlap between cultivar and rootstock indicator genera. Bacterial diversity in grafted grapevines was affected by both cultivar and rootstock identity, but this effect was dependent on which diversity measure was being examined (i.e., α- or β-diversity) and specific rootstock–cultivar combinations. These findings could have functional implications, for instance, if specific combinations varied in their ability to attract beneficial microbial taxa which can control pathogens and/or assist plant performance.

Bio-herbicidal potential of wheat rhizosphere bacteria on Avena fatua L. grass

In order to isolated and identified the bacterial strains from wheat rhizosphere and evaluated the effect of different concentration of bacterial fermentation broth on the wild oats weed growth. This experiment carried out the separation and purification of dominant bacterial strains from the wheat rhizosphere soil, and performed the fermentation broth biological activity assessment by measured the seed germination and plant growth from 20 wheat varieties. The results had shown that the bacterial fermentation broth inhibits the growth of wild oat seedlings and plants to varying degrees, bacterial strains of X3, X4, X8, X12, X16 and X20 has certain level of inhibition activity and X20 has the highest herbicidal effectiveness. According to molecular biology identification, obtained superior bacterial strains X20 was Bacillus as potentially inhibitor for developing of bacterial-based bioherbicides for wild oats weed control management in the wheat field.

Changes in Bacterial Community Structure and Enriched Functional Bacteria Associated With Turfgrass Monoculture

There is increasing attention being paid to utilizing microbial communities to improve plant health while reducing management inputs. Thus, the objectives of this research were to assess changes in the rhizosphere bacterial community structure associated with long-term turfgrass monoculture and to demonstrate the feasibility of using functional bacteria as beneficial biocontrol agents. Large patch disease, caused by the fungal pathogen Rhizoctonia solani AG2-2, is a significant threat to turfgrass cultivation. Rhizosphere samples were collected from 2-, 13- and 25-year turfgrass (Zoysia japonica) monocultures. The 13-year monoculture field had a higher pathogen population density than both the 2- and 25-year monoculture fields. Analyses of the rhizosphere bacterial communities revealed that Streptomyces was dominant in the 2-year field and Burkholderia was enriched in the 25-year field. Based on the culturable rhizosphere bacteria, Streptomyces neyagawaensis J6 and Burkholderia vietnamiensis J10 were obtained from the 2- and 25-year fields, respectively. Application of S. neyagawaensis J6 and B. vietnamiensis J10 led to excellent inhibition of large patch disease as well as enhanced tolerance against drought and temperature stresses. The results showed that the selected bacteria could be developed as biocontrol and abiotic stress tolerance agents for turfgrass cultivation.

Getting to the root of grafting-induced traits

Grafting is an ancient technique that involves the physical joining of genotypically distinct shoot and root systems, in order to achieve a desirable compound plant. This practice is widely used in modern agriculture to improve biotic and abiotic stress tolerance, modify plant architecture, induce precocious flowering and rejuvenate old perennial varieties, boost yield, and more. Beneficial new rootstock-scion combinations are currently identified through an inefficient trial and error process, which presents a significant bottleneck for the application of grafting to combat new environmental challenges. Identifying the mechanisms that underlie beneficial grafting-induced traits will facilitate rapid breeding and genetic engineering of new rootstock x scion combinations that exhibit superior performance across varying agricultural environments.

Opportunities and Challenges in Studies of Host-Pathogen Interactions and Management of Verticillium dahliae in Tomatoes

Tomatoes (Solanum lycopersicum L.) are a valuable horticultural crop that are grown and consumed worldwide. Optimal production is hindered by several factors, among which Verticillium dahliae, the cause of Verticillium wilt, is considered a major biological constraint in temperate production regions. V. dahliae is difficult to mitigate because it is a vascular pathogen, has a broad host range and worldwide distribution, and can persist in soil for years. Understanding pathogen virulence and genetic diversity, host resistance, and plant-pathogen interactions could ultimately inform the development of integrated strategies to manage the disease. In recent years, considerable research has focused on providing new insights into these processes, as well as the development and integration of environment-friendly management approaches. Here, we discuss the current knowledge on the race and population structure of V. dahliae, including pathogenicity factors, host genes, proteins, enzymes involved in defense, and the emergent management strategies and future research directions for managing Verticillium wilt in tomatoes.

Plant Grafting Shapes Complexity and Co-occurrence of Rhizobacterial Assemblages

Grafting is a basic technique which is widely used to increase yield and enhance biotic and abiotic stress tolerance in plant production. The diversity and interactions of rhizobacterial assemblages shaped by grafting are important for the growth of their hosts but remain poorly understood. To test the hypothesis that plant grafting shapes complexity and co-occurrence of rhizobacterial assemblage, four types of plants, including ungrafted bottle gourd (B), ungrafted watermelon (W), grafted watermelon with bottle gourd rootstock (W/B), and grafted bottle gourd with watermelon rootstock (B/W), were cultivated in two soil types in a greenhouse, and the rhizosphere bacterial communities were analyzed by 16S rRNA gene high-throughput sequencing. Both the soil type and grafting significantly influenced the bacterial community composition. Grafting increased bacterial within-sample diversity in both soils. Core enriched operational taxonomic units (OTUs) in the W/B rhizosphere compared with the other three treatments (B, W, and B/W) were mainly affiliated with Alphaproteobacteria, Deltaproteobacteria, and Bacteroidetes, which are likely related to methanol oxidation, methylotrophy, fermentation, and ureolysis. Co-occurrence network analysis proved that grafting increased network complexity, including the number of nodes, edges, and modules. Moreover, grafting strengthened the structural robustness of the network in the rhizosphere, while ungrafted watermelon had the lowest network robustness. Homogeneous selection played a predominant role in bacterial community assembly, and the contribution of dispersal limitation was increased in grafted watermelon with bottle gourd rootstock. Grafting increased the diversity and transformed the network topology of the bacterial community, which indicated that grafting could improve species coexistence in the watermelon rhizosphere.

Shift in rhizospheric and endophytic bacterial communities of tomato caused by salinity and grafting

Saline water has to be used as an alternative resource in modern agriculture due to the increasing lack of fresh water. Approaches that promote the growth of crops under saline conditions have, therefore, become crucial. Grafting has been reported to be effective for this; however, the associated bacterial community remains unclear. To obtain a deeper understanding of the underlying microbial mechanisms, both grafted and non-grafted tomatoes were irrigated with three types of water having different electrical conductivity values. The experiment lasted 2.5 months, after which, the soil chemical properties and tomato heights were assessed. The rhizospheric and endophytic bacterial communities of samples from the different treatments were assessed by Illumina sequencing. The results showed that saline water significantly affected leaf-associated endophytic bacterial communities, whereas rhizosphere and root- and stem-associated bacterial communities were not affected. Increasing salinity increased the abundance of Gammaproteobacteria, but decreased the abundance of Actinobacteria, Alphaproteobacteria, Bacilli, and Acidobacteria at the class level of the leaf-associated bacterial community. Moreover, under higher salinity levels, grafting increased the diversity of the leaf-endophytic bacterial community. Overall, this study provides a comprehensive understanding of the rhizosphere and endophytic bacterial communities of tomato under saline conditions. The results highlight the importance of leaf-endophytic bacteria for salt response in plants. This is an important complementary finding to previous studies on the effect of salinity, which mainly focused on plant rhizosphere and root bacterial communities.

Microbial assemblages associated with the rhizosphere and endosphere of an herbage, Leymus chinensis

Root-associated microbiomes play significant roles in plant productivity, health and ecological services. However, our current understanding of the microbial assemblages in the rhizosphere and endosphere of herbage is still limited. To gain insights into these microbial assemblages, Illumina MiSeq high-throughput sequencing was performed to investigate the characteristics of microbial communities of an herbage, Leymus chinensis. Hierarchical clustering analysis and principal coordinate analysis (PCoA) results showed that microbial communities of the rhizosphere and endosphere samples were clearly distinguished. Rhizosphere soil communities showed a greater sensitivity than root endosphere communities using linear discriminant analysis (LDA) effect size (LEfSe). Rhizosphere and endosphere communities performed their respective functions in the soil as a cohesive collective, and Rhizobiales were observed to function as generalists. Redundancy analysis (RDA) and variance partitioning analysis (VPA) results revealed that the contribution of the interaction between soil physicochemical parameters and soil enzymes was greater than their individual contributions. In summary, this study is the first to elucidate the microbial diversity and community structure of L. chinensis and compare the diversity and composition between rhizospheric and endosphere microbiomes.

Influence of Citrus Scion/Rootstock Genotypes on Arbuscular Mycorrhizal Community Composition under Controlled Environment Condition

Citrus is vegetatively propagated by grafting for commercial production, and most rootstock cultivars of citrus have scarce root hairs, thus heavily relying on mutualistic symbiosis with arbuscular mycorrhizal fungi (AMF) for mineral nutrient uptake. However, the AMF community composition, and its differences under different citrus scion/rootstock genotypes, were largely unknown. In this study, we investigated the citrus root-associated AMF diversity and richness, and assessed the influence of citrus scion/rootstock genotypes on the AMF community composition in a controlled condition, in order to exclude interferences from environmental factors and agricultural practices. As a result, a total of 613,408 Glomeromycota tags were detected in the citrus roots, and 46 AMF species were annotated against the MAARJAM database. Of these, 39 species belonged to Glomus, indicating a dominant role of the Glomus AMF in the symbiosis with citrus. PCoA analysis indicated that the AMF community’s composition was significantly impacted by both citrus scion and rootstock genotypes, but total samples were clustered according to rootstock genotype rather than scion genotype. In addition, AMF α diversity was significantly affected merely by rootstock genotype. Thus, rootstock genotype might exert a greater impact on the AMF community than scion genotype. Taken together, this study provides a comprehensive insight into the AMF community in juvenile citrus plants, and reveals the important effects of citrus genotype on AMF community composition.

Highly diverse root endophyte bacterial community is driven by growth substrate and is plant genotype-independent in common bean (Phaseolus vulgaris L.)

The common bean (Phaseolus vulgaris L.) is the most important grain legume in the human diet with an essential role in sustainable agriculture mostly based on the symbiotic relationship established between this legume and rhizobia, a group of bacteria capable of fixing atmospheric nitrogen in the roots nodules. Moreover, root-associated bacteria play an important role in crop growth, yield, and quality of crop products. This is particularly true for legume crops forming symbiotic relationships with rhizobia, for fixation of atmospheric N₂. The main objective of this work is to assess the substrate and genotype effect in the common bean (Phaseolus vulgaris L.) root bacterial community structure. To achieve this goal, we applied next-generation sequencing coupled with bacterial diversity analysis. The analysis of the bacterial community structures between common bean roots showed marked differences between substrate types regardless of the genotype. Also, we were able to find several phyla conforming to the bacterial community structure of the common bean roots, mainly composed by Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, and Firmicutes. Therefore, we determined that the substrate type was the main factor that influenced the bacterial community structure of the common bean roots, regardless of the genotype, following a substrate-dependent pattern. These guide us to develop efficient and sustainable strategies for crop field management based on the soil characteristics and the bacterial community that it harbors.

Bacterial community characterization of the rhizobiome of plants belonging to Solanaceae family cultivated in desert soils

Purpose

The plant Solanaceae family is one of the most important for global agriculture and nutrition. Within this plant family, two plant species stand out for their economic importance and for human consumption, which are tomato (Solanum lycopersicum) and chili pepper (Capsicum annuum). Moreover, those plants support diverse and characteristic microbial communities that are uniquely suited to the plant habitat and intimately connected to plant health. The main objective of this work is the bacterial community characterization in the rhizobiome of tomato and chili pepper, cultivated in arid environments.

Methods

Five crop fields located in the south of the peninsula of Baja California, Mexico, were sampled. Total DNA was extracted from rhizosphere, rhizoplane, and endophytic root compartment and sequenced by Illumina MiniSeq platform technology applied to 16S rRNA gene V3 region.

Results

We were able to obtain 1,195,426 total reads and 1,725,258 total reads for tomato and chili pepper samples, respectively. The analysis of the bacterial community structures confirmed that the two plant species showed differences in their microbial community structures. Nonetheless, the microbial community structures were directly and equally influenced by the crop field localization of each plant species. Interestingly, we determined that in both plant species, the Proteobacteria was the main phylum.

Conclusion

In conclusion, we found that several bacterial families are part of the core rhizobiome (28 OTUs) for both tomato and chili pepper, but the most abundant were the Pseudomonadaceae family and the Pseudomonas genus, which most probably play a pivotal role in the microbial ecology to benefit both crop plants.

Omics applications: towards a sustainable protection of tomato

Transcriptome data and gene expression analysis have a huge potential in the study of multiple relationships involving plants, pathogens, and pests, including the interactions with beneficial microorganisms such as endophytes or other functional groups. Next-generation sequencing (NGS) and other recent long-read-based sequencing approaches (i.e., nanopore and others) provide unprecedented tools allowing the fast identification of plant information processing systems, in situ and in real time, fundamental for crop management and pest regulation. Other -omics approaches such as metagenomics and metatranscriptomics allow high-resolution insights on the rhizosphere ecology. They may highlight key factors affecting belowground biodiversity or processes, modulating the expression of stress-responsive pathways. The application of miRNAs and other small RNAs is a relatively new field of application, with enormous potential for the selective activation of defense pathways. However, limitations concerning the stability of the RNA molecules and their effective delivery must be overcome.

Myxobacterial Response to Methyljasmonate Exposure Indicates Contribution to Plant Recruitment of Micropredators

Chemical exchanges between plants and microbes within rhizobiomes are critical to the development of community structure. Volatile root exudates such as the phytohormone methyljasmonate (MeJA) contribute to various plant stress responses and have been implicated to play a role in the maintenance of microbial communities. Myxobacteria are competent predators of plant pathogens and are generally considered beneficial to rhizobiomes. While plant recruitment of myxobacteria to stave off pathogens has been suggested, no involved chemical signaling processes are known. Herein we expose predatory myxobacteria to MeJA and employ untargeted mass spectrometry, motility assays, and RNA sequencing to monitor changes in features associated with predation such as specialized metabolism, swarm expansion, and production of lytic enzymes. From a panel of four myxobacteria, we observe the most robust metabolic response from plant-associated Archangium sp. strain Cb G35 with 10 μM MeJA impacting the production of at least 300 metabolites and inducing a ≥ fourfold change in transcription for 56 genes. We also observe that MeJA induces A. sp. motility supporting plant recruitment of a subset of the investigated micropredators. Provided the varying responses to MeJA exposure, our observations indicate that MeJA contributes to the recruitment of select predatory myxobacteria suggesting further efforts are required to explore the microbial impact of plant exudates associated with biotic stress.

Diversity and plant growth-promoting functions of diazotrophic/N-scavenging bacteria isolated from the soils and rhizospheres of two species of Solanum

Studies of the interactions between plants and their microbiome have been conducted worldwide in the search for growth-promoting representative strains for use as biological inputs for agriculture, aiming to achieve more sustainable agriculture practices. With a focus on the isolation of plant growth-promoting (PGP) bacteria with ability to alleviate N stress, representative strains that were found at population densities greater than 10⁴ cells g^-1 and that could grow in N-free semisolid media were isolated from soils under different management conditions and from the roots of tomato (Solanum lycopersicum) and lulo (Solanum quitoense) plants that were grown in those soils. A total of 101 bacterial strains were obtained, after which they were phylogenetically categorized and characterized for their basic PGP mechanisms. All strains belonged to the Proteobacteria phylum in the classes Alphaproteobacteria (61% of isolates), Betaproteobacteria (19% of isolates) and Gammaproteobacteria (20% of isolates), with distribution encompassing nine genera, with the predominant genus being Rhizobium (58.4% of isolates). Strains isolated from conventional horticulture (CH) soil composed three bacterial genera, suggesting a lower diversity for the diazotrophs/N scavenger bacterial community than that observed for soils under organic management (ORG) or secondary forest coverture (SF). Conversely, diazotrophs/N scavenger strains from tomato plants grown in CH soil comprised a higher number of bacterial genera than did strains isolated from tomato plants grown in ORG or SF soils. Furthermore, strains isolated from tomato were phylogenetically more diverse than those from lulo. BOX-PCR fingerprinting of all strains revealed a high genetic diversity for several clonal representatives (four Rhizobium species and one Pseudomonas species). Considering the potential PGP mechanisms, 49 strains (48.5% of the total) produced IAA (2.96–193.97 μg IAA mg protein^-1), 72 strains (71.3%) solubilized FePO₄ (0.40–56.00 mg l^-1), 44 strains (43.5%) solubilized AlPO₄ (0.62–17.05 mg l^-1), and 44 strains produced siderophores (1.06–3.23). Further, 91 isolates (90.1% of total) showed at least one PGP trait, and 68 isolates (67.3%) showed multiple PGP traits. Greenhouse trials using the bacterial collection to inoculate tomato or lulo plants revealed increases in plant biomass (roots, shoots or both plant tissues) elicited by 65 strains (54.5% of the bacterial collection), of which 36 were obtained from the tomato rhizosphere, 15 were obtained from the lulo rhizosphere, and 14 originated from samples of soil that lacked plants. In addition, 18 strains showed positive inoculation effects on both Solanum species, of which 12 were classified as Rhizobium spp. by partial 16S rRNA gene sequencing. Overall, the strategy adopted allowed us to identify the variability in the composition of culturable diazotroph/N-scavenger representatives from soils under different management conditions by using two Solanum species as trap plants. The present results suggest the ability of tomato and lulo plants to enrich their belowground microbiomes with rhizobia representatives and the potential of selected rhizobial strains to promote the growth of Solanum crops under limiting N supply.

Apple rootstocks with different phosphorus efficiency exhibit alterations in rhizosphere bacterial structure

AIMS

The purpose of this study was to select phosphorus-efficient apple rootstocks under phosphorus deficiency and to reveal the effects of different apple rootstocks on the rhizosphere bacterial community.

METHODS AND RESULTS

We used 83 hybrid lines of Malus robusta Rehd. × Malling 9 (M.9) to investigate their physiological traits and the phosphorus deficiency phenotypes of leaves in response to phosphorus deficiency (0·1 mmol l^-1 PO₄ ^3- ). All the plants were cultivated in pots in the greenhouse and watered using drip irrigation. In accordance with the results of investigation, we selected the phosphorus-efficient hybrid lines (PE) and the phosphorus-inefficient hybrid lines (PI) to research their root morphology and root hairs (RH). In addition, we used Illumina MiSeq sequencing to determine the bacterial community of the rhizosphere from different rootstocks. The results showed that the PE plants had better growth characteristics and stronger root plasticity than that of the PI plants, and phosphorus deficiency can stimulate the RH growth of PE plants. There was no significant difference in the rhizosphere bacterial diversity, but we found that the bacterial community structure was significantly different at the genus levels; in addition, 89 genera were found to have significant differences between PE and PI plants, especially Bacillus. The PE rhizosphere had more abundant Bacillus compared to the PI. High positive Pearson correlations with the phosphorus concentration in the plantlets of apple rootstocks were detected for the bacterial genera Bacillus (r: 0·776).

CONCLUSIONS

The phosphorus-efficient apple rootstocks adapted to phosphorus deficiency by shaping the root morphology. Notably, different apple rootstocks showed alteration of the microbes in rhizosphere.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study can provide the materials for exploring the mechanism of apple rootstock phosphorus absorption. In accordance with the different bacterial community compositions, we can develop the inoculants to promote nutrient uptake.

Phycosphere Microbial Succession Patterns and Assembly Mechanisms in a Marine Dinoflagellate Bloom

Given the ecological significance of microorganisms in algal blooming events, it is critical to understand the mechanisms regarding their distribution under different conditions. We tested the hypothesis that microbial community succession is strongly associated with algal bloom stages, and that the assembly mechanisms are cocontrolled by deterministic and stochastic processes. Community structures and underlying ecological processes of microbial populations (attached and free-living bacteria) at three algal bloom stages (pre-, during, and postbloom) over a complete dinoflagellate Scrippsiella trochoidea bloom were investigated. Both attached and free-living taxa had a strong response to the bloom event, and the latter was more sensitive than the former. The contribution of environmental parameters to microbial variability was 40.2%. Interaction analysis showed that complex positive or negative correlation networks exist in phycosphere microbes. These relationships were the potential drivers of mutualist and competitive interactions that impacted bacterial succession. Null model analysis showed that the attached bacterial community primarily exhibited deterministic processes at pre- and during-bloom stages, while dispersal-related processes contributed to a greater extent at the postbloom stage. In the free-living bacterial community, homogeneous selection and dispersal limitation dominated in the initial phase, which gave way to more deterministic processes at the two later stages. Relative contribution analyses further demonstrated that the community turnover of attached bacteria was mainly driven by environmental selection, while stochastic factors had partial effects on the assembly of free-living bacteria. Taken together, these data demonstrated that a robust link exists between bacterioplankton community structure and bloom progression, and phycosphere microbial succession trajectories are cogoverned by both deterministic and random processes.IMPORTANCE Disentangling the mechanisms shaping bacterioplankton communities during a marine ecological event is a core concern for ecologists. Harmful algal bloom (HAB) is a typical ecological disaster, and its formation is significantly influenced by alga-bacterium interactions. Microbial community shifts during the HAB process are relatively well known. However, the assembly processes of microbial communities in an HAB are not fully understood, especially the relative influences of deterministic and stochastic processes. We therefore analyzed the relative contributions of deterministic and stochastic processes during an HAB event. Both free-living and attached bacterial groups had a dramatic response to the HAB, and the relative importance of determinism versus stochasticity varied between the two bacterial groups at various bloom stages. Environmental factors and biotic interactions were the main drivers impacting the microbial shift process. Our results strengthen the understanding of the ecological mechanisms controlling microbial community patterns during the HAB process.

Changes in endophytic bacterial communities during different growth stages of cucumber (Cucumis sativus L.)

Endophytic bacterial diversity in plants presents the level of interaction between culturable and non-culturable endophytic bacteria, thereby providing an appropriate insight into the endophytic environment. This study was conducted to determine the trend of culturable and non-culturable endophytic bacteria at two different sites encompassing four consecutive growth stages. For culturable endophytic bacteria, isolation was carried out using the dilution plate technique, and the obtained colonies were compared using PCR-restriction fragment length polymorphism (RFLP). Different RFLP-types were identified to their nearest neighbour using 16S rRNA sequencing. The non-culturable endophytic bacterial diversity was obtained by next generation sequencing. Results suggested a similar trend among the culturable and non-culturable bacteria for observed operational taxonomic units and diversity indices. It is noticeable that the endophytic bacteria inhabiting in stage 1 disappeared, and instead, different endophytic bacteria appeared. Moreover, the temporal persistence of certain culturable and non-culturable bacteria was also observed. In conclusion, the endophytic bacterial diversity in cucumber initially increased with the plant growth and then decreased at a later stage. Furthermore, it was suggested that plants regulate the number and diversity of endophytes throughout the lifecycle of plants.